PHD-finger family genes in wheat (Triticum aestivum L.): evolutionary conservatism, functional diversification, and active expression in abiotic stress

PHD-finger family genes in wheat (Triticum aestivum L.): evolutionary conservatism, functional diversification, and active expression in abiotic stress | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article PHD-finger family genes in wheat ( Triticum aestivum L.): evolutionary conservatism, functional diversification, and active expression in abiotic stress Fei Pang, Junqi Niu, Zhaoliang Liu, Zhen Wang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-1799303/v2 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 11 Dec, 2022 Read the published version in Frontiers in Plant Science → Version 2 posted You are reading this latest preprint version Show more versions Abstract Plant homeodomain (PHD) transcription factors (TFs) are a class of proteins with conserved Cys4-His-Cys3 domains that play important roles in plant growth and development, and in response to abiotic stresses. Although characterization of PHDs have been performed in plants, little is known about their function in wheat ( Triticum aestivum L.), especially under stress conditions. In the present study, 244 TaPHDs were identified in wheat using comparative genomics. We renamed them TaPHD1-244 based on their chromosomal distribution, and almost all PHD proteins were predicted to be located in the nucleus. According to the unrooted neighbor-joining phylogenetic tree, gene structure, and motif analyses, PHD genes were divided into four clades. A total of 149 TaPHD genes were assigned to arise from duplication events. Furthermore, 230 gene pairs came from wheat itself, and 119, 186, 168, 7, 2, and 6 gene pairs came from six other species ( Hordeum vulgareto, Zea mays , Oryza sativa, Arabidopsis thaliana , Brassica rapa , and Gossypium raimondii , respectively). A total of 548 interacting protein branches were identified to be involved in the protein interaction network. Tissue-specific expression pattern analysis showed that TaPHDs were highly expressed in the stigma and ovary during flowering, suggesting that the TaPHD gene plays an active role in the reproductive growth of wheat. In addition, the qRT-PCR results further confirmed that these TaPHD genes are involved in the abiotic stress response of wheat. In conclusion, our study provides a theoretical basis for deciphering the molecular functions of TaPHDs , particularly in response to abiotic stress. Agronomy Bioinformatics Molecular Biology PHD finger genes wheat phylogenetic analysis expression patterns Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 9 Figure 10 Figure 11 Figure 12 1. Introduction Plants encounter various unfavorable growth conditions during their life cycle, such as pests and diseases, drought, and extreme temperatures. In response to adverse external environments, plants activate in vivo defense response mechanisms by inducing stress-responsive gene expression [1,2]. Many plant-specific transcription factor (TF) family members are involved in plant-specific developmental processes and participate in and regulate the stress response of plants to the external environment, thereby improving their adaptation to adversity [3]. To date, some such transcription factors have been successively isolated from many species of plants, such as AP2/ERF [4], bHLH [5], MYB [6], and WRKY [7]. Among these, the PHD-finger transcription factor family is tissue-specific and plays an important role in plant growth, development, and transcriptional regulation by adversity. The plant homeodomain (PHD) is a conserved zinc finger structural domain in biological evolution and is commonly distributed in eukaryotes ranging from yeast to plants and animals [8-12]. A typical PHD domain consists of 50-80 amino acid residues with a characteristic Cys4-His-Cys3 sequence, which is arranged in a manner similar to RING (Cys3-His-Cys4) and LIM (Cys2-His-Cys5) [13,14]. The most important function of the PHD domain is the specific recognition of various histone modifications and DNA sequences, thus acting in transcriptional regulation and participating in various biological processes in organisms [15-17]. For example, previous studies have shown that, in model plants, proteins containing PHD domains are involved in embryonic meristem germination, root development, photoperiod, vernalization, meiosis, and post-meiotic pollen development. PHD domains plays an important role in plant growth and development [18]. PHD domains are a class of relatively small protein domains. Their relatively conserved cysteine and histidine can stabilize the normal spatial structure by binding zinc ions, so that the three-dimensional conformation of the entire domain is basically spherical [19]. In addition to the conserved Cys4-His-Cys3 residues, PHD proteins usually contain highly diverse sequences. These diverse sequences form genes with different biological functions within the PHD-finger family. For example, the PHD domain–containing protein MMD1 is involved in essential chromatin remodeling and transcriptional events during male meiosis [20]. In Arabidopsis , the ALFIN1-like (AL) protein, which contains the PHD domain, plays a key role in seed germination [21]. Furthermore, the PHD-finger protein VIL1 is involved in the photoperiod and vernalization pathways, as it regulates the expression of related floral repressors [22]. ATX1 and ATX2 have histone methyltransferase activities and regulate the development of roots, leaves, and floral organs, as well as the transcription of some stress genes [23]. Since Schinder first discovered and identified PHD proteins in plants in 1993 [24], an increasing number of PHDs have been reported. To date, 59 members of Oryza stiva [25], 108 members of Gossypium hirsutum [26], 72 members of Solanum tuberosum [27], 60 members of Phyllostachys edulis [28], and 67 members of Zea mays [29] have been identified. It is known that PHD proteins not only participate in the regulation of plant growth and development, but also play an important role in stress response, especially to abiotic stresses such as salt, high-temperature, low-temperature, and drought stress. In rice, overexpression of the OsPHD1 gene can significantly improve tolerance to low-temperature, high-salt, and drought stress [30]. Overexpression of the PHD-finger transcription factor gene OsMsr16 can enhance salt tolerance in rice plants [31]. Wei et al. also found that Arabidopsis thaliana transgenic plants overexpressing soybean GmPHD2 exhibited higher salt tolerance, possibly because overexpression of GmPHD2 enhanced the scavenging of oxidative substances [32]. Furthermore, under abiotic stress, genes in the PHD-finger family in maize, cotton, and poplar show differential expression under salt, drought, and cold stress [26,29,33]. Thus, it can be seen that the PHD family genes play a crucial role in regulating plant resistance to stress. Wheat is a major food crop in the world and plays a crucial role in global food security. It is especially important to tap important resistance genes, breed new resistant wheat varieties, and improve the resistance of wheat itself [34]. The PHD-finger gene family, which is essential for growth and development, has been identified and studied in many crops, but no systematic studies of the PHD gene family in wheat have been performed. In the present study, we identified PHD-finger family members in wheat for the first time and performed a comprehensive and systematic genome-wide analysis, including gene conserved motif analysis, phylogenetic relationships, Gene Ontology (GO) annotation analysis, covariance analysis, reciprocal relationship analysis, and subcellular localization. We also investigated the expression of PHD family proteins during growth and development, their specific expression in each organ, and their expression under multiple stresses of low temperature, high temperature, and drought. We lay the foundation for analyzing the functions of PHD proteins and regulating stress resistance and also provide theoretical references for the excavation of stress resistance genes and stress resistance breeding in wheat. 2. Materials And Methods 2.1 Identification and classification analysis of PHD family genes in wheat Whole genome data for T. aestivum (IWGSC RefSeq_v1.1) were obtained from the Ensembl plant database (http://plants.ensembl.org/info/website/ftp/index.html), and the PHD-finger domain (PF00628) was downloaded from the PFAM database (https://pfam.xfam.org/). The PHD protein sequences from A. thaliana (70) and O. sativa (59) (Supplementary Table S1) [25] were used as query sequences to search against the wheat protein dataset using the BLASTP program, and the threshold was set as E-value < 1e-5. The NCBI-Batch CD-Search [35] (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi), PFAM database, and SMART database (http://smart.embl.de/) were used to further confirm the candidate PHD-finger genes of T. aestivum. There were other spliced transcripts in the candidate genes of these species, and we selected the first splice variant as a representative for subsequent analysis. The protein sequences of the TaPHDs were computed using the ExPASy server [36] to obtain the theoretical isoelectric point (pI), molecular weight (MW), instability index (II), aliphatic index (AI), and grand average hydrophobicity (GRAVY). Plant-mPLoc [37] ( http://www.csbio.sjtu.edu.cn/cgi-bin/PlantmPLoc.cgi ) and BUSCA [38] (Bologna Unified Subcellular Component Annotator, http://busca.biocomp.unibo.it) were used to predict the subcellular localization of the TaPHD proteins. 2. 2 Phylogenetic analyses of TaPHD genes The PHD-finger protein sequences of T. aestivum , A. thaliana , and O. sativa were used for phylogenetic analysis. Jalview 2.11 software (http://www.jalview.org/) with the MUSCLE method with default parameters was utilized to conduct multiple sequence alignment. Evolutionary analysis involved 342 amino acid sequences (all wheat PHD genes, and most rice and Arabidopsis PHD genes). These analyses were conducted in MEGA X [39] using the neighbor-joining method [40]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. The evolutionary distances were computed using the Poisson correction method and were expressed as the number of amino acid substitutions per site. The iTOL website (http://itol.embl.de/) was used to visualize the phylogenetic tree. 2.3 Gene duplication and Ka/Ks analysis of TaPHD genes MCScanX software [41] was used to detect collinear regions between TaPHD genes as well as collinear blocks of TaPHDs with three monocotyledons ( H. vulgareto , Z. mays , and O. sativa ) and three dicotyledons ( A. thaliana , B. rapa , and G. raimondii ). All TaPHD genes were mapped to their respective loci in the wheat genome in a circular diagram using shinyCircos [42]. Gene duplication events of TaPHDs and synteny relationships between the aforementioned species were visualized using TBtools (v1.082) [43]. The Ka/Ks values (non-synonymous substitution rate/synonymous substitution rate) were calculated after identification of duplicated genes, using the method of Nei and Gojobori as implemented in KaKs_calculator [44] based on the coding sequence alignments. Subsequently, the divergence time of collinear gene pairs was calculated using the duplication events formula T = Ks/(2λ × 10 - 6 ) in millions of years (Mya), with λ = 6.5 × 10 - 9 [45]. 2.4 GO annotation and protein–protein interaction network analysis of TaPHD genes GO annotation of TaPHD proteins was available from the KOBAS database ( http://kobas.cbi.pku.edu.cn/kobas3 ) [46]. The full-length amino acid sequence of TaPHD proteins were uploaded to the original program, followed by drawing and annotation. GO annotations were performed for three types of analyses: biological processes, molecular functions, and cellular composition. The GO annotation results were visualized using the online tool OmicStudio (https://www.omicstudio.cn/tool) [47]. All the predicted TaPHD proteins were submitted to the STRING database (https://string-db.org/cgi/input.pl). The minimum required interaction score was set to high confidence (0.700). The max number of interactors was no more than 10 on the first shell. 2.5 Expression of TaPHD genes Transcriptional data for TaPHDs were obtained from the wheat expression website ( http://www.wheat-expression.com/download ) [48,49] and were used to explore the potential biological functions of TaPHD genes in growth and development, abiotic and biotic stress, and other conditions. Systematic clustering analysis was performed based on the log2 of transcripts per million (TPM) values for the 244 TaPHD genes. R was used to display the expression patterns in a heat map, and OmicStudio (https://www.omicstudio.cn/tool) was used to display the histogram, volcano plot, and Venn diagram. 2.6 Quantitative real-time PCR analyses of TaPHD genes in response to environmental stresses In this study, the seeds of the hexaploid common wheat variety “zhengmai 7698” were surface-sterilized with 2% hydrogen peroxide, rinsed thoroughly with distilled water, and germinated with water saturation at 25 °C for 2 days in Petri dishes on three layers of filter paper. The young seedlings were transformed and grown in 1/2 Hoagland's culture solution under a 14 h light (25 °C)/10 h dark (20 °C) photoperiod. When the wheat grew to two leaves and one heart, the plants were subsequently treated with 16% polyethylene glycol 6000 (PEG6000). For cold stress, rice seedlings were exposed to 4 °C for 12 h. For heat stress, rice seedlings were exposed to 40 °C for 12 h. New leaves of the three seedlings were collected as biological replicates, and each treatment had three replicates. Total RNA was extracted using RNAiso Reagent (TaKaRa, Beijing, China) and cDNA was synthesized using the RT Master Mix Perfect RealTime kit (TaKaRa, Beijing, China). Quantitative real-time PCR was performed using the CFX Touch™ Real-Time PCR Detection System (Bio-Rad Laboratories, Hercules, CA, USA) and the SG Fast qPCR Master Mix (Sangon Biotech, Shanghai, China). Relative expression levels were determined using the 2 (-ΔΔCt) method [50], and β-actin was used as the internal control to normalize the expression levels of TaPHD genes. Specific primers used for RT-qPCR are listed in Supplementary Table S2. 2.7 Determination of subcellular localization of TaPHD11, TaPHD19, and TaPHD133 Full-length open reading frames of TaPHD11, TaPHD19 , and TaPHD133 were obtained from “zhengmai 7698” cDNA (Supplementary Table S2). The CDS of TaPHD11, TaPHD19 , and TaPHD133 were cloned into the pJIT16318 vector at the BamHI site using specific primers (Supplementary Table S2). The pJIT16318 vector contained a CaMV 35S promoter and C-terminal GFP. Transient expression assays were conducted as described by Cui , et al. [51]. Approximately 4 × 10 4 mesophyll protoplasts were isolated from 12-day-old wheat seedlings. The transfected protoplasts were incubated at 23 °C for 12 h. GFP fluorescence in the transformed protoplasts was imaged using a confocal laser-scanning microscope (LSM 700; Zeiss). 3. Results 3.1 Identification and classification analysis of PHD genes in wheat In this study, 244 T. aestivum genes were designated PHD genes with two query methods, HMM and BLASTP, used for identification, and three websites, NCBI-Batch CD-Search, PFAM database, and SMART database, used for confirmation (Supplementary Table S3). These PHD genes were renamed TaPHD1 to TaPHD244 , based on their chromosomal locations and physical positions. To further determine the characteristics of TaPHD genes, the ExPASy Server online tool was used to analyze the protein characteristics (Supplementary Table S3). The shortest protein contained 216 amino acids ( TaPHD158, TaPHD175 ) and the longest one contained 2853 amino acids ( TaPHD204 ); the molecular weight was between 24567.82 Da ( TaPHD158 ) and 310347.53 Da ( TaPHD204 ). The protein instability index showed that all PHD genes were unstable proteins. The isoelectric point of TaPHD genes varied markedly from 4.42 ( TaPHD36 ) to 9.65 ( TaPHD78 ), and the aliphatic index varied significantly from 48.13 ( TaPHD26/39/51 ) to 97.51 ( TaPHD42 ). The GRAVY of TaPHD proteins in wheat varied from 0.016 ( TaPHD160 ) to -1.285 ( TaPHD23 ), indicating that they were all hydrophilic proteins, except for TaPHD160 (Supplementary Table S3). We used two methods (Plant-mPLoc and BUSCA) to predict the subcellular localization of the TaPHD proteins. The results showed that a few TaPHDs may be localized in the chloroplast, mitochondrion, or cytoplasm, and most members were predicted to be located in the nucleus (Supplementary Table S3). 3.2 Multiple sequence alignment and phylogenetic analysis of PHD genes Multiple sequence alignments of PHD domains were performed (Figure 1). Approximately 60 amino acids (aa) comprised a PHD domain containing basic Cys4-His-Cys3 sequence motifs in each TaPHD. To evaluate the evolutionary relationships of PHD genes in T. aestivum , O. sativa, and A. thaliana , a neighbor-joining phylogenetic tree was constructed using full-length PHD proteins (Figure 2 and Supplementary Table S1). Phylogenetic analysis showed that PHD family proteins can be divided into four clades (clades 1 to 4). TaPHD members were found in all clades. Clade 1 was the largest, with 95 TaPHD members, and clade 4 was the smallest, with only 38 members. The results showed that there were many small branches under each clade, and almost every small branch had corresponding genes of rice and Arabidopsis . This indicated that the TaPHD gene is not an evolutionary characteristic of monocotyledonous and dicotyledonous plants, and that the PHD gene family was formed before the differentiation of these two types of plants. Protein domains are often functional carriers. According to phylogenetic and domain analyses (NCBI-Batch CD-Search, PFAM, and SMART database), 30 dominant types were identified in all wheat PHD proteins (Table 1). The results showed that among all wheat PHD proteins, 43 contained a typical PHD domain. Next most common, the jas-PHD and alifn-PHD domains had 28 and 25 members, respectively; the PHD-Oberon_cc domain and the PHD-RING domains had 11 members, and the remaining domain types had less than ten members. The results showed that wheat PHD proteins contained a canonical PHD domain or double PHD domains. Owing to their different domains, differentiation in function was achieved. To better understand why PHD-finger genes are abundant in the wheat genome, we analyzed the homoeologous groups in detail (Table 2). A total of 35.8% of wheat genes were present in homoeologous groups of three, also termed triads (A:B:D = 1:1:1) {International Wheat Genome Sequencing Consortium, 2018 #46} . In contrast, 84.8% of the PHD-finger genes identified were present in triads (Table 2). Also, the percentage of PHD-finger genes with homoeolog-specific duplications was lower for PHD-finger genes than for all wheat genes (1.6% vs 5.7%; Table 2). Loss of one homoeolog, on the other hand, was less pronounced in PHD-finger genes (6.6% vs 13.2%; Table 2). Only four PHD-finger genes were orphans/singletons. Thus, the high homoeolog retention rate could partly explain the high number of wheat PHD-finger genes. 3.3 Chromosomal location, gene duplication, and synteny analysis of TaPHD genes Based on the reference GFF3 files, the physical positions of PHD genes on the corresponding chromosomes are shown in Figure 3. The identified TaPHDs could be mapped on every chromosome and evenly across the three sub-genomes. The map shows that chromosomes 5B and 5D harbor the largest number of TaPHD genes (18), whereas chromosome 1D contains the least (6). Gene duplication is an indispensable mechanism by which organisms create new genes with similar or different functions [53]. Therefore, we analyzed the duplication events that occurred in the TaPHD gene family. A total of 230 PHD gene pairs from wheat were identified as duplicated (Figure 4, Supplementary Table S4). These similar PHD gene pairs had the same domain type and appeared in the same branch of the phylogenetic tree. Tandem and segment duplications are critical for the evolution of gene families to adapt to different environmental conditions. Interestingly, all the TaPHD gene pairs were associated with segmental duplication events. This suggests that this was the main route for expanding PHD genes in wheat and the many homologous genes on different wheat chromosomes suggest the high conservation of the family. To further infer the evolutionary origin and homology of the wheat PHD family, we constructed a collinear chart comparing six species with wheat, including three monocotyledons ( H. vulgareto , Z. mays , and O. sativa ) and three dicotyledons ( A. thaliana , B. rapa , and G. raimondii ) (Figure 5, Supplementary Table S4). We identified pairwise homologues of the TaPHD genes and detected 119, 186, 168, 7, 2, and 6 pairs of homologous genes from H. vulgareto, Z. mays , O. sativa, A. thaliana , B. rapa , and G. raimondii , respectively (Figure 5, Supplementary Table S4). This implies that TaPHD genes share a strong evolutionary relationship with ZmPHDs , HvPHDs , and OsPHDs . Furthermore, these results indicated that the PHD gene family was differentiated between monocotyledonous and dicotyledonous plants. This also indicated that TaPHD genes had a strong evolutionary relationship with ZmPHDs , HvPHDs , and OsPHDs. The average differentiation time was as barley (12.78 Mya) < rice (22.09 Mya) < maize (60.87 Mya). Ka/Ks, the non-synonymous substitution ratio, determines the selection pressure for duplicated genes. According to the results (Supplementary Table S4), only very few TaPHD gene pairs had Ka/Ks ratios >1, suggesting that the evolution of TaPHD genes was accompanied by strong purifying selection. The Ka/Ks ratios between wheat and three monocotyledonous plants were calculated based on the collinear gene pairs. Except for very few genes, the values of the other collinear gene pairs were all below 1, which confirmed that the evolution of the wheat PHD gene family underwent strong purifying selection. However, the Ka/Ks ratios of the collinear gene pairs between wheat and the three dicots could not be calculated properly. This is because most synonymous mutation sites have synonymous mutations; that is, the degree of sequence divergence and evolutionary distance is too large. Some TaPHD genes have formed at least five homologous gene pairs, such as TaPHD9 , which may have played key roles in the evolution of the PHD gene family (Figure 5, Supplementary Table S4). 3.4 GO annotation analysis and protein–protein interaction network of TaPHD gene s We performed GO annotation analysis of the 244 TaPHD proteins, revealing that they may participate in a range of cellular components, molecular functions, and biological processes (Figure 6, Supplementary Table S5). The 244 TaPHD proteins were assigned a total of 105 GO terms. In biological processes, the three most highly enriched categories were related to the regulation of DNA-templated transcription, heat acclimation, and chromatin organization. Developmental growth and jasmonic acid–mediated systemic resistance were also particularly enriched. In the cellular component category, the most highly enriched categories were related to the nucleus, and 85% of the TaPHDs could participate in this process, whereas less than 10% of TaPHDs were involved in plasmodesma. Regarding molecular functions, the 65 most enriched TaPHDs were involved in histone binding, 28 TaPHDs were involved in chromatin binding, and 81 TaPHDs were related to protein binding. To understand protein–protein interactions between TaPHDs and other proteins in wheat, we constructed a protein–protein interaction network (Figure 7, Supplementary Table S6). A total of 89 TaPHD proteins and 548 interacting protein branches were identified. According to the strength of the interaction, we divided the 89 proteins into four interaction regions, which are represented by different colors, as shown in Figure 7. Some TaPHDs, such as TaPHD15, TaPHD145, and TaPHD162, could interact with up to 28 proteins, suggesting that these TaPHD proteins play a significant role in the regulation of protein networks. Interestingly, we found that these proteins had a PHD domain or a PHD-SWIB-Plus3-GYF domain. Therefore, we believe that such domains are likely to play an important role in the PHD family. 3.5 Expression analysis of TaPHD genes during growth and development RNA-sequencing is a powerful tool for exploring certain gene transcription patterns using high-throughput sequencing methods [54]. Systematic clustering analysis was performed based on the log2 of TPM values for 244 TaPHD genes (Figure 8A, Supplementary Table S7). The data showed that TaPHD gene expression showed great differences with the change in the growth period. In general, the expression of TaPHDs can be divided into three categories: the first group contains members that are widely expressed in many tissues under multiple developmental stage conditions, the second group contains those that are highly induced only at specific growth and development stages, and the last group includes members that do not appear to be expressed during growth and development. For example, TaPHD100 , TaPHD108 , and TaPHD122 had high expression during most growth and developmental processes, except in the endosperm. Of course, there were also some genes ( TaPHD222 and TaPHD232 ) that had higher expression only in shoots and roots. Furthermore, some genes, such as TaPHD68 , TaPHD78 , and TaPHD86 , were basically not expressed, which implies that these genes may have functional redundancy. To further study the expression differences of this family in different stages and organs of wheat, we counted the number of high, medium, and low expression genes in each period and organ (Figure 8B). The data showed that the number of highly expressed genes was the largest in the stigma and ovary, reaching as high as 60, followed by a spike in the boot period, reaching 41. The lowest number of highly expressed genes (none) was found in the flag leaf blade at night in the flag leaf stage. Our results suggest that some TaPHDs may play important roles in many biological processes during wheat growth, especially during anthesis. 3.6 Expression responses of TaPHD genes to abiotic/biotic stress The differential expression of TaPHDs under different conditions is shown in Figure 9A-F (Supplementary Table S8). During biological stress, we found that inoculation with Fusarium , powdery mildew, pathogen associated molecular patterns (PAMP), crown rot, Septoria , or stripe rust caused few changes in the expression of TaPHD genes. This suggests that TaPHD family members may not be associated with disease resistance. Under abiotic stress, there are many TaPHD genes whose expression changes are more obvious under high-temperature, drought, and cold conditions (Figure 9G-K, Supplementary Table S8). For example, after high-temperature treatment, the expression levels of many TaPHD genes ( TaPHD26 , TaPHD75 , TaPHD100, TaPHD115, TaPHD117 , and TaPHD167 ) were significantly altered compared to those in the experimental control group. In the drought starvation treatment, TaPHD11, TaPHD19, TaPHD99, TaPHD141, TaPHD153 , and TaPHD171 expression levels changed significantly. However, in the phosphorus starvation treatment, there were few changes in the expression of TaPHD genes. To further understand whether there is an intersection between the differential genes of the PHD family under drought, high-temperature, and low-temperature treatments, we drew a Venn diagram of DEGs in TaPHD genes during the four different transcriptomes (Figure 10, Supplementary Table S9). The data showed that TaPHD215 and TaPHD223 were significantly altered in every treatment. TaPHD30, TaPHD96, TaPHD180, TaPHD174 , and TaPHD239 gene expression varied greatly between the two drought and heat treatments. In addition, in cold and heat stress environments, the expression levels of five genes ( TaPHD109, TaPHD118, TaPHD120, TaPHD167 , and TaPHD178 ) were significantly changed. 3.7 qRT-PCR confirmed the response capability of TaPHD genes to abiotic stress conditions To elucidate the possible regulatory mechanisms of TaPHD genes under cold, drought, and heat conditions, we performed qRT-PCR analysis of 20 genes (Figure 11). The results showed that all 20 TaPHDs responded to different stress conditions and had different manifestations. Under low temperature stress induced by 4°C, the expression of five TaPHD s was significantly upregulated at different time points, and the expression of six TaPHD s was significantly downregulated at different time points compared with the control. In contrast, under 40°C-induced high-temperature stress, the expression of 12 TaPHD s was significantly upregulated at different time points compared with the control. The expression of five TaPHDs was inhibited at different time points. This indicated that compared with low temperature stress, high temperature stress could induce more changes in the expression of TaPHD s and could upregulate the expression more. In wheat under 16% PEG stress, the expression of ten TaPHD s was significantly upregulated at different time points. The expression of seven TaPHD s was inhibited at different time points. Among them, TaPHD72 was most significantly inhibited, and it was downregulated fourfold at 6 h and 12 h after treatment. The expression levels of TaPHD69 and TaPHD135 significantly increased after the three treatments. However, the expression levels of TaPHD23 and TaPHD141 significantly decreased after the three treatments. In addition, TaPHD99 was strongly upregulated or downregulated by high temperature, low temperature, and PEG, and we speculated that this might be a key regulator of abiotic induction. In conclusion, we verified the effect of PHD-finger gene expression on the effect of three abiotic stresses in wheat using qRT-PCR. These results indicate that PHD-finger genes play an important role in coping with abiotic stress in wheat. 3.8 Subcellular localization of TaPHD11, TaPHD19, and TaPHD133 Previous studies have shown that most PHD finger proteins are localized in the nucleus, and only a few are localized in the membranes or other organelles [25,33,57]. For example, ZmPHD14 and ZmPHD19 are localized to the nucleus [29]. Also, GmPHD1 to GmPHD6 target the nucleus, and their nuclear localization requires the PHD domain [32]. To better understand the functions of TaPHDs, we used Plant-mPLoc and BUSCA to predict their subcellular localization. The results showed that more than 90% of the TaPHD proteins were localized in the nucleus (Table S1). In Arabidopsis thaliana , the PHD genes AL5 and AL6 play a very important role in improving the tolerance of plants to abiotic stress. Therefore, we selected TaPHD11 and TaPHD19, which are highly homologous to AtALs , for subcellular localization of wheat protoplasts. As shown in Figure 12, this suggests that, in wheat, the proteins TaPHD11 and TaPHD19 not only function in the nucleus but also in the membrane. In addition, research has shown that PHD finger ING2 is a phosphoinositide binding module and a nuclear PtdInsP receptor and suggests that PHD-phosphoinositide interactions directly regulate nuclear responses to DNA damage [57]. However, we studied the protein TaPHD133, which is highly homologous to ING1, and found that it is localized not only in the nucleus, but also in the membrane. In summary, the subcellular localization of PHD proteins in wheat differs from that in other species. 4. Discussion As an important transcription factor in organisms, the PHD gene family not only plays a key role in regulating plant growth and development but also plays an important regulatory role when plants face biotic and abiotic stresses [18]. In this study, we identified 244 TaPHD gene members in the wheat genome for the first time (Supplementary Table S3), and the vast majority of the TaPHD proteins were located in the nucleus. In terms of the number of genes, the number of TaPHD genes increased significantly compared with other species. This is because the origin of wheat involves two polyploidy events, resulting in the existing allohexaploid bread wheat. However, compared with the 59 and 67 PHD members in the diploid gramineous crops rice and maize, respectively, it is not multiplied, indicating that the PHD gene in wheat has a more exaggerated expansion and evolution. Gene duplication events are important for the rapid expansion and evolution of plant gene families [58]. About 70-80% of angiosperms experience duplication events [59,60], and in common wheat ( Triticum aestivum L.), more than 85% of the sequences are duplicates [61]. Physical localization on chromosomes and covariance analysis (Figure 4 and 5) revealed the presence of a large number of segmental duplication events during the evolution of TaPHD genes, suggesting that segmental duplication contributes to the amplification of TaPHD genes. The proportion of TaPHDs with a 1:1:1 ratio of the three subgenomes A:B:D accounted for 84.8% of the total proportion (Table 2), which was much higher than the 35.8% observed for the whole wheat genome, indicating that the PHD gene family is highly conserved in the three subgenomes compared to other genes. In terms of the covariance and evolutionary relationship of wheat PHD genes among species (Figure 5), the PHD-finger family diverged between monocotyledonous and dicotyledonous species, with the average divergence time from the monocotyledonous species as barley (12.78 Mya) < rice (22.09 Mya) < maize (60.87 Mya), indicating a more similar genetic structure to barley. Phylogenetic analysis showed that PHD proteins in three species (including Arabidopsis , O. stiva , and T. aestivum ), which are distant from each other, could be divided into four large evolutionary branches, and each group of evolutionary branches contained many smaller evolutionary branches. From the results, there were some small branches containing only wheat PHD genes, which was consistent with previous findings that wheat PHD genes had more exaggerated expansion and evolution. When the PHD genes with different chaperone structural domains were subdivided (Table 1), the fold divergences were also different; for example, ING1, ING2, ROS1, EBS, and PKL were expanded 3-fold, while SHL1 was expanded 6-fold, and VIN3 and SIZ1 were expanded 9-fold and 11-fold, respectively. It is likely that the presence of many redundant genes has contributed to the stability of the genome of the hexaploid wheat species [62]. Genes perform their functions through transcription and translation, and the expression patterns of genes reflect their function. PHD genes can regulate the growth and development of plants; therefore, their expression in different plant tissues has also attracted much attention. Studies have shown that the expression patterns of the PHD gene family in rice, maize, potato, and cotton are concentrated in different tissue types [25-27]. In rice, the expression levels of OsPHD s were relatively high in pre-emergence inflorescences and pistils, and the number of lowly expressed OsPHD s was significantly higher in the seed stage (10 days) compared with that in the other periods [25]. In potato, considerable differences in expression are observed between individual StPHD genes from different tissues. For example, StPHD27 is abundantly expressed in roots, shoots, and stamens, but has lower expression levels in petals, carpels, and leaves [27]. In cotton, GhPHD s genes have the highest expression levels in ovule and fiber tissues, suggesting that GhPHD s may be involved in regulating ovule and fiber development [26]. This study showed that the TaPHD gene expression in various tissues of wheat showed great differences with the growth period; in particular, the TaPHD gene expression was highest in the stigma and ovary at the flowering stage. This may be because a large number of PHD proteins in the PHD family regulate plant reproductive and developmental processes. For example, MMD1, MS1, VIM1, and SHL1 in Arabidopsis have been shown to play key roles in the reproductive growth stage [20,63,64]. Moreover, TaPHD100 , TaPHD108 , and TaPHD122 were highly expressed during the whole growth period. These three genes are highly orthologous to AtAL6 and AtAL7 . In Arabidopsis , AtAL6 and AtAL7 are methylated by histones via the PHD domain, and the modification sites H3K4me3 and H3K4me2 bind to regulate the expression of target genes. Alifn-PHD domain proteins bind to di- or trimethylated histone H3 (H3K4me3/2) and affect plant growth and development in Arabidopsis [52]. Furthermore, PWWP-PHD-SET domain proteins have histone methyltransferase activities and regulate the development of roots, leaves, and floral organs, as well as the transcription of some stress genes [23]. Therefore, TaPHD100 , TaPHD108 , and TaPHD122 may play important roles in regulating the growth and development of wheat histone methylation [65]. In addition, TaPHD222 and TaPHD232 are only highly expressed in shoots and roots; these two genes are highly orthologous to ORC1A/B, whereas in Arabidopsis , the ORC1A/B protein binds methyl groups through the PHD domain and functions as a transcriptional activator [66]. Therefore, we infer that TaPHD222 and TaPHD232 are essential for root and shoot development. However, their function during development requires further verification. The PHD family not only regulates plant growth and development but also responds to abiotic stresses. Existing research shows that PHD family transcription factors also play an important role in coping with abiotic stress. For example, the PHD genes AL5 and AL6 in Arabidopsis bind to the promoter regions of downstream target genes, thereby inhibiting various signaling pathways to improve the tolerance of plants to abiotic stresses, such as low temperature, drought, and high salt [56,57]. AtSIZ1 accumulates high levels of SUMOylated proteins through an ABA-independent pathway in response to abiotic stresses such as drought, low temperature, and heat shock [67]. In rice, the cis-acting elements DRE/CRT in the OsPHD13 and OsPHD52 promoters are upregulated by as much as 15-fold under low-temperature stress. Overexpression of OsPHD1 can significantly improve plant tolerance to stress (drought, high salt, and low temperature) [30]. In maize, the expression of subfamily IX TaPHD s responds to salt, drought, and ABA stress [29]. In this study, TaPHD11 and TaPHD19 , which are highly homologous to ALs , were upregulated only under induction by PEG treatment. This suggests that there are differences in the responses of PHD genes to abiotic stresses among species. Through transcriptome data, we found that 122 TaPHD s showed significant responses to low temperatures, drought, or high temperatures. Among them, 45 TaPHDs genes were significantly changed under two or three treatments, indicating that TaPHD s play an active role in plant responses to low-temperature, drought, or high-temperature stress. In order to better verify the adaptability of TaPHDs to the above three abiotic stresses, we selected a representative cultivar "zhengmai 7698" from the Huanghuai wheat area of China and performed qRT-PCR analysis. We found that TaPHD11 and TaPHD19 , which are highly homologous to AtALs , were significantly upregulated only under drought treatment, which is different from the results of the previous study in Arabidopsis {Chandrika, 2013 #5}{Wei, 2015 #52}, indicating that ALs seem to have different responses to abiotic stress in monocotyledonous and dicotyledonous plants. At the same time, subcellular localization experiments also showed that TaPHD11 and TaPHD19 were localized in the nucleus and cell membrane, indicating that they function not only in the nucleus but also in the cell membrane of wheat. TaPHD69 , which is highly homologous to AtSIZ1 , can be significantly upregulated under low-temperature, drought, and high-temperature conditions. The accumulation of TaPHD69 seems to be beneficial for plants to cope with abiotic stress, which is similar to the function of AtSIZ1 in Arabidopsis . 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Tables Table 1 Types, names, and numbers of wheat PHD-finger genes Domain type Wheat triad Rice orthologs Arabidopsis thaliana orthologs Gene number Chr Genomes PHD TaPHD1/TaPHD8/TaPHD15 3 1 ABD TaPHD5/TaPHD12 2 1 AB TaPHD21/TaPHD34/TaPHD46 3 2 ABD TaPHD62/TaPHD73/TaPHD84 OsPHD5 3 3 ABD TaPHD82 1 3 D TaPHD94/TaPHD114/TaPHD128 OsPHD24 3 4 ABD TaPHD218/TaPHD226/TaPHD237 OsPHD24 3 7 ABD TaPHD98/TaPHD110/TaPHD124 3 4 ABD TaPHD99/TaPHD109/TaPHD123 OsPHD55 AtPHD6 3 4 ABD TaPHD101/TaPHD107/TaPHD121 OsPHD19 MS1,MMD1 3 4 ABD TaPHD143/TaPHD160/TaPHD177 OsPHD52 MS1,MMD1 3 5 ABD TaPHD103 1 4 A TaPHD137/TaPHD154/TaPHD172 3 5 ABD TaPHD146/TaPHD163/TaPHD180 OsPHD58 AtPHD54 3 5 ABD TaPHD168/TaPHD185 2 5 BD TaPHD186 OsPHD11 1 5 D TaPHD192/TaPHD201/TaPHD209 OsPHD14,OsPHD37 AtPHD8,AtPHD37 3 6 ABD PHD-PHD TaPHD135/TaPHD152/TaPHD170 OsPHD59 AtPHD32,AtPHD40 3 5 ABD TaPHD144/TaPHD161/TaPHD178 AtPHD29 3 5 ABD TaPHD216/TaPHD224/TaPHD235 OsPHD48 3 7 ABD Alifn-PHD TaPHD4/TaPHD11/TaPHD18 OsPHD30 AL1,AL2 3 1 ABD TaPHD6/TaPHD13/TaPHD19 OsPHD31 AL6,AL7 3 1 ABD TaPHD26/TaPHD39/TaPHD51 OsPHD44 AL3.AL4,AL5 3 2 ABD TaPHD31/TaPHD44/TaPHD56 AL1,AL2,AL3.AL4,AL5,AL6,AL7 3 2 ABD TaPHD64/TaPHD75/TaPHD86 OsPHD7 AL6,AL7 3 3 ABD TaPHD100/TaPHD108/TaPHD122 OsPHD56 AL6,AL7 3 4 ABD TaPHD167/TaPHD184 OsPHD23,OsPHD42 AL1,AL2 2 5 BD TaPHD104/TaPHD229/TaPHD230/TaPHD243/TaPHD244 AL1,AL2,AL3.AL4,AL5,AL6,AL7 5 4(7) A(DD)UU ARID-PHD TaPHD142/TaPHD159/TaPHD176 3 5 ABD RING-PHD TaPHD23/TaPHD36/TaPHD48 OsPHD46 AtPHD30 3 2 ABD TaPHD93/TaPHD115/TaPHD129 OsPHD17 AtPHD30 3 4 ABD ING-PHD TaPHD105/TaPHD119/TaPHD133 OsPHD16 ING1 3 4 ABD TaPHD148/TaPHD165/TaPHD182 OsPHD21 ING2 3 5 ABD BAH-PHD TaPHD27/TaPHD40/TaPHD53 OsPHD41 SHL1 3 2 ABD TaPHD141/TaPHD158/TaPHD175 OsPHD49,OsPHD51 EBS 3 5 ABD TaPHD149/TaPHD166/TaPHD183 OsPHD22 SHL1 3 5 ABD Jas-PHD TaPHD28/TaPHD41/TaPHD52 OsPHD40 AtPHD1,AtPHD61,AtPHD62 3 2 ABD TaPHD147/TaPHD164/TaPHD181 OsPHD20 AtPHD1,AtPHD61,AtPHD62 3 5 ABD TaPHD30/TaPHD43/TaPHD55 OsPHD25 3 2 ABD TaPHD33/TaPHD45/TaPHD58 ROS4 3 2 ABD TaPHD22/TaPHD35/TaPHD47 OsPHD47 AtPHD68,AtPHD70 3 2 ABD TaPHD92/TaPHD116/TaPHD130 OsPHD47 AtPHD68,AtPHD70 3 4 ABD TaPHD66/TaPHD76/TaPHD88 OsPHD9 3 3 ABD TaPHD68/TaPHD78 OsPHD9 2 3 AB TaPHD106/TaPHD212 OsPHD32 AtPHD24,AtPHD26,AtPHD27,AtPHD41 2 4(7) A(A) TaPHD220/TaPHD227/TaPHD238 OsPHD38 AtPHD24,AtPHD26,AtPHD27,AtPHD41 3 7 ABD DDT-PHD TaPHD25/TaPHD38/TaPHD50 OsPHD45 DDP1,DDP2 3 2 ABD TaPHD97/TaPHD112/TaPHD125 OsPHD54 DDP3 3 4 ABD TaPHD138/TaPHD155/TaPHD173 OsPHD54 DDP3 3 5 ABD zf-HC5HC2H-PHD TaPHD59/TaPHD70/TaPHD80 OsPHD1 3 3 ABD PHD-Oberon_cc TaPHD91/TaPHD118/TaPHD132 3 4 ABD TaPHD95/TaPHD111/TaPHD127 OBE1,OBE2 3 4 ABD TaPHD136/TaPHD153/TaPHD171 OBE1,OBE2 3 5 ABD TaPHD117/TaPHD131 2 4 BD PHD-FN3 TaPHD3/TaPHD10/TaPHD17 VIN3 3 1 ABD TaPHD134/TaPHD151/TaPHD169 VIN3 3 5 ABD TaPHD190/TaPHD199/TaPHD207 VIN3 3 6 ABD PHD-SANT TaPHD63/TaPHD74/TaPHD85 3 3 ABD TaPHD194/TaPHD203/TaPHD211 3 6 ABD PHD-WHIM1 TaPHD102/TaPHD191/TaPHD200/TaPHD208 MBD9 4 6(4) (A)ABD PHD-SET TaPHD67/TaPHD77/TaPHD89 OsPHD8 ATXR5,ATXR6 3 3 ABD TaPHD187/TaPHD196/TaPHD242 OsPHD10 ATXR5,ATXR6 3 6 AB(U) PWWP-PHD-SET TaPHD60/TaPHD71/TaPHD81 OsPHD2,OsPHD4 ATX3,ATX4,ATX5 3 3 ABD PWWP-FYRN-FYRC-PHD-SET TaPHD140/TaPHD157/TaPHD174 OsPHD50 ATX1,ATX2 3 5 ABD PHD-BAH TaPHD234 1 7 D PHD-BAH-AAA TaPHD214/TaPHD222/TaPHD232 OsPHD33 ORC1A,ORC1B 3 7 ABD PHD-homeodomain TaPHD7/TaPHD14/TaPHD20 PRHA 3 1 ABD TaPHD61/TaPHD72/TaPHD83 OsPHD35 HAT3.1 3 3 ABD TaPHD189/TaPHD198/TaPHD206 3 6 ABD PHD-PLN03142 TaPHD65/TaPHD87 2 3 AD TaPHD195/TaPHD204/TaPHD241 3 6 ABD PHD-RING TaPHD2/TaPHD9/TaPHD16 OsPHD29 SIZ1 3 1 ABD TaPHD69/TaPHD79/TaPHD90 SIZ1 3 3 ABD TaPHD96/TaPHD113/TaPHD126 SIZ1 3 4 ABD TaPHD139/TaPHD156 SIZ1 2 5 AB PHD-JmjC-PLU1 TaPHD219/TaPHD228/TaPHD239 3 7 ABD AAA_34-PHD-Helicase_C_4 TaPHD32/TaPHD57 OsPHD27 EMB1135 2 2 AD TaPHD217/TaPHD225/TaPHD236 OsPHD27 EMB1135 3 7 ABD PHD-zf-HC5HC2H-zf-HC5HC2H TaPHD193/TaPHD202/TaPHD210 OsPHD15,OsPHD34 AtPHD18 3 6 ABD TaPHD215/TaPHD223/TaPHD233 3 7 ABD BRCT-BRCT-PHD TaPHD24/TaPHD37/TaPHD49 OsPHD18 3 2 ABD TaPHD188/TaPHD197/TaPHD205 OsPHD18 3 6 ABD PHD-SWIB-GYF-Plus3 TaPHD120/TaPHD150/TaPHD240 3 4(5) (A)BU PHD-SWIB-Plus3-GYF TaPHD145/TaPHD162/TaPHD179 3 5 ABD PHD-Chromo-Helicase_C-DUF TaPHD213/TaPHD221/TaPHD231 PKL 3 7 ABD PHD-Cohesin_HEAT-Nipped-B_C TaPHD29/TaPHD42/TaPHD54 EMB2773 3 2 ABD Table 2 Groups of homoeologous PHD-finger genes in wheat Homoeologous group (A: B: D) All wheat genes 1 Wheat PHD-finger genes (all) Number of groups Number of genes % of genes 2 1: 1: 1 35.8% 69 207 84.8 n: 1: 1/1: n: 1/1: 1: n 3 5.7% 1 4 1.6 1: 1: 0/1: 0: 1/0: 1: 1 13.2% 8 16 6.6 Other ratios 4 8.0% 3 11 4.5 Orphans/singletons 37.1% 4 4 1.6 Not categorized 5 - - 2 0.8 99.8% 244 100.0 Note: 1 According to IWGSC (2018). 2 Percentage calculated with 244 genes. 3 For n > 1. 4 E.g., n:1:n or 0:1:n, n > 1. 5 See Table 1 and Table S3. Supplementary Files TableS1.xlsx TableS2.xlsx TableS3.xlsx TableS4.xlsx TableS5.xlsx TableS6.xlsx TableS7.xlsx TableS8.xlsx TableS9.xlsx Cite Share Download PDF Status: Published Journal Publication published 11 Dec, 2022 Read the published version in Frontiers in Plant Science → Version 2 posted You are reading this latest preprint version Show more versions Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-1799303","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":117373220,"identity":"eb7f75d7-4409-4cb0-8b9c-9ddf45adfc91","order_by":0,"name":"Fei Pang","email":"","orcid":"","institution":"Yulin Normal University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Fei","middleName":"","lastName":"Pang","suffix":""},{"id":117373227,"identity":"7e3f263a-acf3-4fa6-9f76-1809abe44130","order_by":1,"name":"Junqi Niu","email":"","orcid":"","institution":"Yulin Normal University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Junqi","middleName":"","lastName":"Niu","suffix":""},{"id":117373223,"identity":"fcd6a8bc-172b-40ef-a664-cf3930a5a621","order_by":2,"name":"Zhaoliang Liu","email":"","orcid":"","institution":"Yulin Normal University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Zhaoliang","middleName":"","lastName":"Liu","suffix":""},{"id":117373231,"identity":"b68dc1cc-7fdd-435c-ab33-097bae7b940c","order_by":3,"name":"Zhen Wang","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA+ElEQVRIiWNgGAWjYJAC5j8VNjxszPwPDiRUSMjJE6WH50yaDB97D+OBD2csjA0biNHC23bYRo7nDPPBmW0ViQwHCKg2OH728AvJtjQeNoncA4d550kkMDYwP3x0A5+WM3lpFgbngH6RyEs4zLtNIo+dgc3YOAePFrMDOWYGCWUgWxIMQFqKGRt42KTxajn/xszgANthqJY5EokNBwhpuZFj/LChDaiF54zBwZkNRGixv/HGjJnhDNBh7G0JBz4ckzA2bCbgF8n+HOPPDBU29vLNzIc/JNTUycmzNz98jE8LELBJoPKZ8SsHK/lAWM0oGAWjYBSMaAAAcSVOtLlG2dIAAAAASUVORK5CYII=","orcid":"","institution":"Yulin Normal University","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Zhen","middleName":"","lastName":"Wang","suffix":""}],"badges":[],"createdAt":"2022-06-27 10:19:39","currentVersionCode":2,"declarations":"","doi":"10.21203/rs.3.rs-1799303/v2","doiUrl":"https://doi.org/10.21203/rs.3.rs-1799303/v2","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.3389/fpls.2022.1016831","type":"published","date":"2022-12-12T00:00:00+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":24684677,"identity":"55150bdb-f64c-432f-a319-65373874ca3b","added_by":"auto","created_at":"2022-08-02 19:04:06","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1312953,"visible":true,"origin":"","legend":"\u003cp\u003eProtein sequence multiple alignment of the PHD-finger domains in TaPHD family proteins. The multiple alignment was conducted with the amino acid sequences within the predicted PHD domains by using Jalview software. The conserved amino acids (Cys4-His-Cys3) within the PHD-finger domains are shaded in red and blue.\u0026nbsp;\u003c/p\u003e","description":"","filename":"Figure1domain.png","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/73471496bb45d28aff0f7478.png"},{"id":24684679,"identity":"a4016786-076d-4fa4-b574-541deb62bb86","added_by":"auto","created_at":"2022-08-02 19:04:06","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":160366,"visible":true,"origin":"","legend":"\u003cp\u003ePhylogenetic tree of \u003cem\u003ePHD\u003c/em\u003e genes in wheat, rice, and\u003cem\u003e Arabidopsis\u003c/em\u003e. The tree was analyzed in MEGA X by using the neighbor-joining method. The PHDs from wheat, rice, and \u003cem\u003eArabidopsis\u003c/em\u003e are distinguished with black, red, and green dots. The PHD proteins were grouped into four distinct clades (clades 1-4), which are indicated by colored branches.\u003c/p\u003e","description":"","filename":"Figure2TaAtOsPHD244NJEvolutionarytree.png","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/eebeae6bd570fb1fa9d92945.png"},{"id":24685131,"identity":"12ab0f38-a5bf-4d3e-bbf0-5f0ef2b0095c","added_by":"auto","created_at":"2022-08-02 19:14:06","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1602831,"visible":true,"origin":"","legend":"\u003cp\u003eChromosomal localization of the \u003cem\u003eTaPHDs.\u003c/em\u003e The light blue column represents the chromosome. The depth of blue in the columns represent the density of genes on the chromosome.\u0026nbsp;\u003c/p\u003e","description":"","filename":"Figure3Selfcircle.png","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/2da042ea04a9ceac3343f301.png"},{"id":24685579,"identity":"0c23346f-3e88-400e-8d5f-f0d62302cbf2","added_by":"auto","created_at":"2022-08-02 19:19:06","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":791464,"visible":true,"origin":"","legend":"\u003cp\u003eSynteny analysis of \u003cem\u003ePHD \u003c/em\u003egenes in wheat. All \u003cem\u003eTaPHD\u003c/em\u003e genes were mapped to their respective locus in the wheat genome in a circular diagram using shinyCircos [42]. Subgenomes are indicated by different shades of blue (outer track), and chromosomal segments are indicated by shades of gray (inner track). Homoeologous \u003cem\u003ePHD\u003c/em\u003e genes were inferred by phylogeny (for details see the Materials and Methods section) and linked with chromosome-specific colors.\u003c/p\u003e","description":"","filename":"Figure4Collinearanalysistotal.png","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/39b9d97eeac946965d0fd58c.png"},{"id":24685134,"identity":"36204386-f8a9-402f-8e79-6ccb3937a1a4","added_by":"auto","created_at":"2022-08-02 19:14:06","extension":"jpg","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":5913215,"visible":true,"origin":"","legend":"\u003cp\u003eSynteny analysis of \u003cem\u003ePHD \u003c/em\u003egenes between wheat and six representative plants (maize, barley, rice,\u003cem\u003e Arabidopsis\u003c/em\u003e, cotton,\u003cem\u003e \u003c/em\u003eand\u003cem\u003e Brassica rapa\u003c/em\u003e). Each different species is replaced with a different color. The gray line in the background indicates a collinear block in the genome of wheat and other plants, while the line highlights the isomorphic \u003cem\u003ePHD \u003c/em\u003egene pair. Homoeologous \u003cem\u003ePHD\u003c/em\u003e genes were inferred by phylogeny (for details see the Materials and Methods section) and linked with chromosome-specific colors.\u0026nbsp;\u003c/p\u003e","description":"","filename":"Figure5GeneLocation.jpg","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/be7490b3b1f7334c1553cf9f.jpg"},{"id":24685577,"identity":"99ac997a-39fa-4955-b33a-e4f1319990b3","added_by":"auto","created_at":"2022-08-02 19:19:06","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":139543,"visible":true,"origin":"","legend":"\u003cp\u003eFunctional annotation analysis of \u003cem\u003eTaPHD \u003c/em\u003egenes. Gene Ontology (GO) classification based on \u003cem\u003eTaPHD \u003c/em\u003egene annotation. The GO terms are grouped into three main categories: purple for Biological Processes, red for Cellular Components, and yellow for Molecular Function.\u003c/p\u003e","description":"","filename":"Figure6Go.png","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/73125d906f1c427ee409863d.png"},{"id":24685580,"identity":"c065e6e2-5b9e-476d-a40f-516315ad30de","added_by":"auto","created_at":"2022-08-02 19:19:06","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":11704816,"visible":true,"origin":"","legend":"\u003cp\u003ePredicted protein association networks analyses of TaPHD proteins. The four colors represent different interaction areas. The nodes represent the proteins, and the lines represent the protein–protein associations. Light blue and purple lines represent the known interactions from the curated database or experimentally determined interactions; green, red, and blue lines represent gene neighborhood, gene fusions, and gene co-occurrence, indicating that the proteins have the predicted interactions; yellow, black, and light blue lines represent textiming, co-expression, and protein homology, respectively.\u003c/p\u003e","description":"","filename":"Figure7ProteinInteracting.png","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/c16a95324ed8ff6af8c6ae30.png"},{"id":24684696,"identity":"cd0d1785-4b63-48e2-8fc0-d2b6f483bbda","added_by":"auto","created_at":"2022-08-02 19:04:06","extension":"png","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":388112,"visible":true,"origin":"","legend":"\u003cp\u003eThe expression of \u003cem\u003eTaPHD\u003c/em\u003es during different biological stress. Volcano map of expression profiles for 244 \u003cem\u003eTaPHD \u003c/em\u003egenes under different biological/abiotic stresses, including \u003cem\u003eFusarium\u003c/em\u003e infection, crown rot infection, powdery mildew infection, stripe rust infection, \u003cem\u003eSeptoria \u003c/em\u003e(\u003cem\u003eSeptoria tritici\u003c/em\u003e infection and \u003cem\u003eZymoseptoria tritici\u003c/em\u003e infection), PAMP (chitin and flg22 infection), cold stress, drought-1 (drought stress in Giza 168), drought-2 (drought stress in Gemmiza 10), heat stress, and phosphorus starvation. DEGs were defined as Fold Change \u0026gt; 1 and FDR \u0026lt; 0.05.\u003c/p\u003e","description":"","filename":"Figure9DiseaseStress.png","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/673d41af7cc0770f72cc8d4f.png"},{"id":24685636,"identity":"116b1bfb-050d-429c-a831-3ab1b1a132c9","added_by":"auto","created_at":"2022-08-02 19:24:06","extension":"png","order_by":10,"title":"Figure 10","display":"","copyAsset":false,"role":"figure","size":70446,"visible":true,"origin":"","legend":"\u003cp\u003eVenn diagram of DEGs in \u003cem\u003eTaPHD \u003c/em\u003egenes during different abiotic stress. DEGs of \u003cem\u003eTaPHD \u003c/em\u003egenes in different abiotic stress conditions, including cold stress, drought-1 (drought stress in Giza), drought-2 (drought stress in Gemmiza), and heat stress.\u003c/p\u003e","description":"","filename":"Figure10ColdDroughtHeatVenn.png","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/0c2219b701ca596de2a45311.png"},{"id":24685138,"identity":"0dba21f8-0ffe-4a2d-9bf7-aa55a4816fed","added_by":"auto","created_at":"2022-08-02 19:14:06","extension":"tif","order_by":11,"title":"Figure 11","display":"","copyAsset":false,"role":"figure","size":2194163,"visible":true,"origin":"","legend":"\u003cp\u003eRelative expression levels of 20 genes under three different treatments. Expression of \u003cem\u003eTaPHD\u003c/em\u003e genes in wheat were detected after 4℃, 16% PEG, and 40℃ treatments for 0, 1, 6, and 12 h.\u003c/p\u003e","description":"","filename":"Figure11qPCR.tif","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/0262ab89ca75ff1512f63ad3.tif"},{"id":24684886,"identity":"30f4b902-75ec-412e-a7c0-398c27fdb3b7","added_by":"auto","created_at":"2022-08-02 19:09:06","extension":"tif","order_by":12,"title":"Figure 12","display":"","copyAsset":false,"role":"figure","size":1311439,"visible":true,"origin":"","legend":"\u003cp\u003eThe subcellular location of \u003cem\u003eTaPHD11\u003c/em\u003e, \u003cem\u003eTaPHD19\u003c/em\u003e, and \u003cem\u003eTaPHD133\u003c/em\u003e. Localization of TaPHD proteins under normal conditions. Images were observed under a confocal laser scanning microscope (LSM 700, Zeiss). Scale bars = 10 μm.\u003c/p\u003e","description":"","filename":"Figure12Subcellularlocalization.tif","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/4902ead1927c70b62f33ba1f.tif"},{"id":33044231,"identity":"5265092e-0c8a-4d76-8658-bc05686002a6","added_by":"auto","created_at":"2023-02-16 17:06:31","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":7178344,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/9c19a793-d4fa-47f5-9679-588e22253c6d.pdf"},{"id":24684877,"identity":"118d3256-a62c-42a6-a538-17dd0c1bd68e","added_by":"auto","created_at":"2022-08-02 19:09:06","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":75588,"visible":true,"origin":"","legend":"","description":"","filename":"TableS1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/198cc2915eae8465317bd81c.xlsx"},{"id":24684678,"identity":"c8c0106b-6207-4872-b638-d76ecb1b3ae6","added_by":"auto","created_at":"2022-08-02 19:04:06","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":11330,"visible":true,"origin":"","legend":"","description":"","filename":"TableS2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/8621adf1b592fbeb613f66d1.xlsx"},{"id":24684684,"identity":"ded886d7-1413-4484-9faf-dc5a8efc0473","added_by":"auto","created_at":"2022-08-02 19:04:06","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":34930,"visible":true,"origin":"","legend":"","description":"","filename":"TableS3.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/7e1741d260c57d3383c010a7.xlsx"},{"id":24684687,"identity":"2610ba05-e0e5-4e70-b4e3-5cb3cec391fc","added_by":"auto","created_at":"2022-08-02 19:04:06","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":84565,"visible":true,"origin":"","legend":"","description":"","filename":"TableS4.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/12149779cba3d88120b6260d.xlsx"},{"id":24685635,"identity":"d4525234-765f-4225-942b-b276136f424c","added_by":"auto","created_at":"2022-08-02 19:24:06","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":20750,"visible":true,"origin":"","legend":"","description":"","filename":"TableS5.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/cb6e324f6e2ed3d6e6704af1.xlsx"},{"id":24684874,"identity":"86dc109a-fa7d-43f6-b16d-2d1cb719f7b7","added_by":"auto","created_at":"2022-08-02 19:09:06","extension":"xlsx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":46252,"visible":true,"origin":"","legend":"","description":"","filename":"TableS6.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/8d3997d5f40a205175f5509c.xlsx"},{"id":24684697,"identity":"3e54df7b-dec1-4d01-b0b1-7790bf2d0fe1","added_by":"auto","created_at":"2022-08-02 19:04:06","extension":"xlsx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":376192,"visible":true,"origin":"","legend":"","description":"","filename":"TableS7.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/98377d77cec70095714011d0.xlsx"},{"id":24684880,"identity":"f4617e51-4264-4099-b808-a0f45df62990","added_by":"auto","created_at":"2022-08-02 19:09:06","extension":"xlsx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":1794962,"visible":true,"origin":"","legend":"","description":"","filename":"TableS8.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/10a19c6cb1a9aeec871f586b.xlsx"},{"id":24684689,"identity":"6b9f366d-eb76-44b2-9df4-3244ddd3ac54","added_by":"auto","created_at":"2022-08-02 19:04:06","extension":"xlsx","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":9877,"visible":true,"origin":"","legend":"","description":"","filename":"TableS9.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-1799303/v2/3d9baa0988e71a152cbca05f.xlsx"}],"financialInterests":"","formattedTitle":"\u003cp\u003e\u003cem\u003ePHD-finger\u003c/em\u003e family genes in wheat (\u003cem\u003eTriticum aestivum\u003c/em\u003e L.): evolutionary conservatism, functional diversification, and active expression in abiotic stress\u003c/p\u003e","fulltext":[{"header":"1. Introduction","content":"\u003cp\u003ePlants encounter various unfavorable growth conditions during their life cycle, such as pests and diseases, drought, and extreme temperatures. In response to adverse external environments, plants activate in vivo defense response mechanisms by inducing stress-responsive gene expression\u0026nbsp;[1,2]. Many plant-specific transcription factor (TF) family members are involved in plant-specific developmental processes and participate in and regulate the stress response of plants to the external environment, thereby improving\u0026nbsp;their adaptation to adversity\u0026nbsp;[3]. To date, some such transcription factors have been successively isolated from many species of plants, such as AP2/ERF\u0026nbsp;[4], bHLH\u0026nbsp;[5], MYB\u0026nbsp;[6],\u0026nbsp;and WRKY\u0026nbsp;[7]. Among these, the PHD-finger transcription factor family is tissue-specific and plays an important role in plant growth, development, and transcriptional regulation by adversity. The plant homeodomain (PHD) is a conserved zinc finger structural domain in biological evolution and is commonly distributed in eukaryotes ranging from yeast to plants and animals\u0026nbsp;[8-12]. A typical PHD domain consists of 50-80 amino acid residues with a characteristic Cys4-His-Cys3 sequence, which is arranged in a manner similar to RING (Cys3-His-Cys4) and LIM (Cys2-His-Cys5)\u0026nbsp;[13,14]. The most important function of the PHD domain is the specific recognition of various histone modifications and DNA sequences, thus acting in transcriptional regulation and participating in various biological processes in organisms\u0026nbsp;[15-17]. For example, previous studies have shown that, in model plants, proteins containing PHD domains are involved in embryonic meristem germination, root development, photoperiod, vernalization, meiosis, and post-meiotic pollen development. PHD domains plays an important role in plant growth and development\u0026nbsp;[18].\u003c/p\u003e\n\u003cp\u003ePHD domains are a class of relatively small protein domains. Their relatively conserved cysteine and histidine can stabilize the normal spatial structure by binding zinc ions, so that the three-dimensional conformation of the entire domain is basically spherical\u0026nbsp;[19]. In addition to the conserved Cys4-His-Cys3 residues, PHD proteins usually contain highly diverse sequences. These diverse sequences form genes with different biological functions\u0026nbsp;within the\u0026nbsp;\u003cem\u003ePHD-finger\u003c/em\u003e family. For example, the PHD domain\u0026ndash;containing protein MMD1 is involved in essential chromatin remodeling and transcriptional events during male meiosis\u0026nbsp;[20]. In \u003cem\u003eArabidopsis\u003c/em\u003e,\u0026nbsp;the ALFIN1-like (AL) protein, which contains the PHD domain, plays a key role in seed germination\u0026nbsp;[21]. Furthermore, the PHD-finger protein VIL1 is involved in\u0026nbsp;the photoperiod and vernalization pathways, as it regulates the expression of related floral repressors\u0026nbsp;[22]. ATX1 and ATX2 have histone methyltransferase activities and regulate the development of roots, leaves, and floral organs,\u0026nbsp;as well as the transcription of some stress genes\u0026nbsp;[23].\u003c/p\u003e\n\u003cp\u003eSince Schinder first discovered and identified PHD proteins in plants in 1993\u0026nbsp;[24], an increasing number of \u003cem\u003ePHDs\u003c/em\u003e have been reported. To date, 59 members of \u003cem\u003eOryza stiva\u0026nbsp;\u003c/em\u003e[25], 108 members of \u003cem\u003eGossypium hirsutum\u0026nbsp;\u003c/em\u003e[26], 72 members of \u003cem\u003eSolanum tuberosum\u0026nbsp;\u003c/em\u003e[27], 60 members of \u003cem\u003ePhyllostachys edulis\u0026nbsp;\u003c/em\u003e[28], and 67 members of \u003cem\u003eZea mays\u0026nbsp;\u003c/em\u003e[29]\u0026nbsp;have been identified. It is known that PHD proteins not only participate in the regulation of plant growth and development, but also play an important role in stress response, especially to abiotic stresses such as salt, high-temperature, low-temperature, and drought stress. In rice, overexpression of the \u003cem\u003eOsPHD1\u003c/em\u003e gene can significantly improve tolerance to low-temperature, high-salt, and drought stress\u0026nbsp;[30]. Overexpression of the PHD-finger\u003cem\u003e\u0026nbsp;\u003c/em\u003etranscription factor gene \u003cem\u003eOsMsr16\u003c/em\u003e can enhance salt tolerance in rice plants\u0026nbsp;[31]. Wei et al. also found that \u003cem\u003eArabidopsis thaliana\u003c/em\u003e transgenic plants overexpressing soybean \u003cem\u003eGmPHD2\u003c/em\u003e exhibited higher salt tolerance, possibly because overexpression of \u003cem\u003eGmPHD2\u003c/em\u003e enhanced the scavenging of oxidative substances\u0026nbsp;[32]. Furthermore, under abiotic stress, genes in the \u003cem\u003ePHD-finger\u003c/em\u003e family in maize, cotton, and poplar show\u0026nbsp;differential expression under salt, drought, and cold stress\u0026nbsp;[26,29,33]. Thus, it can be seen that the \u003cem\u003ePHD\u003c/em\u003e family genes play a crucial role in regulating plant resistance to stress.\u003c/p\u003e\n\u003cp\u003eWheat is a major food crop in the world and plays a crucial role in global food security. It is especially important to tap important resistance genes, breed new resistant wheat varieties, and improve the resistance of wheat itself\u0026nbsp;[34].\u0026nbsp;The\u0026nbsp;\u003cem\u003ePHD-finger\u003c/em\u003e gene family, which is essential for growth and development, has been identified and studied in many crops, but no systematic studies of the \u003cem\u003ePHD\u003c/em\u003e gene family in wheat have been performed. In the present study, we identified \u003cem\u003ePHD-finger\u003c/em\u003e family members in wheat for the first time and performed a comprehensive and systematic genome-wide analysis, including gene conserved motif analysis, phylogenetic relationships, Gene Ontology (GO) annotation analysis, covariance analysis, reciprocal relationship analysis, and subcellular localization. We also investigated the expression of PHD family proteins during growth and development, their specific expression in each organ, and their expression under multiple stresses of low temperature, high temperature, and drought. We lay the foundation for analyzing the functions of PHD proteins and regulating stress resistance and also provide theoretical references for the excavation of stress resistance genes and stress resistance breeding in wheat.\u003c/p\u003e"},{"header":"2. Materials And Methods","content":"\u003cp\u003e\u003cstrong\u003e2.1\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eIdentification and\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eclassification analysis\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;of \u003cem\u003ePHD\u0026nbsp;\u003c/em\u003efamily genes in wheat\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWhole genome data for \u003cem\u003eT. aestivum\u003c/em\u003e (IWGSC\u0026nbsp;RefSeq_v1.1)\u0026nbsp;were obtained from the Ensembl plant database\u0026nbsp;(http://plants.ensembl.org/info/website/ftp/index.html), and the\u0026nbsp;PHD-finger domain (PF00628) was downloaded from the PFAM database (https://pfam.xfam.org/). The PHD protein sequences from \u003cem\u003eA. thaliana\u0026nbsp;\u003c/em\u003e(70) and \u003cem\u003eO. sativa\u0026nbsp;\u003c/em\u003e(59) (Supplementary\u0026nbsp;Table S1)\u0026nbsp;[25]\u0026nbsp;were used as query sequences to search against the wheat protein dataset using the BLASTP program, and the threshold was set as\u0026nbsp;E-value\u0026nbsp;\u003cem\u003e\u0026lt;\u0026nbsp;\u003c/em\u003e1e-5. The NCBI-Batch CD-Search\u0026nbsp;[35]\u003csup\u003e\u0026nbsp;\u003c/sup\u003e(https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi),\u0026nbsp;PFAM database,\u0026nbsp;and SMART database\u0026nbsp;(http://smart.embl.de/) were used to further confirm the candidate \u003cem\u003ePHD-finger\u003c/em\u003e genes of\u0026nbsp;\u003cem\u003eT. aestivum.\u0026nbsp;\u003c/em\u003eThere were other spliced transcripts in the candidate genes of these species, and we selected the first splice variant as a representative for subsequent analysis.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThe protein sequences of the TaPHDs were computed\u0026nbsp;using the\u0026nbsp;ExPASy server\u0026nbsp;[36]\u003csup\u003e\u0026nbsp;\u003c/sup\u003eto obtain the theoretical isoelectric point (pI), molecular weight (MW), instability index\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e(II),\u0026nbsp;aliphatic index\u0026nbsp;(AI),\u0026nbsp;and grand average hydrophobicity (GRAVY).\u0026nbsp;Plant-mPLoc\u0026nbsp;[37]\u0026nbsp;(\u003ca href=\"http://www.csbio.sjtu.edu.cn/cgi-bin/PlantmPLoc.cgi\"\u003ehttp://www.csbio.sjtu.edu.cn/cgi-bin/PlantmPLoc.cgi\u003c/a\u003e)\u0026nbsp;and BUSCA\u0026nbsp;[38]\u0026nbsp;(Bologna Unified Subcellular Component\u0026nbsp;Annotator, http://busca.biocomp.unibo.it) were used to predict the subcellular localization of the TaPHD proteins.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.\u003c/strong\u003e\u003cstrong\u003e2 Phylogenetic analyses of \u003cem\u003eTaPHD\u003c/em\u003e genes\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe\u0026nbsp;PHD-finger protein sequences of \u003cem\u003eT. aestivum\u003c/em\u003e, \u003cem\u003eA. thaliana\u003c/em\u003e,\u003cem\u003e\u0026nbsp;\u003c/em\u003eand\u003cem\u003e\u0026nbsp;O. sativa\u003c/em\u003e were used for phylogenetic analysis. Jalview 2.11 software\u0026nbsp;(http://www.jalview.org/) with the MUSCLE method with default parameters was utilized to conduct multiple sequence alignment.\u0026nbsp;Evolutionary analysis involved 342 amino acid sequences (all wheat \u003cem\u003ePHD\u003c/em\u003e genes, and most\u0026nbsp;rice and \u003cem\u003eArabidopsis\u003c/em\u003e \u003cem\u003ePHD\u0026nbsp;\u003c/em\u003egenes). These analyses were conducted in MEGA X\u0026nbsp;[39]\u0026nbsp;using the neighbor-joining method\u0026nbsp;[40]. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. The evolutionary distances were computed using the Poisson correction method and were expressed as the number of amino acid substitutions per site.\u0026nbsp;The\u0026nbsp;iTOL website (http://itol.embl.de/) was used to visualize the phylogenetic tree.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.3 Gene duplication and\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eKa/Ks analysis of\u003cem\u003e\u0026nbsp;TaPHD\u003c/em\u003e\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;genes\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eMCScanX software\u0026nbsp;[41]\u0026nbsp;was used to detect collinear regions between \u003cem\u003eTaPHD\u003c/em\u003e genes as well as collinear blocks of \u003cem\u003eTaPHDs\u003c/em\u003e with\u0026nbsp;three monocotyledons (\u003cem\u003eH. vulgareto\u003c/em\u003e, \u003cem\u003eZ. mays\u003c/em\u003e, and \u003cem\u003eO. sativa\u003c/em\u003e) and three dicotyledons (\u003cem\u003eA. thaliana\u003c/em\u003e, \u003cem\u003eB. rapa\u003c/em\u003e, and \u003cem\u003eG. raimondii\u003c/em\u003e).\u0026nbsp;All \u003cem\u003eTaPHD\u003c/em\u003e genes were mapped to their respective loci in the wheat genome in a circular diagram using shinyCircos\u0026nbsp;[42].\u0026nbsp;Gene duplication events of \u003cem\u003eTaPHDs\u003c/em\u003e and synteny relationships between the aforementioned species were visualized using TBtools\u0026nbsp;(v1.082)\u0026nbsp;[43].\u0026nbsp;The Ka/Ks values (non-synonymous substitution rate/synonymous substitution rate) were calculated after identification of duplicated genes,\u0026nbsp;using\u0026nbsp;the method of\u0026nbsp;Nei and Gojobori as implemented in KaKs_calculator\u0026nbsp;[44]\u003cem\u003e\u0026nbsp;\u003c/em\u003ebased on the coding sequence alignments. Subsequently,\u0026nbsp;the divergence time of collinear gene pairs was calculated using the\u0026nbsp;duplication events formula\u0026nbsp;T = Ks/(2\u0026lambda;\u0026nbsp;\u0026times; 10\u003csup\u003e-\u003c/sup\u003e\u003csup\u003e6\u003c/sup\u003e)\u0026nbsp;in millions of years (Mya), with \u0026lambda;\u0026nbsp;= 6.5 \u0026times; 10\u003csup\u003e-\u003c/sup\u003e\u003csup\u003e9\u003c/sup\u003e [45].\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.4 GO annotation and protein\u0026ndash;protein interaction network analysis of \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eGO annotation of TaPHD proteins was available from the KOBAS database (\u003ca href=\"http://kobas.cbi.pku.edu.cn/kobas3\"\u003ehttp://kobas.cbi.pku.edu.cn/kobas3\u003c/a\u003e)\u0026nbsp;[46]. The full-length amino acid sequence of TaPHD proteins were uploaded to the original program, followed by drawing and annotation. GO annotations\u0026nbsp;were performed for three types of analyses: biological processes, molecular functions, and cellular composition. The GO annotation results were visualized using the\u0026nbsp;online tool\u0026nbsp;OmicStudio (https://www.omicstudio.cn/tool)\u0026nbsp;[47]. All\u0026nbsp;the predicted\u0026nbsp;TaPHD proteins were submitted to the STRING database (https://string-db.org/cgi/input.pl). The minimum required interaction score was set to\u0026nbsp;high confidence (0.700). The max number of interactors was no more than 10 on the first shell.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.5 Expression of \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTranscriptional data for \u003cem\u003eTaPHDs\u003c/em\u003e were obtained from\u0026nbsp;the wheat expression website (\u003ca href=\"http://www.wheat-expression.com/download\"\u003ehttp://www.wheat-expression.com/download\u003c/a\u003e)\u0026nbsp;[48,49]\u0026nbsp;and were used to explore the potential biological functions of\u0026nbsp;\u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes in growth and development,\u0026nbsp;abiotic and biotic\u003cem\u003e\u0026nbsp;\u003c/em\u003estress, and other conditions. Systematic clustering analysis was performed based on\u0026nbsp;the log2 of\u0026nbsp;transcripts per million (TPM) values for\u0026nbsp;the\u0026nbsp;244\u0026nbsp;\u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes.\u0026nbsp;R was used to display the expression patterns in a heat map, and OmicStudio (https://www.omicstudio.cn/tool)\u0026nbsp;was used to display the histogram, volcano plot,\u0026nbsp;and Venn diagram.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.6\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eQuantitative real-time PCR analyses of \u003cem\u003eTaPHD\u003c/em\u003e genes in response to environmental stresses\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eIn this study, the\u0026nbsp;seeds\u0026nbsp;of\u0026nbsp;the\u0026nbsp;hexaploid common wheat variety\u0026nbsp;\u0026ldquo;zhengmai 7698\u0026rdquo;\u0026nbsp;were\u0026nbsp;surface-sterilized with 2% hydrogen peroxide, rinsed thoroughly with distilled water, and germinated with water saturation at 25\u0026nbsp;\u0026deg;C for 2 days in Petri dishes on three layers of filter paper.\u0026nbsp;The young seedlings were transformed and\u0026nbsp;grown in 1/2 Hoagland\u0026apos;s culture solution under a 14 h light (25 \u0026deg;C)/10 h dark (20 \u0026deg;C) photoperiod.\u0026nbsp;When the wheat grew to two leaves and one heart, the plants were subsequently treated with 16% polyethylene glycol 6000 (PEG6000).\u0026nbsp;For cold stress, rice seedlings were exposed to 4 \u0026deg;C for 12 h. For heat stress, rice seedlings were exposed to 40 \u0026deg;C for 12 h.\u0026nbsp;New leaves of\u0026nbsp;the\u0026nbsp;three seedlings were collected as biological replicates, and each treatment had three replicates.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eTotal RNA was extracted using\u0026nbsp;RNAiso Reagent (TaKaRa, Beijing, China)\u0026nbsp;and cDNA was synthesized using\u0026nbsp;the RT Master Mix Perfect RealTime kit (TaKaRa, Beijing, China). Quantitative real-time PCR was performed using the CFX Touch\u0026trade; Real-Time PCR Detection System (Bio-Rad Laboratories, Hercules, CA, USA)\u0026nbsp;and\u0026nbsp;the\u0026nbsp;SG Fast qPCR Master Mix (Sangon Biotech, Shanghai, China). Relative expression levels were determined using the 2\u003csup\u003e(-\u0026Delta;\u0026Delta;Ct)\u0026nbsp;\u003c/sup\u003emethod\u0026nbsp;[50],\u0026nbsp;and \u0026beta;-actin was used as the internal control\u0026nbsp;to normalize the expression levels of\u0026nbsp;\u003cem\u003eTaPHD\u003c/em\u003e genes. Specific primers used for RT-qPCR are listed in\u0026nbsp;Supplementary Table S2.\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.7 Determination of subcellular localization of TaPHD11, TaPHD19, and TaPHD133\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eFull-length open reading frames of\u0026nbsp;\u003cem\u003eTaPHD11, TaPHD19\u003c/em\u003e,\u003cem\u003e\u0026nbsp;\u003c/em\u003eand\u003cem\u003e\u0026nbsp;TaPHD133\u003c/em\u003e were obtained from\u0026nbsp;\u0026ldquo;zhengmai 7698\u0026rdquo;\u0026nbsp;cDNA\u0026nbsp;(Supplementary\u0026nbsp;Table S2). The CDS of\u003cem\u003e\u0026nbsp;\u003c/em\u003e\u003cem\u003eTaPHD11, TaPHD19\u003c/em\u003e,\u003cem\u003e\u0026nbsp;\u003c/em\u003eand\u003cem\u003e\u0026nbsp;TaPHD133\u003c/em\u003e were cloned\u0026nbsp;into\u0026nbsp;the\u0026nbsp;pJIT16318 vector at the\u0026nbsp;BamHI\u0026nbsp;site using specific primers\u0026nbsp;(Supplementary\u0026nbsp;Table S2).\u0026nbsp;The\u0026nbsp;pJIT16318 vector contained a CaMV 35S promoter and C-terminal GFP. Transient expression assays were conducted as described by\u0026nbsp;Cui\u003cem\u003e, et al.\u003c/em\u003e [51]. Approximately 4 \u0026times; 10\u003csup\u003e4\u0026nbsp;\u003c/sup\u003emesophyll protoplasts were isolated from 12-day-old wheat seedlings. The transfected protoplasts were incubated at 23 \u0026deg;C for 12 h. GFP fluorescence in the transformed protoplasts was imaged using a confocal laser-scanning microscope (LSM 700; Zeiss).\u003c/p\u003e"},{"header":"3. Results","content":"\u003cp\u003e\u003cstrong\u003e3.1\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eIdentification and classification analysis of \u003cem\u003ePHD\u003c/em\u003e genes in wheat\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eIn this study, 244\u0026nbsp;\u003cem\u003eT. aestivum\u003c/em\u003e genes were\u0026nbsp;designated \u003cem\u003ePHD\u003c/em\u003e genes with two query methods, HMM and BLASTP,\u0026nbsp;used for identification,\u0026nbsp;and three websites, NCBI-Batch CD-Search, PFAM database, and\u0026nbsp;SMART database, used for confirmation (Supplementary\u0026nbsp;Table S3).\u0026nbsp;These \u003cem\u003ePHD\u003c/em\u003e genes were renamed \u003cem\u003eTaPHD1\u003c/em\u003e to \u003cem\u003eTaPHD244\u003c/em\u003e,\u003cem\u003e\u0026nbsp;\u003c/em\u003ebased on\u0026nbsp;their chromosomal locations and\u0026nbsp;physical\u0026nbsp;positions.\u003c/p\u003e\n\u003cp\u003eTo further determine the characteristics of \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes,\u0026nbsp;the\u0026nbsp;ExPASy Server online tool was used to analyze the protein characteristics\u0026nbsp;(Supplementary\u0026nbsp;Table S3). The shortest protein contained 216 amino acids (\u003cem\u003eTaPHD158, TaPHD175\u003c/em\u003e) and the longest one contained 2853 amino acids (\u003cem\u003eTaPHD204\u003c/em\u003e); the molecular weight was between 24567.82 Da (\u003cem\u003eTaPHD158\u003c/em\u003e) and 310347.53 Da (\u003cem\u003eTaPHD204\u003c/em\u003e). The protein instability index showed that all \u003cem\u003ePHD\u0026nbsp;\u003c/em\u003egenes were unstable proteins. The isoelectric point of \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes varied markedly from 4.42 (\u003cem\u003eTaPHD36\u003c/em\u003e) to 9.65 (\u003cem\u003eTaPHD78\u003c/em\u003e), and the aliphatic index varied significantly from 48.13 (\u003cem\u003eTaPHD26/39/51\u003c/em\u003e) to 97.51 (\u003cem\u003eTaPHD42\u003c/em\u003e). The GRAVY of TaPHD\u003cem\u003e\u0026nbsp;\u003c/em\u003eproteins in wheat varied from 0.016 (\u003cem\u003eTaPHD160\u003c/em\u003e) to -1.285 (\u003cem\u003eTaPHD23\u003c/em\u003e), indicating that they were all hydrophilic proteins, except for \u003cem\u003eTaPHD160\u003c/em\u003e (Supplementary\u0026nbsp;Table S3). We used two methods (Plant-mPLoc and BUSCA) to predict the subcellular localization of\u0026nbsp;the\u0026nbsp;TaPHD proteins. The results showed that a\u0026nbsp;few TaPHDs may be localized in the chloroplast, mitochondrion,\u0026nbsp;or cytoplasm, and most members were predicted to\u0026nbsp;be located in the nucleus\u0026nbsp;(Supplementary\u0026nbsp;Table S3).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.2\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eMultiple sequence alignment and phylogenetic analysis of \u003cem\u003ePHD\u003c/em\u003e genes\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eMultiple sequence alignments of\u0026nbsp;PHD\u0026nbsp;domains\u0026nbsp;were performed\u0026nbsp;(Figure 1). Approximately 60 amino acids (aa) comprised a PHD domain containing basic Cys4-His-Cys3\u0026nbsp;sequence motifs\u0026nbsp;in each TaPHD.\u003c/p\u003e\n\u003cp\u003eTo evaluate the evolutionary relationships of \u003cem\u003ePHD\u003c/em\u003e genes in\u0026nbsp;\u003cem\u003eT. aestivum\u003c/em\u003e,\u003cem\u003e\u0026nbsp;O. sativa,\u003c/em\u003e and\u003cem\u003e\u0026nbsp;A. thaliana\u003c/em\u003e, a neighbor-joining phylogenetic tree was constructed using\u0026nbsp;full-length PHD proteins (Figure 2 and Supplementary Table S1). Phylogenetic analysis showed that \u003cem\u003ePHD\u003c/em\u003e family proteins can be divided into four clades (clades\u0026nbsp;1 to 4). \u003cem\u003eTaPHD\u003c/em\u003e members were found in all clades. Clade 1 was the largest, with 95 \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003emembers, and clade 4 was the smallest, with only 38 members. The results showed that there\u0026nbsp;were many small branches under each clade, and almost every small branch had\u0026nbsp;corresponding genes of rice and \u003cem\u003eArabidopsis\u003c/em\u003e. This indicated that\u003cem\u003e\u0026nbsp;\u003c/em\u003ethe \u003cem\u003eTaPHD\u003c/em\u003e gene is not an evolutionary characteristic of monocotyledonous and dicotyledonous plants, and\u0026nbsp;that the\u0026nbsp;\u003cem\u003ePHD\u0026nbsp;\u003c/em\u003egene family was formed before the differentiation of these two types of plants.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eProtein domains are often functional carriers. According to phylogenetic and domain analyses (NCBI-Batch CD-Search, PFAM, and SMART database), 30 dominant\u0026nbsp;types were identified in all wheat PHD proteins (Table 1). The results showed that among all wheat PHD proteins, 43 contained a typical PHD domain. Next most common, the jas-PHD and alifn-PHD domains had 28 and 25 members, respectively; the PHD-Oberon_cc domain and the PHD-RING domains had 11 members, and the remaining domain types had less than ten members. The results showed that wheat PHD proteins contained a canonical PHD domain or double PHD domains. Owing to their different\u0026nbsp;domains,\u0026nbsp;differentiation in function was achieved.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eTo better understand why \u003cem\u003ePHD-finger\u003c/em\u003e genes are abundant in the wheat genome, we analyzed\u0026nbsp;the homoeologous groups in detail (Table 2). A total of\u0026nbsp;35.8%\u0026nbsp;of wheat genes were present in homoeologous groups of three, also termed triads (A:B:D = 1:1:1) {International Wheat Genome Sequencing Consortium, 2018 #46} . In contrast, 84.8% of the \u003cem\u003ePHD-finger\u0026nbsp;\u003c/em\u003egenes identified were present in\u0026nbsp;triads (Table 2). Also, the percentage of\u0026nbsp;\u003cem\u003ePHD-finger\u003c/em\u003e genes with homoeolog-specific duplications was lower for \u003cem\u003ePHD-finger\u003c/em\u003e genes than for all wheat genes (1.6% vs 5.7%; Table 2). Loss of one homoeolog, on the other hand, was less pronounced in \u003cem\u003ePHD-finger\u003c/em\u003e genes (6.6% vs 13.2%; Table 2). Only four \u003cem\u003ePHD-finger\u0026nbsp;\u003c/em\u003egenes were orphans/singletons. Thus, the high homoeolog retention rate could partly explain the high number of wheat \u003cem\u003ePHD-finger\u0026nbsp;\u003c/em\u003egenes.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.3 Chromosomal location, gene duplication, and synteny analysis of \u003cem\u003eTaPHD\u003c/em\u003e genes\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eBased on\u0026nbsp;the reference GFF3 files, the physical positions of \u003cem\u003ePHD\u003c/em\u003e genes on\u0026nbsp;the corresponding chromosomes\u0026nbsp;are shown in\u0026nbsp;Figure 3.\u0026nbsp;The identified \u003cem\u003eTaPHDs\u003c/em\u003e could be mapped on every chromosome and\u0026nbsp;evenly across the three sub-genomes. The map shows that chromosomes\u0026nbsp;5B\u0026nbsp;and 5D harbor the largest number of \u003cem\u003eTaPHD\u003c/em\u003e genes (18),\u0026nbsp;whereas chromosome 1D contains the least (6).\u003c/p\u003e\n\u003cp\u003eGene duplication is an indispensable mechanism by which organisms create new genes with similar or different functions\u0026nbsp;[53].\u0026nbsp;Therefore, we analyzed the duplication events that occurred in the \u003cem\u003eTaPHD\u003c/em\u003e gene family.\u0026nbsp;A total of\u0026nbsp;230\u0026nbsp;\u003cem\u003ePHD\u003c/em\u003e gene pairs from wheat were identified as duplicated (Figure 4, Supplementary Table S4). These similar \u003cem\u003ePHD\u003c/em\u003e gene pairs had\u0026nbsp;the same\u0026nbsp;domain type and appeared in the same branch of the phylogenetic tree. Tandem and segment duplications are critical for the evolution of gene families to adapt to different environmental conditions.\u0026nbsp;Interestingly, all the \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egene pairs were associated with segmental duplication events.\u0026nbsp;This suggests that this was the main route for expanding \u003cem\u003ePHD\u003c/em\u003e genes in wheat and the many homologous genes on different wheat chromosomes suggest the high conservation of the family.\u0026nbsp;To further infer the\u0026nbsp;evolutionary origin\u0026nbsp;and homology of the wheat \u003cem\u003ePHD\u003c/em\u003e family, we constructed\u0026nbsp;a collinear chart comparing\u0026nbsp;six species\u0026nbsp;with wheat, including three\u0026nbsp;monocotyledons\u0026nbsp;(\u003cem\u003eH. vulgareto\u003c/em\u003e, \u003cem\u003eZ. mays\u003c/em\u003e, and \u003cem\u003eO. sativa\u003c/em\u003e) and three dicotyledons (\u003cem\u003eA. thaliana\u003c/em\u003e, \u003cem\u003eB. rapa\u003c/em\u003e, and \u003cem\u003eG. raimondii\u003c/em\u003e)\u0026nbsp;(Figure 5, Supplementary Table S4). We identified pairwise homologues of the \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes\u0026nbsp;and detected\u0026nbsp;119, 186, 168, 7, 2,\u0026nbsp;and 6 pairs of homologous genes from\u0026nbsp;\u003cem\u003eH. vulgareto, Z. mays\u003c/em\u003e, \u003cem\u003eO. sativa,\u003c/em\u003e \u003cem\u003eA. thaliana\u003c/em\u003e, \u003cem\u003eB. rapa\u003c/em\u003e, and \u003cem\u003eG. raimondii\u003c/em\u003e, respectively (Figure 5, Supplementary Table S4).\u0026nbsp;This implies that \u003cem\u003eTaPHD\u003c/em\u003e genes share a strong evolutionary relationship with \u003cem\u003eZmPHDs\u003c/em\u003e, \u003cem\u003eHvPHDs\u003c/em\u003e, and \u003cem\u003eOsPHDs\u003c/em\u003e. Furthermore, these results indicated that the\u0026nbsp;\u003cem\u003ePHD\u003c/em\u003e gene family was differentiated between monocotyledonous and dicotyledonous plants. This also indicated that \u003cem\u003eTaPHD\u003c/em\u003e genes had\u0026nbsp;a strong evolutionary relationship with\u0026nbsp;\u003cem\u003eZmPHDs\u003c/em\u003e, \u003cem\u003eHvPHDs\u003c/em\u003e, and \u003cem\u003eOsPHDs.\u0026nbsp;\u003c/em\u003eThe average differentiation time\u003cem\u003e\u0026nbsp;\u003c/em\u003ewas as barley\u003cem\u003e\u0026nbsp;\u003c/em\u003e(12.78 Mya) \u0026lt; rice\u003cem\u003e\u0026nbsp;\u003c/em\u003e(22.09 Mya) \u0026lt; maize (60.87 Mya).\u003c/p\u003e\n\u003cp\u003eKa/Ks, the non-synonymous substitution ratio, determines the selection pressure for duplicated genes. According to the results\u0026nbsp;(Supplementary Table S4), only very few \u003cem\u003eTaPHD\u003c/em\u003e gene pairs had Ka/Ks ratios \u0026gt;1, suggesting that the evolution of \u003cem\u003eTaPHD\u003c/em\u003e genes was accompanied by strong purifying selection. The Ka/Ks ratios between wheat and three monocotyledonous plants were calculated based on the collinear gene pairs. Except for very few genes, the values of the other collinear gene pairs were all below 1, which confirmed that the evolution of the wheat \u003cem\u003ePHD\u003c/em\u003e gene family underwent strong purifying selection. However, the Ka/Ks ratios of the collinear gene pairs between wheat and\u0026nbsp;the\u0026nbsp;three dicots could not be calculated properly. This is because most synonymous mutation sites have synonymous mutations; that is, the degree of sequence divergence and evolutionary distance is too large. Some\u0026nbsp;\u003cem\u003eTaPHD\u003c/em\u003e genes have formed at least five homologous gene pairs, such as \u003cem\u003eTaPHD9\u003c/em\u003e, which may\u0026nbsp;have played key roles in the evolution of the\u0026nbsp;\u003cem\u003ePHD\u003c/em\u003e gene family (Figure 5, Supplementary Table S4).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.4\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eGO annotation analysis and protein\u0026ndash;protein interaction network of \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egene\u003cem\u003es\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe performed GO annotation analysis of the 244 TaPHD proteins, revealing that they may participate in a range of cellular components, molecular functions, and biological processes\u0026nbsp;(Figure 6, Supplementary Table S5). The 244 TaPHD proteins were assigned a total of 105 GO terms. In biological processes,\u0026nbsp;the\u0026nbsp;three most highly\u0026nbsp;enriched categories were related to\u0026nbsp;the\u0026nbsp;regulation of DNA-templated transcription, heat acclimation,\u0026nbsp;and chromatin organization.\u0026nbsp;Developmental growth and jasmonic acid\u0026ndash;mediated systemic resistance were also\u0026nbsp;particularly enriched. In the cellular component category, the most highly enriched categories were related to\u0026nbsp;the nucleus, and\u0026nbsp;85% of the \u003cem\u003eTaPHDs\u003c/em\u003e could participate in this process, whereas less than 10% of \u003cem\u003eTaPHDs\u003c/em\u003e were involved in plasmodesma. Regarding molecular functions,\u0026nbsp;the\u0026nbsp;65 most enriched\u0026nbsp;\u003cem\u003eTaPHDs\u003c/em\u003e were involved in histone binding, 28 \u003cem\u003eTaPHDs\u003c/em\u003e were involved in chromatin binding,\u0026nbsp;and 81 \u003cem\u003eTaPHDs\u003c/em\u003e were\u0026nbsp;related to\u0026nbsp;protein binding.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eTo understand protein\u0026ndash;protein interactions between TaPHDs and other proteins in wheat, we constructed a protein\u0026ndash;protein interaction network (Figure 7, Supplementary Table S6).\u0026nbsp;A total of\u0026nbsp;89 TaPHD proteins and 548 interacting protein branches were identified. According to the strength of the interaction, we divided the 89 proteins into four interaction regions, which are represented by different colors, as shown in Figure 7.\u0026nbsp;Some TaPHDs, such as\u0026nbsp;TaPHD15, TaPHD145,\u0026nbsp;and TaPHD162,\u0026nbsp;could interact with up to 28 proteins, suggesting that these TaPHD proteins play a significant role in the regulation of protein networks. Interestingly, we found that these proteins had\u0026nbsp;a\u0026nbsp;PHD domain or\u0026nbsp;a\u0026nbsp;PHD-SWIB-Plus3-GYF domain. Therefore, we believe that such domains are likely to play\u0026nbsp;an important role\u0026nbsp;in\u0026nbsp;the PHD family.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.5 Expression analysis of \u003cem\u003eTaPHD\u003c/em\u003e genes during growth and development\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eRNA-sequencing is a powerful tool for exploring certain gene transcription patterns using high-throughput sequencing methods\u0026nbsp;[54].\u003cem\u003e\u0026nbsp;\u003c/em\u003eSystematic clustering analysis was performed based on\u0026nbsp;the log2 of\u0026nbsp;TPM values for 244\u0026nbsp;\u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes (Figure 8A,\u0026nbsp;Supplementary Table S7). The data showed that \u003cem\u003eTaPHD\u003c/em\u003e gene expression showed great differences with the change in\u0026nbsp;the growth period.\u0026nbsp;In general, the expression of\u0026nbsp;\u003cem\u003eTaPHDs\u0026nbsp;\u003c/em\u003ecan be divided into three categories: the first group contains members that are widely expressed in many tissues under multiple developmental stage conditions, the second group contains those that are highly induced only at specific growth and development stages,\u0026nbsp;and the last group\u0026nbsp;includes members that do not appear to\u0026nbsp;be expressed during\u0026nbsp;growth and development.\u0026nbsp;For example,\u0026nbsp;\u003cem\u003eTaPHD100\u003c/em\u003e,\u0026nbsp;\u003cem\u003eTaPHD108\u003c/em\u003e, and\u0026nbsp;\u003cem\u003eTaPHD122\u003c/em\u003e had high expression during most growth and developmental processes, except in\u0026nbsp;the\u0026nbsp;endosperm. Of course, there were also some genes (\u003cem\u003eTaPHD222\u003c/em\u003e and\u003cem\u003e\u0026nbsp;TaPHD232\u003c/em\u003e) that had higher expression only\u0026nbsp;in shoots and roots. Furthermore, some genes, such as\u0026nbsp;\u003cem\u003eTaPHD68\u003c/em\u003e,\u0026nbsp;\u003cem\u003eTaPHD78\u003c/em\u003e, and\u0026nbsp;\u003cem\u003eTaPHD86\u003c/em\u003e, were\u003cem\u003e\u0026nbsp;\u003c/em\u003ebasically not expressed, which implies that these genes may have functional redundancy.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eTo further study the expression differences of this family in different stages and organs of wheat, we counted the number of high, medium, and low expression genes in each period and organ\u0026nbsp;(Figure 8B).\u0026nbsp;The data showed that the number of highly expressed genes was the largest in\u0026nbsp;the\u0026nbsp;stigma and ovary, reaching as high as 60, followed by\u0026nbsp;a spike\u0026nbsp;in\u0026nbsp;the\u0026nbsp;boot period, reaching 41. The lowest number of highly expressed genes (none) was found in the flag leaf blade at night in\u0026nbsp;the\u0026nbsp;flag leaf stage. Our results suggest that some \u003cem\u003eTaPHDs\u0026nbsp;\u003c/em\u003emay play important roles in many biological processes during wheat growth, especially during anthesis.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.6 Expression responses of \u003cem\u003eTaPHD\u003c/em\u003e genes to abiotic/biotic stress\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe differential expression of\u0026nbsp;\u003cem\u003eTaPHDs\u0026nbsp;\u003c/em\u003eunder different conditions is shown in\u0026nbsp;Figure 9A-F (Supplementary Table S8). During biological stress, we found that inoculation with \u003cem\u003eFusarium\u003c/em\u003e, powdery mildew, pathogen associated molecular patterns (PAMP), crown rot, \u003cem\u003eSeptoria\u003c/em\u003e,\u0026nbsp;or stripe rust\u0026nbsp;caused few changes in the expression of \u003cem\u003eTaPHD\u003c/em\u003e genes. This suggests that \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003efamily members may not be associated with disease resistance.\u003c/p\u003e\n\u003cp\u003eUnder abiotic stress, there are many\u003cem\u003e\u0026nbsp;TaPHD\u003c/em\u003e genes whose expression changes are more obvious under high-temperature, drought, and cold conditions\u0026nbsp;(Figure 9G-K,\u0026nbsp;Supplementary Table S8).\u0026nbsp;For example, after high-temperature treatment, the expression levels of\u0026nbsp;many\u0026nbsp;\u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes (\u003cem\u003eTaPHD26\u003c/em\u003e,\u0026nbsp;\u003cem\u003eTaPHD75\u003c/em\u003e,\u0026nbsp;\u003cem\u003eTaPHD100, TaPHD115, TaPHD117\u003c/em\u003e,\u003cem\u003e\u0026nbsp;\u003c/em\u003eand\u003cem\u003e\u0026nbsp;TaPHD167\u003c/em\u003e) were significantly altered compared to those in the experimental control group. In the drought starvation\u0026nbsp;treatment,\u0026nbsp;\u003cem\u003eTaPHD11, TaPHD19, TaPHD99,\u003c/em\u003e \u003cem\u003eTaPHD141, TaPHD153\u003c/em\u003e,\u003cem\u003e\u0026nbsp;\u003c/em\u003eand\u003cem\u003e\u0026nbsp;TaPHD171\u003c/em\u003e expression levels\u003cem\u003e\u0026nbsp;\u003c/em\u003echanged significantly. However, in the phosphorus starvation\u0026nbsp;treatment,\u0026nbsp;there were\u0026nbsp;few changes in the expression of \u003cem\u003eTaPHD\u003c/em\u003e genes. To further understand whether there is an intersection between the differential genes of the \u003cem\u003ePHD\u003c/em\u003e family under drought, high-temperature, and low-temperature treatments, we drew a Venn diagram of DEGs in \u003cem\u003eTaPHD\u003c/em\u003e genes during\u0026nbsp;the\u0026nbsp;four different transcriptomes\u0026nbsp;(Figure 10,\u0026nbsp;Supplementary Table S9).\u0026nbsp;The data showed that \u003cem\u003eTaPHD215\u0026nbsp;\u003c/em\u003eand\u003cem\u003e\u0026nbsp;TaPHD223\u0026nbsp;\u003c/em\u003ewere significantly altered in every treatment. \u003cem\u003eTaPHD30, TaPHD96, TaPHD180, TaPHD174\u003c/em\u003e, and \u003cem\u003eTaPHD239\u003c/em\u003e gene expression varied greatly between the two drought and heat treatments.\u0026nbsp;In addition, in cold and heat stress environments, the expression\u0026nbsp;levels of five genes (\u003cem\u003eTaPHD109, TaPHD118, TaPHD120, TaPHD167\u003c/em\u003e,\u003cem\u003e\u0026nbsp;\u003c/em\u003eand\u003cem\u003e\u0026nbsp;TaPHD178\u003c/em\u003e) were significantly changed.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.7 qRT-PCR confirmed the response capability of \u003cem\u003eTaPHD\u0026nbsp;\u003c/em\u003egenes to abiotic stress conditions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTo elucidate the possible regulatory mechanisms of\u003cem\u003e\u0026nbsp;TaPHD\u003c/em\u003e genes under cold, drought, and heat conditions, we performed qRT-PCR analysis of 20 genes\u0026nbsp;(Figure 11).\u0026nbsp;The results showed that all 20 \u003cem\u003eTaPHDs\u003c/em\u003e responded to different stress conditions and had different manifestations. Under low temperature stress induced by 4\u0026deg;C, the expression of five \u003cem\u003eTaPHD\u003c/em\u003es was significantly upregulated at different time points, and the expression of six \u003cem\u003eTaPHD\u003c/em\u003es was significantly downregulated at different time points compared with the control. In contrast, under 40\u0026deg;C-induced high-temperature stress, the expression of 12 \u003cem\u003eTaPHD\u003c/em\u003es was significantly upregulated at different time points compared with the control. The expression of\u0026nbsp;five \u003cem\u003eTaPHDs\u003c/em\u003e was inhibited at different time points. This indicated that compared with low temperature stress, high temperature stress could induce more changes in the expression of \u003cem\u003eTaPHD\u003c/em\u003es and could upregulate the expression more. In wheat under 16% PEG stress, the expression of ten \u003cem\u003eTaPHD\u003c/em\u003es was significantly upregulated at different time points. The expression of seven \u003cem\u003eTaPHD\u003c/em\u003es was inhibited at different time points. Among them, \u003cem\u003eTaPHD72\u003c/em\u003e was most significantly inhibited, and it was downregulated fourfold at 6 h and 12 h after treatment. The expression levels of \u003cem\u003eTaPHD69\u0026nbsp;\u003c/em\u003eand \u003cem\u003eTaPHD135\u003c/em\u003e significantly increased after\u0026nbsp;the three treatments. However, the expression levels of\u0026nbsp;\u003cem\u003eTaPHD23\u003c/em\u003e and \u003cem\u003eTaPHD141\u003c/em\u003e significantly decreased after\u0026nbsp;the three treatments.\u0026nbsp;In addition, \u003cem\u003eTaPHD99\u003c/em\u003e was strongly upregulated or downregulated by high temperature, low temperature, and PEG, and we speculated that this\u0026nbsp;might be a key regulator of abiotic induction. In conclusion, we verified the effect of \u003cem\u003ePHD-finger\u003c/em\u003e gene expression on the effect of three abiotic stresses in wheat using qRT-PCR. These results indicate that \u003cem\u003ePHD-finger\u0026nbsp;\u003c/em\u003egenes play an important role in coping with abiotic stress\u0026nbsp;in wheat.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.8 Subcellular localization of TaPHD11, TaPHD19, and TaPHD133\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePrevious studies have shown that most PHD finger proteins are localized in the nucleus, and only a few are localized in\u0026nbsp;the membranes or other organelles\u0026nbsp;[25,33,57]. For example, ZmPHD14 and ZmPHD19 are localized to the nucleus\u0026nbsp;[29]. Also, GmPHD1 to GmPHD6 target the nucleus, and their nuclear localization requires the PHD domain\u0026nbsp;[32].\u0026nbsp;To better understand the functions\u0026nbsp;of TaPHDs, we used\u0026nbsp;Plant-mPLoc and BUSCA\u0026nbsp;to predict their subcellular localization. The results showed that more than 90% of\u0026nbsp;the\u0026nbsp;TaPHD proteins were localized in the nucleus\u0026nbsp;(Table S1).\u0026nbsp;In \u003cem\u003eArabidopsis thaliana\u003c/em\u003e, the \u003cem\u003ePHD\u003c/em\u003e genes \u003cem\u003eAL5\u003c/em\u003e and \u003cem\u003eAL6\u003c/em\u003e play a very important role in improving the tolerance of plants to abiotic stress. Therefore, we selected TaPHD11 and TaPHD19, which are highly homologous to \u003cem\u003eAtALs\u003c/em\u003e, for subcellular localization of wheat protoplasts. As shown in Figure 12, this suggests that, in wheat, the proteins TaPHD11 and TaPHD19 not only function in the nucleus but also in the membrane. In addition, research has shown that PHD finger ING2 is a phosphoinositide binding module and a nuclear PtdInsP receptor and suggests that PHD-phosphoinositide interactions directly regulate nuclear responses to DNA damage [57]. However, we studied the protein TaPHD133, which is highly homologous to ING1, and found that it is localized not only in the nucleus, but also in the membrane. In summary, the subcellular localization of PHD proteins in wheat differs from that in other species.\u003c/p\u003e"},{"header":"4. Discussion","content":"\u003cp\u003eAs an important transcription factor in organisms, the \u003cem\u003ePHD\u003c/em\u003e gene family not only plays a key role in regulating plant growth and development but also plays an important regulatory role when plants face biotic and abiotic stresses\u0026nbsp;[18]. In this study, we identified 244 \u003cem\u003eTaPHD\u003c/em\u003e gene members in the wheat genome\u0026nbsp;for the first time (Supplementary\u0026nbsp;Table S3), and the vast majority of\u0026nbsp;the\u0026nbsp;TaPHD proteins were located in the nucleus. In terms of the number of genes, the number of \u003cem\u003eTaPHD\u003c/em\u003e genes increased significantly compared with other species. This is because the origin of wheat involves two polyploidy events, resulting in the existing allohexaploid bread wheat. However, compared with the 59 and 67 \u003cem\u003ePHD\u003c/em\u003e members in the diploid gramineous crops rice and maize, respectively, it is not multiplied, indicating that the \u003cem\u003ePHD\u003c/em\u003e gene in wheat has a more exaggerated expansion and evolution.\u0026nbsp;Gene duplication events are important for the rapid expansion and evolution of plant gene families\u0026nbsp;[58]. About 70-80% of angiosperms experience duplication events\u0026nbsp;[59,60], and in common wheat (\u003cem\u003eTriticum aestivum\u003c/em\u003e L.), more than 85% of the sequences are duplicates\u0026nbsp;[61]. Physical localization on chromosomes and covariance analysis (Figure 4 and 5) revealed the presence of a large number of segmental duplication events during the evolution of\u0026nbsp;\u003cem\u003eTaPHD\u003c/em\u003e genes, suggesting that segmental duplication contributes to the amplification of \u003cem\u003eTaPHD\u003c/em\u003e genes. The proportion of \u003cem\u003eTaPHDs\u003c/em\u003e with a 1:1:1 ratio of the three subgenomes A:B:D accounted for 84.8% of the total proportion (Table 2), which was much higher than the 35.8% observed for the whole wheat genome, indicating that the \u003cem\u003ePHD\u003c/em\u003e gene family is highly conserved in the three subgenomes compared to other genes. In terms of the covariance and evolutionary relationship of wheat \u003cem\u003ePHD\u003c/em\u003e genes among species (Figure 5), the \u003cem\u003ePHD-finger\u003c/em\u003e family diverged between monocotyledonous and dicotyledonous species, with the average divergence time from the monocotyledonous species as\u0026nbsp;barley\u0026nbsp;(12.78 Mya) \u0026lt; rice (22.09 Mya) \u0026lt; maize (60.87 Mya), indicating a more similar genetic structure to barley.\u003c/p\u003e\n\u003cp\u003ePhylogenetic analysis showed that PHD proteins in three species (including \u003cem\u003eArabidopsis\u003c/em\u003e, \u003cem\u003eO. stiva\u003c/em\u003e, and \u003cem\u003eT. aestivum\u003c/em\u003e), which are distant from each other, could be divided into four large evolutionary branches, and each group of evolutionary branches contained many smaller evolutionary branches. From the results, there were some small branches containing only wheat \u003cem\u003ePHD\u0026nbsp;\u003c/em\u003egenes, which was consistent with previous findings that wheat \u003cem\u003ePHD\u003c/em\u003e genes had more exaggerated expansion and evolution. When the \u003cem\u003ePHD\u003c/em\u003e genes with different chaperone structural domains were subdivided (Table 1), the fold divergences were also different; for example, ING1, ING2, ROS1, EBS, and PKL were expanded 3-fold, while SHL1 was expanded 6-fold, and\u0026nbsp;VIN3 and SIZ1 were expanded 9-fold and 11-fold, respectively. It is\u0026nbsp;likely that the presence of many redundant genes has contributed to the stability of the genome of the hexaploid wheat species\u0026nbsp;[62].\u003c/p\u003e\n\u003cp\u003eGenes perform their functions through transcription and translation, and the expression patterns of genes reflect their function. \u003cem\u003ePHD\u003c/em\u003e genes can regulate the growth and development of plants; therefore, their expression in different plant tissues has also attracted much attention. Studies have shown that the expression patterns of the \u003cem\u003ePHD\u003c/em\u003e gene family in rice, maize, potato, and cotton are concentrated in different tissue types\u0026nbsp;[25-27]. In rice, the expression levels of \u003cem\u003eOsPHD\u003c/em\u003es were relatively high in pre-emergence inflorescences and pistils, and the number of lowly expressed \u003cem\u003eOsPHD\u003c/em\u003es was significantly higher in the seed stage (10 days) compared with that in the other periods\u0026nbsp;[25]. In potato, considerable differences\u0026nbsp;in expression are\u0026nbsp;observed between individual \u003cem\u003eStPHD\u003c/em\u003e genes from different tissues. For example, \u003cem\u003eStPHD27\u003c/em\u003e is abundantly expressed in roots, shoots, and stamens, but has lower expression levels in petals, carpels, and leaves\u0026nbsp;[27]. In cotton, \u003cem\u003eGhPHD\u003c/em\u003es genes have the highest expression levels in ovule and fiber tissues, suggesting that\u0026nbsp;\u003cem\u003eGhPHD\u003c/em\u003es may be involved in regulating ovule and fiber development\u0026nbsp;[26].\u0026nbsp;This study showed that the \u003cem\u003eTaPHD\u003c/em\u003e gene expression in various tissues of wheat showed great differences with the growth period; in particular, the \u003cem\u003eTaPHD\u003c/em\u003e gene expression was highest in the stigma and ovary at the flowering stage. This may be because a large number of PHD proteins in the \u003cem\u003ePHD\u003c/em\u003e family regulate plant reproductive and developmental processes. For example, MMD1, MS1, VIM1, and SHL1 in\u0026nbsp;\u003cem\u003eArabidopsis\u003c/em\u003e have been shown to play key roles in the reproductive growth stage\u0026nbsp;[20,63,64]. Moreover, \u003cem\u003eTaPHD100\u003c/em\u003e, \u003cem\u003eTaPHD108\u003c/em\u003e, and \u003cem\u003eTaPHD122\u003c/em\u003e were highly expressed during the whole growth period. These three genes are highly orthologous to \u003cem\u003eAtAL6\u003c/em\u003e and \u003cem\u003eAtAL7\u003c/em\u003e. In \u003cem\u003eArabidopsis\u003c/em\u003e, \u003cem\u003eAtAL6\u003c/em\u003e and \u003cem\u003eAtAL7\u003c/em\u003e are methylated by histones via the PHD domain, and the modification sites H3K4me3 and H3K4me2 bind to regulate the expression of target genes.\u0026nbsp;Alifn-PHD domain proteins bind to di- or trimethylated histone H3 (H3K4me3/2) and affect plant growth and development in \u003cem\u003eArabidopsis\u003c/em\u003e [52]. Furthermore, PWWP-PHD-SET domain proteins have histone methyltransferase activities and regulate the development of roots, leaves, and floral organs, as well as the transcription of some stress genes\u0026nbsp;\u0026nbsp;[23].\u0026nbsp;Therefore, \u003cem\u003eTaPHD100\u003c/em\u003e, \u003cem\u003eTaPHD108\u003c/em\u003e, and \u003cem\u003eTaPHD122\u003c/em\u003e may play important roles in\u0026nbsp;regulating the growth and development of wheat histone methylation\u0026nbsp;[65]. In addition, \u003cem\u003eTaPHD222\u003c/em\u003e and \u003cem\u003eTaPHD232\u003c/em\u003e are only highly expressed in shoots and roots; these two genes are highly orthologous to ORC1A/B,\u0026nbsp;whereas in \u003cem\u003eArabidopsis\u003c/em\u003e, the ORC1A/B protein binds methyl groups through the PHD domain and\u0026nbsp;functions as a transcriptional activator\u0026nbsp;[66]. Therefore, we infer\u0026nbsp;that\u0026nbsp;\u003cem\u003eTaPHD222\u003c/em\u003e and \u003cem\u003eTaPHD232\u0026nbsp;\u003c/em\u003eare essential for root and shoot development. However, their function during development requires further verification.\u003c/p\u003e\n\u003cp\u003eThe PHD family not only regulates plant growth and development but also responds to abiotic stresses. Existing research shows that PHD family transcription factors also play an important role in coping with abiotic stress. For example, the \u003cem\u003ePHD\u003c/em\u003e genes \u003cem\u003eAL5\u003c/em\u003e and \u003cem\u003eAL6\u003c/em\u003e in \u003cem\u003eArabidopsis\u003c/em\u003e bind to the promoter regions of downstream target genes, thereby inhibiting various signaling pathways to improve the tolerance of plants to abiotic stresses, such as low temperature, drought, and high salt\u0026nbsp;[56,57]. \u003cem\u003eAtSIZ1\u003c/em\u003e accumulates high levels of SUMOylated proteins through an ABA-independent pathway in response to abiotic stresses such as drought, low temperature, and heat shock\u0026nbsp;[67].\u0026nbsp;In rice, the cis-acting elements DRE/CRT in the \u003cem\u003eOsPHD13\u003c/em\u003e and \u003cem\u003eOsPHD52\u003c/em\u003e promoters are upregulated by as much as 15-fold under low-temperature stress. Overexpression of \u003cem\u003eOsPHD1\u003c/em\u003e can significantly improve plant tolerance to stress (drought, high salt, and low temperature)\u0026nbsp;[30]. In maize, the expression of subfamily IX \u003cem\u003eTaPHD\u003c/em\u003es responds to salt, drought, and ABA stress\u0026nbsp;[29].\u0026nbsp;In this study, \u003cem\u003eTaPHD11\u003c/em\u003e and \u003cem\u003eTaPHD19\u003c/em\u003e, which are highly homologous to \u003cem\u003eALs\u003c/em\u003e, were upregulated\u0026nbsp;only under induction by PEG treatment. This suggests that there are differences in the responses of\u0026nbsp;\u003cem\u003ePHD\u003c/em\u003e genes to abiotic stresses among species.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThrough transcriptome data, we found that 122 \u003cem\u003eTaPHD\u003c/em\u003es showed significant responses to low temperatures, drought, or high temperatures. Among them, 45\u0026nbsp;\u003cem\u003eTaPHDs\u003c/em\u003e genes were significantly changed under two or three treatments, indicating that \u003cem\u003eTaPHD\u003c/em\u003es play an active role in plant responses to low-temperature, drought, or high-temperature stress. In order to better verify the adaptability of\u0026nbsp;\u003cem\u003eTaPHDs\u003c/em\u003e to the above three abiotic stresses, we selected a representative cultivar \u0026quot;zhengmai 7698\u0026quot; from the Huanghuai wheat area of China and performed qRT-PCR analysis. We found that \u003cem\u003eTaPHD11\u003c/em\u003e and \u003cem\u003eTaPHD19\u003c/em\u003e, which are highly homologous to \u003cem\u003eAtALs\u003c/em\u003e, were significantly upregulated only under drought treatment, which is different from the results of the previous study in \u003cem\u003eArabidopsis\u0026nbsp;\u003c/em\u003e{Chandrika, 2013 #5}{Wei, 2015 #52}, indicating that ALs seem to have different responses to abiotic stress in monocotyledonous and dicotyledonous plants. At the same time, subcellular localization experiments also showed that \u003cem\u003eTaPHD11\u003c/em\u003e and \u003cem\u003eTaPHD19\u003c/em\u003e were localized in the nucleus and cell membrane, indicating that they function not only in the nucleus but also in the cell membrane of wheat. \u003cem\u003eTaPHD69\u003c/em\u003e, which is highly homologous to \u003cem\u003eAtSIZ1\u003c/em\u003e, can be significantly upregulated under low-temperature, drought, and high-temperature\u0026nbsp;conditions. The accumulation of \u003cem\u003eTaPHD69\u003c/em\u003e seems to be beneficial for plants to cope with abiotic stress, which is similar to the function of \u003cem\u003eAtSIZ1\u003c/em\u003e in \u003cem\u003eArabidopsis\u003c/em\u003e. \u003cem\u003eTaPHD117\u003c/em\u003e was significantly upregulated under high-temperature and drought treatments and significantly downregulated under low-temperature treatment, and had distinct expression patterns in response to different treatments. Therefore, whether \u003cem\u003eTaPHDs\u003c/em\u003e act as key genes in\u0026nbsp;the roots to cope with abiotic stress\u0026nbsp;requires further verification. Taken together, our results suggest that \u003cem\u003eTaPHDs\u003c/em\u003e have potential functions in plant responses to abiotic stress.\u003c/p\u003e"},{"header":"References","content":"\u003cp\u003e1.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Zhu, Y.-X.; Gong, H.-J.; Yin, J.-L. Role of silicon in mediating salt tolerance in plants: a review. \u003cem\u003ePlants\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2019\u003c/strong\u003e, \u003cem\u003e8\u003c/em\u003e, 147.\u003c/p\u003e\n\u003cp\u003e2.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;Fujita, M.; Fujita, Y.; Noutoshi, Y.; Takahashi, F.; Narusaka, Y.; Yamaguchi-Shinozaki, K.; Shinozaki, K. 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Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa. \u003cem\u003ePlanta\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2000\u003c/strong\u003e, \u003cem\u003e210\u003c/em\u003e, 416-422.\u003c/p\u003e\n\u003cp\u003e53.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Song, S.; Hao, L.; Zhao, P.; Xu, Y.; Zhong, N.; Zhang, H.; Liu, N. Genome-wide identification, expression profiling and evolutionary analysis of auxin response factor gene family in potato (\u003cem\u003eSolanum tuberosum\u003c/em\u003e Group Phureja). \u003cem\u003eScientific Reports\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2019\u003c/strong\u003e, \u003cem\u003e9\u003c/em\u003e, 1755.\u003c/p\u003e\n\u003cp\u003e54.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Wang, Z.; Gerstein, M.; Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. \u003cem\u003eNature Reviews Genetics\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2009\u003c/strong\u003e, \u003cem\u003e10\u003c/em\u003e, 57-63.\u003c/p\u003e\n\u003cp\u003e55.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Chandrika, N.N.P.; Sundaravelpandian, K.; Yu, S.M.; Schmidt, W. ALFIN‐LIKE 6 is involved in root hair elongation during phosphate deficiency in Arabidopsis. \u003cem\u003eNew Phytologist\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2013\u003c/strong\u003e, \u003cem\u003e198\u003c/em\u003e, 709-720.\u003c/p\u003e\n\u003cp\u003e56.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Wei, W.; Zhang, Y.Q.; Tao, J.J.; Chen, H.W.; Li, Q.T.; Zhang, W.K.; Ma, B.; Lin, Q.; Zhang, J.S.; Chen, S.Y. The Alfin‐like homeodomain finger protein AL5 suppresses multiple negative factors to confer abiotic stress tolerance in Arabidopsis. \u003cem\u003eThe Plant Journal\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2015\u003c/strong\u003e, \u003cem\u003e81\u003c/em\u003e, 871-883.\u003c/p\u003e\n\u003cp\u003e57.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Gozani, O.; Karuman, P.; Jones, D.R.; Ivanov, D.; Cha, J.; Lugovskoy, A.A.; Baird, C.L.; Zhu, H.; Field, S.J.; Lessnick, S.L. The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor. \u003cem\u003eCell\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2003\u003c/strong\u003e, \u003cem\u003e114\u003c/em\u003e, 99-111.\u003c/p\u003e\n\u003cp\u003e58.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Cannon, S.B.; Mitra, A.; Baumgarten, A.; Young, N.D.; May, G. The roles of segmental and tandem gene duplication in the evolution of large gene families in \u003cem\u003eArabidopsis thaliana\u003c/em\u003e. \u003cem\u003eBMC Plant Biology\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2004\u003c/strong\u003e, \u003cem\u003e4\u003c/em\u003e, 10.\u003c/p\u003e\n\u003cp\u003e59.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Blanc, G.; Hokamp, K.; Wolfe, K.H. A recent polyploidy superimposed on older large-scale duplications in the \u003cem\u003eArabidopsis\u003c/em\u003e genome. \u003cem\u003eGenome Research\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2003\u003c/strong\u003e, \u003cem\u003e13\u003c/em\u003e, 137-144.\u003c/p\u003e\n\u003cp\u003e60.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Bowers, J.E.; Chapman, B.A.; Rong, J.; Paterson, A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. \u003cem\u003eNature\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2003\u003c/strong\u003e, \u003cem\u003e422\u003c/em\u003e, 433-438.\u003c/p\u003e\n\u003cp\u003e61.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Walkowiak, S.; Gao, L.; Monat, C.; Haberer, G.; Kassa, M.T.; Brinton, J.; Ramirez-Gonzalez, R.H.; Kolodziej, M.C.; Delorean, E.; Thambugala, D. Multiple wheat genomes reveal global variation in modern breeding. \u003cem\u003eNature\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2020\u003c/strong\u003e, \u003cem\u003e588\u003c/em\u003e, 277-283.\u003c/p\u003e\n\u003cp\u003e62.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Consortium, I.W.G.S.; Appels, R.; Eversole, K.; Stein, N.; Feuillet, C.; Keller, B.; Rogers, J.; Pozniak, C.J.; Choulet, F.; Distelfeld, A. Shifting the limits in wheat research and breeding using a fully annotated reference genome. \u003cem\u003eScience\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2018\u003c/strong\u003e, \u003cem\u003e361\u003c/em\u003e, eaar7191.\u003c/p\u003e\n\u003cp\u003e63.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Woo, H.R.; Pontes, O.; Pikaard, C.S.; Richards, E.J. VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization. \u003cem\u003eGenes \u0026amp; Development\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2007\u003c/strong\u003e, \u003cem\u003e21\u003c/em\u003e, 267-277.\u003c/p\u003e\n\u003cp\u003e64.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Fern\u0026aacute;ndez G\u0026oacute;mez, J.; Wilson, Z.A. A barley PHD finger transcription factor that confers male sterility by affecting tapetal development. \u003cem\u003ePlant Biotechnology Journal\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2014\u003c/strong\u003e, \u003cem\u003e12\u003c/em\u003e, 765-777.\u003c/p\u003e\n\u003cp\u003e65.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Lee, W.Y.; Lee, D.; Chung, W.I.; Kwon, C.S. Arabidopsis ING and Alfin1‐like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers. \u003cem\u003eThe Plant Journal\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2009\u003c/strong\u003e, \u003cem\u003e58\u003c/em\u003e, 511-524.\u003c/p\u003e\n\u003cp\u003e66.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;de La Paz Sanchez, M.; Gutierrez, C. \u003cem\u003eArabidopsis\u003c/em\u003e ORC1 is a PHD-containing H3K4me3 effector that regulates transcription. \u003cem\u003eProceedings of the National Academy of Sciences\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2009\u003c/strong\u003e, \u003cem\u003e106\u003c/em\u003e, 2065-2070.\u003c/p\u003e\n\u003cp\u003e67.\u0026nbsp; \u0026nbsp; \u0026nbsp; \u0026nbsp;\u0026nbsp;Catala, R.; Ouyang, J.; Abreu, I.A.; Hu, Y.; Seo, H.; Zhang, X.; Chua, N.-H. The \u003cem\u003eArabidopsis\u003c/em\u003e E3 SUMO ligase SIZ1 regulates plant growth and drought responses. \u003cem\u003eThe Plant Cell\u0026nbsp;\u003c/em\u003e\u003cstrong\u003e2007\u003c/strong\u003e, \u003cem\u003e19\u003c/em\u003e, 2952-2966.\u003c/p\u003e"},{"header":"Tables","content":"\u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style='font-size:13px;font-family:\"Times New Roman\",serif;color:#242021;'\u003eTable 1\u003c/span\u003e\u003c/strong\u003e\u003cstrong\u003e\u003cspan style='font-size:13px;font-family:\"Arial\",sans-serif;color:#242021;'\u003e\u0026nbsp;\u003c/span\u003e\u003c/strong\u003e\u003cstrong\u003e\u003cspan style='font-size:13px;font-family:\"AdvPSSXR\",serif;color:#242021;'\u003eTypes, names, and numbers of wheat \u003cem\u003ePHD-finger\u003c/em\u003e genes\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cdiv align=\"center\" style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\n \u003ctable style=\"border: none;width:490.85pt;border-collapse:collapse;\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:74.75pt;border-top:solid windowtext 1.0pt;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style=\"font-size:11px;color:black;\"\u003eDomain type\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;border-top:solid windowtext 1.0pt;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style=\"font-size:11px;color:#242021;\"\u003eWheat triad\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;border-top:solid windowtext 1.0pt;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style=\"font-size:11px;color:#242021;\"\u003eRice orthologs\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;border-top:solid windowtext 1.0pt;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style=\"font-size:11px;color:#242021;\"\u003eArabidopsis thaliana orthologs\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;border-top:solid windowtext 1.0pt;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style=\"font-size:11px;color:#242021;\"\u003eGene number\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;border-top:solid windowtext 1.0pt;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style=\"font-size:11px;color:#242021;\"\u003eChr\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;border-top:solid windowtext 1.0pt;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style=\"font-size:11px;color:#242021;\"\u003eGenomes\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"17\" style=\"width:74.75pt;border:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003ePHD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;border:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD1/TaPHD8/TaPHD15\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;border:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;border:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;border:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;border:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;border:none;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD5/TaPHD12\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAB\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD21/TaPHD34/TaPHD46\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD62/TaPHD73/TaPHD84\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n 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5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e7\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"8\" style=\"width:74.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAlifn-PHD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD4/TaPHD11/TaPHD18\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD30\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAL1,AL2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD6/TaPHD13/TaPHD19\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD31\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAL6,AL7\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD26/TaPHD39/TaPHD51\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD44\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAL3.AL4,AL5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD31/TaPHD44/TaPHD56\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAL1,AL2,AL3.AL4,AL5,AL6,AL7\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD64/TaPHD75/TaPHD86\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD7\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAL6,AL7\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD100/TaPHD108/TaPHD122\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD56\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAL6,AL7\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e4\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD167/TaPHD184\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD23,OsPHD42\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAL1,AL2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eBD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"2\" style=\"width:179.15pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD104/TaPHD229/TaPHD230/TaPHD243/TaPHD244\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAL1,AL2,AL3.AL4,AL5,AL6,AL7\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e4(7)\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eA(DD)UU\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:74.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eARID-PHD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD142/TaPHD159/TaPHD176\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" style=\"width:74.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp 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style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD30/TaPHD43/TaPHD55\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD25\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n 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style=\"font-size:9px;color:black;\"\u003eTaPHD33/TaPHD45/TaPHD58\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eROS4\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD22/TaPHD35/TaPHD47\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD47\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAtPHD68,AtPHD70\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD92/TaPHD116/TaPHD130\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD47\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eAtPHD68,AtPHD70\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e4\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd 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style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD97/TaPHD112/TaPHD125\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD54\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eDDP3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e4\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD138/TaPHD155/TaPHD173\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd 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style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:74.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003ezf-HC5HC2H-PHD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD59/TaPHD70/TaPHD80\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan 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style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD95/TaPHD111/TaPHD127\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOBE1,OBE2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e4\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD136/TaPHD153/TaPHD171\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOBE1,OBE2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD117/TaPHD131\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e4\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eBD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"3\" style=\"width:74.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003ePHD-FN3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD3/TaPHD10/TaPHD17\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eVIN3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD134/TaPHD151/TaPHD169\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eVIN3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD190/TaPHD199/TaPHD207\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eVIN3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e6\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" style=\"width:74.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003ePHD-SANT\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD63/TaPHD74/TaPHD85\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD194/TaPHD203/TaPHD211\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e6\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:74.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003ePHD-WHIM1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"2\" style=\"width:179.15pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD102/TaPHD191/TaPHD200/TaPHD208\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eMBD9\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e4\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e6(4)\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e(A)ABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" style=\"width:74.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003ePHD-SET\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD67/TaPHD77/TaPHD89\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eOsPHD8\u003c/span\u003e\u003c/p\u003e\n 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\u003c/td\u003e\n \u003ctd style=\"width:69.4pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003ePKL\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e7\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;padding:0in 5.4pt 0in 5.4pt;height:13.8pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width:74.75pt;border:none;border-bottom:solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt;height:.75pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003ePHD-Cohesin_HEAT-Nipped-B_C\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:109.75pt;border:none;border-bottom:solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt;height:.75pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eTaPHD29/TaPHD42/TaPHD54\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:69.4pt;border:none;border-bottom:solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt;height:.75pt;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003ctd style=\"width:118.5pt;border:none;border-bottom:solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt;height:.75pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eEMB2773\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:.55in;border:none;border-bottom:solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt;height:.75pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:33.6pt;border:none;border-bottom:solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt;height:.75pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:center;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003e2\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width:45.25pt;border:none;border-bottom:solid windowtext 1.0pt;padding:0in 5.4pt 0in 5.4pt;height:.75pt;\"\u003e\n \u003cp style=\"margin:0in;text-align:left;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style=\"font-size:9px;color:black;\"\u003eABD\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n\u003c/div\u003e\n\u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style='font-size:13px;font-family:\"Times New Roman\",serif;color:#242021;'\u003e\u0026nbsp;\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style='font-size:13px;font-family:\"Times New Roman\",serif;color:#242021;'\u003eTable 2 Groups of homoeologous \u003cem\u003ePHD-finger\u003c/em\u003e genes in wheat\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003ctable style=\"width:423.1pt;border-collapse:collapse;border:none;\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" style=\"width: 120.5pt;border-color: windowtext currentcolor;border-style: solid none;border-width: 1pt medium;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003eHomoeologous group\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:#242021;'\u003e\u003cbr\u003e \u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-family:\"Times New Roman\",serif;'\u003e(A: B: D)\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 85.05pt;border-color: windowtext currentcolor;border-style: solid none;border-width: 1pt medium;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003eAll wheat genes\u003csup\u003e1\u003c/sup\u003e\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd colspan=\"3\" style=\"width: 217.55pt;border-color: windowtext currentcolor;border-style: solid none;border-width: 1pt medium;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003eWheat\u0026nbsp;\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003cstrong\u003e\u003cem\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:#242021;'\u003ePHD-finger\u003c/span\u003e\u003c/em\u003e\u003c/strong\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003e\u0026nbsp;\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:#242021;'\u003egenes\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-family:\"Times New Roman\",serif;'\u003e\u0026nbsp;(all)\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 77.95pt;border-color: currentcolor currentcolor windowtext;border-style: none none solid;border-width: medium medium 1pt;border-image: none 100% / 1 / 0 stretch;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 18.65pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003eNumber of groups\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border-color: windowtext currentcolor;border-style: solid none;border-width: 1pt medium;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 18.65pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003eNumber of genes\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.6pt;border-color: windowtext currentcolor;border-style: solid none;border-width: 1pt medium;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 18.65pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003e% of genes\u003csup\u003e2\u003c/sup\u003e\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 120.5pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 17.6pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003e1: 1: 1\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85.05pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 17.6pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:#242021;'\u003e35.8%\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 77.95pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 17.6pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e69\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 17.6pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e207\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.6pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 17.6pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e84.8\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 120.5pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.45pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:#242021;'\u003en: 1: 1/1: n: 1/1: 1: n\u003csup\u003e3\u003c/sup\u003e\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85.05pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.45pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:#242021;'\u003e5.7%\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 77.95pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.45pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e1\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.45pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e4\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.6pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.45pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e1.6\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 120.5pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003e1: 1: 0/1: 0: 1/0: 1: 1\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85.05pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:#242021;'\u003e13.2%\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 77.95pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e8\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e16\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.6pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e6.6\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 120.5pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003eOther ratios\u003csup\u003e4\u003c/sup\u003e\u003c/span\u003e\u003c/strong\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85.05pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:#242021;'\u003e8.0%\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 77.95pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e3\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e11\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.6pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e4.5\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 120.5pt;border: medium none;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.45pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003eOrphans/singletons\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 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stretch;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cstrong\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003e\u0026nbsp;\u003c/span\u003e\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 85.05pt;border-color: currentcolor currentcolor windowtext;border-style: none none solid;border-width: medium medium 1pt;border-image: none 100% / 1 / 0 stretch;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-family:\"AdvPSSXR\",serif;color:#242021;font-weight:normal;font-style:normal;'\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003e99.8%\u003c/span\u003e\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 77.95pt;border-color: currentcolor currentcolor windowtext;border-style: none none solid;border-width: medium medium 1pt;border-image: none 100% / 1 / 0 stretch;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;'\u003e\u0026nbsp;\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78pt;border-color: currentcolor currentcolor windowtext;border-style: none none solid;border-width: medium medium 1pt;border-image: none 100% / 1 / 0 stretch;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e244\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 61.6pt;border-color: currentcolor currentcolor windowtext;border-style: none none solid;border-width: medium medium 1pt;border-image: none 100% / 1 / 0 stretch;background: white none repeat scroll 0% 0%;padding: 0in 5.4pt;height: 16.95pt;vertical-align: top;\"\u003e\n \u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:12px;font-family:\"Times New Roman\",serif;color:black;'\u003e100.0\u003c/span\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp style=\"margin:0in;text-align:justify;font-size:14px;font-family:DengXian;\"\u003e\u003cspan style='font-size:11px;font-family:\"Times New Roman\",serif;color:#242021;'\u003eNote: \u003csup\u003e1\u003c/sup\u003eAccording to IWGSC (2018). \u003csup\u003e2\u003c/sup\u003ePercentage calculated with 244 genes. \u003csup\u003e3\u003c/sup\u003eFor n \u0026gt; 1. \u003csup\u003e4\u003c/sup\u003eE.g., n:1:n or 0:1:n, n \u0026gt; 1. \u003csup\u003e5\u003c/sup\u003eSee Table 1 and Table S3.\u003c/span\u003e\u003c/p\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"Yulin Normal University","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"PHD finger genes, wheat, phylogenetic analysis, expression patterns","lastPublishedDoi":"10.21203/rs.3.rs-1799303/v2","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-1799303/v2","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003ePlant homeodomain (PHD) transcription factors (TFs) are a class of proteins with conserved Cys4-His-Cys3 domains that play important roles in plant growth and development, and in response to abiotic stresses. Although characterization of \u003cem\u003ePHDs\u003c/em\u003e have been performed in plants, little is known about their function in wheat (\u003cem\u003eTriticum aestivum\u003c/em\u003e L.), especially under stress conditions. In the present study, 244 \u003cem\u003eTaPHDs\u003c/em\u003e were identified in wheat using comparative genomics. We renamed them \u003cem\u003eTaPHD1-244\u003c/em\u003e based on their chromosomal distribution, and almost all PHD proteins were predicted to be located in the nucleus. According to the unrooted neighbor-joining phylogenetic tree, gene structure, and motif analyses, \u003cem\u003ePHD\u003c/em\u003e genes were divided into four clades. A total of 149 \u003cem\u003eTaPHD\u003c/em\u003e genes were assigned to arise from duplication events. Furthermore, 230 gene pairs came from wheat itself, and 119, 186, 168, 7, 2, and 6 gene pairs came from six other species (\u003cem\u003eHordeum vulgareto, Zea mays\u003c/em\u003e, \u003cem\u003eOryza sativa, Arabidopsis thaliana\u003c/em\u003e, \u003cem\u003eBrassica rapa\u003c/em\u003e, and \u003cem\u003eGossypium raimondii\u003c/em\u003e, respectively). A total of 548 interacting protein branches were identified to be involved in the protein interaction network. Tissue-specific expression pattern analysis showed that \u003cem\u003eTaPHDs\u003c/em\u003e were highly expressed in the stigma and ovary during flowering, suggesting that the \u003cem\u003eTaPHD\u003c/em\u003e gene plays an active role in the reproductive growth of wheat. In addition, the qRT-PCR results further confirmed that these \u003cem\u003eTaPHD\u003c/em\u003e genes are involved in the abiotic stress response of wheat. In conclusion, our study provides a theoretical basis for deciphering the molecular functions of \u003cem\u003eTaPHDs\u003c/em\u003e, particularly in response to abiotic stress.\u003c/p\u003e","manuscriptTitle":"PHD-finger family genes in wheat (Triticum aestivum L.): evolutionary conservatism, functional diversification, and active expression in abiotic stress","msid":"","msnumber":"","nonDraftVersions":[{"code":2,"date":"2022-08-02 19:04:04","doi":"10.21203/rs.3.rs-1799303/v2","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}},{"code":1,"date":"2022-06-29 16:54:21","doi":"10.21203/rs.3.rs-1799303/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"2b8dec0a-3dc0-4666-a44c-ee21ca6f6f27","owner":[],"postedDate":"August 2nd, 2022","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":14402807,"name":"Agronomy"},{"id":14402808,"name":"Bioinformatics"},{"id":14402809,"name":"Molecular Biology"}],"tags":[],"updatedAt":"2023-02-16T17:06:23+00:00","versionOfRecord":{"articleIdentity":"rs-1799303","link":"https://doi.org/10.3389/fpls.2022.1016831","journal":{"identity":"frontiers-in-plant-science","isVorOnly":true,"title":"Frontiers in Plant Science"},"publishedOn":"2022-12-12 00:00:00","publishedOnDateReadable":"December 12th, 2022"},"versionCreatedAt":"2022-08-02 19:04:04","video":"","vorDoi":"10.3389/fpls.2022.1016831","vorDoiUrl":"https://doi.org/10.3389/fpls.2022.1016831","workflowStages":[]},"version":"v2","identity":"rs-1799303","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-1799303","identity":"rs-1799303","version":["v2"]},"buildId":"WrCJVZZCHTDjtuVLN7oU0","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}