OrchidBase 6.0: Increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis

OrchidBase 6.0: Increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis | 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 OrchidBase 6.0: Increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis You-Yi Chen, Ye Sun, Chung-I Li, Shao-Ting Lin, Hao-Chen Zheng, and 24 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-5454452/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 02 Jan, 2025 Read the published version in BMC Plant Biology → Version 1 posted 14 You are reading this latest preprint version Abstract Background: Containing the largest number of species, the orchid family provides not only material for studying plant evolution and environmental adaptation, but also economically and culturally important ornamental plants for the human society. Previously, we collected genomic and transcriptomic information on Apostasia shenzhenica , Dendrobium catenatum , Phalaenopsis equestris , and two species of Platanthera that belong to three different subfamilies of Orchidaceae, and developed user-friendly tools to explore orchid genetic sequences in OrchidBase. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study. Description: Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense , C. ensifolium and C. goeringii , were sequenced de novo , assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses. Conclusion: OrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data. Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Introduction Cymbidium contains approximately 80 species and belongs to the subfamily Epidendroideae of the family Orchidaceae. This genus is distributed in tropical and subtropical Asia (northern India, China, Japan, Malaysia, the Philippines, and Borneo) and further south in Papua New Guinea and Northern Australia [ 1 , 2 ]. The cultivation of Cymbidium can be traced back to the time of Confucius, approximately 2,500 years ago (B.C. 500). Through the accumulation of cultural and scientific development over several thousand years, Cymbidium species and hybrids have become one of the most commercially important orchids, not only in the floriculture industry but also in medicinal applications globally. Cymbidium shows diversified lifestyles for adaptation to the environment, including epiphytic; lithophytic; terrestrial; and rarely, leafless mycoheterotrophy lifestyles [ 3 , 4 ]. C. goeringii , C. ensifolium , and C. sinense are terrestrial plants that are the most popular flowering ornamental orchids and are widely cultivated for their beauty and fragrance [ 5 ]. Therefore, the genome sequences of these three Cymbidium species have been selected for decoding and used to explore the molecular mechanisms of flowering, floral shape morphogenesis, and flower odor biosynthesis [ 6 – 8 ]. OrchidBase was created for the storage, management, and efficient usage of orchid genetic information. The data were primarily generated using first-generation sequencing technology. Sanger sequencing was performed on samples derived from Phalaenopsis reproductive organs [ 9 ]. OrchidBase 2.0 was constructed using transcriptomes derived from the floral buds of two species in each of the five subfamilies of Orchidaceae using next-generation sequencing (Solexa Illumina, San Diego, CA, USA) [ 10 ]. With the advancement in sequencing technology, the cost of sequencing has reduced, and the sequence production speed has greatly increased. As a result, orchid whole-genome sequencing has been accomplished [ 6 – 8 , 11 – 14 ]. Based on these orchid genomes and their transcriptomic sequences, OrchidBase has been updated with new sequences and newly developed tools for mining information embedded in these sequences [ 15 – 17 ]. In addition to OrchidBase, which provides orchid genomes and transcriptomes for analysis, several databases offer similar datasets and tools for mining specific orchid species, such as Orchidstra for P. aphrodite [ 18 – 20 ], OncidiumOrchidGenomeBase for Oncidium [ 21 ], and GelFAP for Gastrodia elata [ 22 – 25 ]. In OrchidBase 6.0, the genomes of three Cymbidium species, namely, C. sinense , C, ensifolium , and C. gorengii , belonging to the Epidendroideae family, and their relative transcriptomes derived from various floral developmental stages and tissues have been included (Fig. 1 ). Furthermore, new tools, including transcription regulation analysis (promoters, transcription factors, and downstream targets), advanced transcriptome analysis, and advanced BLAST tools, have been developed for the functional analysis of orchid genes. The content of the OrchidBase 6.0 is summarized in Table 1 . The information and tools launched in OrchidBase 6.0 are extensive and will be an excellent resource for orchid biology research. Table 1 Summary of data and tools that could be browsed and used for the eight orchid species (Pha. equestris, D. catenatum, Apo. shenzhenica, P. zijinensis, P. guangdongensis, C. sinense, C. ensifolium and C. goeringii) Transcriptome Gene ID, FPKM and TPM values in various tissues Genome browser Scaffold ID, Scaffold sequence, Gene model, miRNA Gene annotation Gene ID, Gene sequence, BLAST top hit descriptions, KEGG pathway, GO terms, Interpro description, Swissprot description, TrEMBL description, miRNA Metabolism pathway Gene ID, Genes mapped to the KEGG pathways Synteny Gene ID, Physical positions of genes Gene order Gene ID, Physical positions of genes miRNA-targets information miRNA gene ID, Structure of miRNA, Target gene IDs of miRNA, Binding sites in the target genes of a miRNA Regulation Gene ID, Promoter binding site prediction Tools BLASTN, BLASTX, tBLASTX, BLASTP, tBLASTN, pfam ID, pfam description, Expanded database content C. sinense, C, ensifolium , and C. gorengii each have a karyotype of 2N = 2X = 40. We generated 429 Gb of data using Nanopore technology [ 26 ] and 670 Gb using Hi-C sequencing technology for C. sinense ; 351 Gb using PacBio technology and 349 Gb using Hi-C technology for C. ensifolium ; and 478 Gb using PacBio technology and 296 Gb using Hi-C technology for C. gorengii . The genome assemblies were 3.45 Gb, with a contig N50 value of 1.11 Mb; 3.63 Gb, with a contig N50 value of 1.21 Mb; and 4.07 Gb, with a contig N50 value of 1.04 Mb for the C. sinense , C. ensifolium and C. gorengii genomes, respectively (Table 2 ) [ 6 – 8 ]. Twenty pseudochromosomes were constructed for each Cymbidium species based on the assembled sequences. The raw data and whole-genome-assembled scaffold sequences of C. sinense and C. gorengii were downloaded from BioProject PRJNA743748 and PRJNA749652, respectively, and deposited in the National Center for Biotechnology Information database. The corresponding data for C. ensifolium (BioProject/GSA PRJCA005355/CRA004327) was downloaded from the National Genomics Data Center. The statistics for the added orchid genomes are presented in OrchidBase 6.0 ( http://cosbi.ee.ncku.edu.tw/orchibase6/ ). Based on these datasets, 29,638, 29,073, and 29,272 protein-coding genes were predicted for the genomes of C. sinense , C. ensifolium , and C. gorengii , respectively. Furthermore, 200, 71, and 147 miRNA candidates have been identified in the C. sinense, C. ensifolium , and C. gorengii genomes, respectively [ 6 – 8 ]. Each predicted gene and miRNA was assigned a specific ID. Specific genes or miRNAs can be selected to investigate their annotated functions associated with biological processes. Table 2 Comparisons of the assembled genomes among eight orchid species in the OrchidBase 6.0 Orchid species Assembled genome size N50 length of Scaffold (Mb) N50 length of contig size Number of predicted genes Reference Phalaenoipsis equestris 1.03 Gb 1.22 45.8 Kb 29,545 Zhang et al . 2017 Dendrobium catenatum 1.12 Gb 1.06 51.7 Kb 29,257 Zhang et al ., 2017 Apostasia shenzhenica 349 Mb 3.03 80.1 Kb 21,841 Zhang et al ., 2017 Platanthera zijinensis 4.19 Gb nd 1.77 Mb 24,513 Li et al ., 2022 Platanthera guangdongensis 4.20 Gb nd 1.57 Mb 22,559 Li et al ., 2022 Cymbidium sinense 3.45 Gb nd 1.11 Mb 29,638 Yang et al ., 2021 Cymbidium ensifolium 3.63 Gb nd 1.21 Mb 29,073 Ai et al ., 2021 Cymbidium goeringii 4.07 Gb nd 1.04 Mb 29,272 Ye et al ., 2021 nd: not determined The transcriptomic data derived from the three Cymbidium species were downloaded from BioProjects PRJNA743748 ( C. sinense ), PRJNA749652 ( C. gorengii ) and BioProject/GSA PRJCA005355/CRA004327 ( C. ensifolium ). All RNA sequencing reads were mapped to the predicted genes and calculated as transcripts per million (TPM), fragments per kilobase of transcript per million mapped reads (FPKM), or raw counts for each gene in various tissues and at different developmental stages to provide the gene expression profiles. This biological information was integrated into the updated version of OrchidBase 6.0. Identification of transcription factor (TF) genes in the genomes of orchid species To identify orchid genes encoding TFs, we retrieved the TF protein sequences of Arabidopsis thaliana and Oryza sativa subsp. japonica from PlantTFDB 5.0 ( https://planttfdb.gao-lab.org/index.php ). In total, 2,296 and 2,408 TF sequences from A. thaliana and O. sativa subsp. japonica , respectively, were used as queries in BLASTP searches against each of the predicted proteomes of eight orchids, with an E value of 10 − 5 to obtain 13,169 putative orchid TF genes that could be categorized into different subfamilies (Supplementary Table 1). To predict TF binding sites, the region 2,000 bp upstream of the translation start site of each gene was annotated for each orchid species genome. These data were retrieved and searched using the Match™ program [ 27 ] based on the position weight matrices created in PlantPan 3.0 [ 28 ]. In total, 1,786 and 420 TFmatrixIDs were predicted for each orchid species using Arabidopsis and rice model plants, respectively (Table 3 ). Furthermore, approximately 37–77 million TF binding sites in the orchid genomes were predicted using the Arabidopsis matrix, and 15–28 million binding sites were predicted using the rice matrix (Table 3 ). Table 3 The number of predicted TFmatrixID and TF binding site at the promoter of each orchid genome Orchid species Compared model plant species Number of hit TFmatrix ID and TF binding site at the promoter of each orchid species Number of TF binding sites at promoter Aps. shenzhenica A. thaliana 1,786 45,452,473 P. zijinensis A. thaliana 1,786 51,027,954 P. guangdongensis A. thaliana 1,786 37,226,223 Pha. equestris A. thaliana 1,786 51,218,142 D. catenatum A. thaliana 1,786 53,846,987 C. sinense A. thaliana 1,786 65,068,952 C. ensifolium A. thaliana 1,786 63,385,827 C. goeringii A. thaliana 1,786 76,868,231 A. shenzhenica O. sativa 420 16,847,177 P. zijinensis O. sativa 420 21,110,631 P. guangdongensis O. sativa 420 15,589,098 Pha. equestris O. sativa 420 19,206,180 D. catenatum O. sativa 420 19,977,158 C. sinense O. sativa 420 23,942,903 C. ensifolium O. sativa 420 23,455,231 C. goeringii O. sativa 420 28,271,112 Table 4 The number of predicted TFmatrixID and TF binding site at the promoter of each orchid genome. Orchid species Compared model plant species Number of hit TFmatrix ID and TF binding site at the promoter of each orchid species Number of TF binding sites at promoter Aps. shenzhenica A. thaliana 1,786 45,452,473 P. zijinensis A. thaliana 1,786 51,027,954 P. guangdongensis A. thaliana 1,786 37,226,223 Pha. equestris A. thaliana 1,786 51,218,142 D. catenatum A. thaliana 1,786 53,846,987 C. sinense A. thaliana 1,786 65,068,952 C. ensifolium A. thaliana 1,786 63,385,827 C. goeringii A. thaliana 1,786 76,868,231 A. shenzhenica O. sativa 420 16,847,177 P. zijinensis O. sativa 420 21,110,631 P. guangdongensis O. sativa 420 15,589,098 Pha. equestris O. sativa 420 19,206,180 D. catenatum O. sativa 420 19,977,158 C. sinense O. sativa 420 23,942,903 C. ensifolium O. sativa 420 23,455,231 C. goeringii O. sativa 420 28,271,112 Searching the genome information for the three species of Cymbidium in the database The genome information for the three Cymbidium species in OrchidBase 6.0 can be accessed using the assembled pseudochromosomes and predicted genes. Through the web interface, the newly added orchid genome information in OrchidBase 6.0 can be freely obtained. The information can be linked via the “Orchid Genome” icon (Fig. 3 , Step 1). Using this interface, users are able to select one of the five existing orchid genomes ( Pha. equestris , D. catenatum , Aps. shenzhenica , P. zijinensis , and P. guangdongensis ), and from the three newly added Cymbidium genomes ( C. sinense, C. ensifolium, and C. gorengii ) (Fig. 3 , Step 2). Users can then access the genome browser (Fig. 3 , Step 3) and obtain information about gene annotation (Fig. 3 , Step 4), metabolic pathways (Fig. 3 , Step 5), synteny (Fig. 3 , step 6), gene order (Fig. 3 , Step 7), miRNAs (Fig. 3 , Step 8), and regulation (Fig. 3 , Step 9) by searching the orchid genome. Comparative analysis can then be performed using the selected orchid genomes. The genome browser and gene annotation, metabolic pathway, synteny, gene order, and miRNA information were introduced in the previous versions of OrchidBase [ 16 , 17 ]. In the following sections, we explain in detail the new “Regulation” function, the updated transcriptome information, and advanced BLAST and Domain searches, which can be found in the Tools menu. Data content and “Regulation” web interface The OrchidBase 6.0 database update provides a “Regulation” function for each orchid genome. This function allows users to predict genes that may be regulated by different types of TFs and the binding sites at which the corresponding TFs bind to the promoters. Regulation analysis provides a graphical interface for displaying the relationships between genes, the binding sites and sequences at their individual promoters, and the corresponding TFs (Fig. 4 ). To use the Regulation Analysis page, users can click on the orchid genome (Fig. 4 , Step 1) and choose one of the orchid species (Fig. 4 , Step 2). They will then be navigated to the main function page for genome analysis and enter the “Regulation” page (Fig. 4 , Step 3). On the “Regulation” page, users can select one of the TF reference libraries ( A. thaliana or O. sativa ) (Fig. 4 , Step 4), which means that the identified TFs in each of the orchid genomes were based on orthologs in Arabidopsis or rice. One orchid species (Fig. 4 , Step 5) can be chosen or maintained, as shown in Fig. 4 , Step 2. If users are interested in gene ID analysis, they can fill in the “Search” box (Fig. 4 , Step 6). In this study, the gene ID cymsin_Mol016808 , a gene encoding SEPTALLA ( SEP )-like MADS-box protein, was used as an example. The results for the example showed that 274 TFs could bind to the promoter of cymsin_Mol016808 . By clicking on these 274 TFs (Fig. 4 , Step 7), users can observe a table characterizing different TF families and the number of corresponding members that potentially regulate the expression of cymsin_Mol016808 (Fig. 4 , Steps 8 and 9). Users can choose any of the TF families, and AP2, ERF, and ERF (3) can be selected (Fig. 4 , Step 10). On the same page, a new table under the TF families table shows the IDs of three genes encoding AP2, ERF, and ERF TFs that bind to specific sequences in the cymsin_Mol016808 promoter, and the IDs of their ortholog genes in Arabidopsis (Fig. 4 , Step 11). Clicking on the binding site directs users to PlantPAN 3.0, where they can see the TFmatrixID logo and access additional information related to the binding sites (Fig. 4 , Steps 12 and 13). Under the TF table, users can further visualize a graph of the binding positions and sequences of the TF (Fig. 4 , Steps 14–16). Different TFs are shown in different colors. Updated transcriptome The previous version of the transcriptome in OrchidBase only provided the FPKM of each gene in each sequenced orchid genome [ 15 – 17 ]. In the current version, we provide the TPM and raw counts for the expression of each gene as well as different presentation styles for the gene expression data. The user can navigate to the transcriptome and choose one of the orchids (Fig. 5 , Step 1). This page shows the expression of each gene in different tissues and organs. Users can select the data type with the contig (raw count), TPM, or FPKM (Fig. 5 , Step 2), and then click “Search” (Fig. 5 , Step 3). Alternatively, they can enter the gene ID, if they know it, in the “Search” box (Fig. 5 , Step 4). The subsequent page then shows the expression patterns that the users would like to see (Fig. 5 , Step 5). Users can further click “Gene ID” (Fig. 5 , Step 6) to hyperlink to the gene annotation (Fig. 5 , step 7). They can even type several Gene IDs or keywords in the “Search” box to explore multiple gene expression patterns (Fig. 5 , Step 8). After clicking “View/Search” (Fig. 5 , Step 9), users can obtain the transcriptome of assigned genes listed in the table under the “Search” box (Fig. 5 , Step 10). Users can choose the values used to measure the expression levels (Fig. 5 , Step 11) and further select items from various tissues or organs (Fig. 5 , Step 12) to investigate their expression patterns. The button under the table is designed to “Refresh or Reset” (Fig. 5 , Step 13). In addition to the table describing the expression patterns of the assigned genes, we designed several graphic modes to visualize the transcripts of the genes, including a heatmap (Fig. 5 , Steps 14 and 15), bar chart (Fig. 5 , Steps 16 and 17), principal component analysis (PCA) results (Fig. 5 , Steps 18 and 19), and hierarchical clustering (Fig. 5 , Steps 20 and 21). Overall, this page provides an interface for users to explore gene expression patterns using TPM, FPKM, or raw counts, and users can obtain gene annotations using the gene ID. Advanced BLAST BLAST is one of the most popular pairwise alignment tools to search for similar sequences stored in databases [ 29 ]. However, scientists would like to know the expression patterns of hit sequences to further infer their functions. Here, we combined the BLAST tool with different expression patterns to display tools that simultaneously reveal the biological significance of the genes. Users can visit “Tools” (Fig. 6 , Step 1), and select one of the sequenced orchid genomes. Here, we selected C. ensifolium using nucleotide BLAST as an example (Fig. 6 , Step 2). Based on the nucleotide BLAST search (Fig. 6 , Step 3), users can select one of the nucleotide BLAST programs (Fig. 6 , Step 4), paste the nucleotide sequence (Fig. 6 , Step 5), and click BLAST (Fig. 6 , step 6). In the BLAST results page (Fig. 6 , Step 7), users would click the hit “Gene ID” (Fig. 6 , Step 8) to link to the gene annotation (Fig. 6 , Step 9), or click the “View Detail” icon to obtain the sequence alignment (Fig. 6 , Steps 10 and 11). Additionally, users can tick any one of the hit gene IDs (Fig. 6 , Step 12) and click “Show Expression Profile” at the bottom of the table (Fig. 6 , Step 13). The subsequent page provides various graphic presentations of the updated transcriptomes described above (Fig. 6 , Steps 14–26). In summary, this tool not only contributes to pairwise alignment results, but also provides additional gene annotation and expression profiles of the hit sequences. Domain search Protein domains are fundamental units of protein structure, folding, function, evolution, and design. They are considered homologous sequences encoded in different gene contexts that have remained intact at the sequence level throughout evolution. Based on these concepts, we designed the tool “Domain Search” to characterize the protein-coding sequences based on the Pfam and InterPro classifications. For example, with the “Domain Research” tool, users can click on “Tools” (Fig. 7 , Step 1) and choose one of the orchid species in the panel of Tools_Domain Search (InterProScan or Pfam) (Fig. 7 , Step 2). Protein sequences can be pasted in the box (Fig. 7 , Step 3), and Pfam or Interproscan can be chosen. After clicking “Submit” (Fig. 7 , Step 4), the page shows an additional table presenting the hit sequence ID in the genome of the selected species (Fig. 7 , Step 5). The page also allows users to choose either the Jaccard, intersection, or union method (Fig. 7 , Step 6) for similarity comparison and to determine how the domains are screened for the inclusion of the query. The unique design of this tool includes the “Domain Search” and the expression patterns of the hit sequences (Fig. 7 , Step 7). Users can further click “Show Similar Gene” (Fig. 7 , Step 8), tick the genes of interest (Fig. 7 , Step 9), and click “Show Expression Profile” (Fig. 7 , Step 10). The additional table page provides various graphical presentations of the expression pattern, such as the updated transcriptome described above (Fig. 7 , Steps 11–23). A case study One of the most well-known orchid characteristics is their delicate floral organ labellum, which attracts pollinators for precision pollination and humans for art appreciation. Several models have been described for the MADS-box genes involved in labellum development, such as the Orchid Tepal Model [ 30 ], Orchid Code [ 31 ], the HOT (Homeotic Orchid Tepal) model [ 32 ], and P (perianth)-code [ 33 ]. One of the B-class MADS-box genes, PeMADS4 in Phalaenopsis , has been proposed as a candidate labellum identity gene that is not excluded from the models. However, the genes that regulate the expression of PeMADS4 orthologs in the labellum of orchids remain unclear. In this study, we screened for TFs that could bind to the promoters of PeMADS4 orthologs in C. sinense . First, we clicked “Orchid Genome”, chose one of the orchid species, C. sinense (Fig. 5 , Step 1), and clicked “Regulation” (Fig. 5 , Step 2). The ortholog ID ( cymsin_Mol018952 ) of PeMADS4 in C. sinense was identified using BLAST (data not shown). We then selected the “TF Reference Library” as A. thaliana and selected the library as C. sinense , or directly entered cymsin_Mol018952 as the gene ID in the “Search” box (Fig. 5 , Step 3). This page shows the annotation of cymsin_Mol018952 and the number (242) of TFs that are possible regulators of cymsin_Mol018952 expression. We clicked the 242 TFs (Fig. 5 , Step 4), and then “MADS box, MIKC(8)” (Fig. 5 , Step 5), because a previous study reported that MADS-box genes also have the ability to regulate the expression of self- or other MADS-box genes [ 32 ]. After choosing the second Cymbidium MADS-box gene cymsin_Mol006225 (Fig. 5 , Step 6), and clicking the third matrix ID “TFmatrixID_0508” (Fig. 5 , Step 7), we could see the page linked to PlantPan 3.0 showing the binding logo and Arabidopsis TFs binding to it. Conclusions and future directions We added the whole-genome sequences of the Cymbidium species, C. sinense , C. ensifolium , and C. goeringii , and their transcriptomes to OrchidBase 6.0. Additionally, two functions for genome comparisons and miRNA characterization were developed in this study. These additions increased the number of Cymbidium genomes in OrchidBase and has provided tools for exploring the knowledge embedded in nucleotide sequences, providing the opportunity for users to obtain novel insights into the conservation and diversification of orchid genomes. We will continue to increase the number of orchid whole-genome sequences in OrchidBase and add omics analysis tools for use by plant scientists. Declarations Ethics declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Availability of data and materials The raw data and whole genome-assembled scaffold sequences of the C. sinense and C. goeringii (PRJNA743748 and PRJNA749652) were downloaded from the National Center for Biotechnology Information (NCBI) database. The related genomic data of C. ensifolium (BioProject/GSA PRJCA005355/CRA004327) was retrieved from the National Genomics Data Center (NGDC). The transcriptomics data derived from the three Cymbidium species were also downloaded from BioProjects PRJNA743748, PRJNA749652, and BioProject/GSA PRJCA005355/CRA004327. Data availability All data generated or analyzed during this study are included in this published article. Competing interests Authors declare that they have no competing interests. Funding This work was funded by the Ministry of Science and Technology, Taiwan, (MOST 110-2313-B-006-002-MY3, 110-2221-E-006-198-MY3, 110-2622-B-006-009-, 111-2313-B-006-003, NSTC 112-2313-B-006-003-, and 113-2313-B-006-003-), National Cheng Kung University, Taiwan (D113-F1738), and National Key R&D Program of China (Grant No.2019YFD1000400) and the National Natural Science Foundation of China [no. 31870199]. Authors' contributions SL, ZJL, WSW, and WCT conceived the project idea, directed the project, generated analyzing ideas and wrote the paper. YYC and YS analyzed the data and wrote the paper. CIL, YYH, STL, and HY contributed to the project idea and did the transcriptomic analysis. HCZ, ZBZ, BRL and CLH established the platform for data analyzed and provided the required hardware. CNC and WCC contributed TFmatrix and TF binding site statistical analyses, HC, FXY, GFZ, QZ, CYZ, ZZ, YA, LYW, DC, XH, MZH and DHP collected the data and contributed the project idea. The author(s) read and approved the final manuscript. Acknowledgement This research was also supported in part by Higher Education Sprout Project, Ministry of Education to the Headquarters of University Advancement at National Cheng Kung University, Taiwan. References Liu Z, Chen S, Ru Z. The genus Cymbidium in China. Beijing, China: Science Press. pp.1 – 342; 2006. Du Puy D, Cribb P. The genus Cymbidium. London and Portland, Oregon: Christopher Helm and Timber Press. pp.1 – 236; 1988. Thakur S, Dutt HC. Cymbidium macrorhizon lindl. (Orchidaceae): a new record for flora of jammu and Kashmir, India. Natl Acad Sci Lett. 2021;44:271–74. Bidartondo MI. The evolutionary ecology of mycoheterotrophy. New Phytol. 2005;167:335–52. Huang WT, Fang ZM, Zeng SJ, Zhang JX, Wu KL, Chen ZL, et al. Molecular cloning and functional analysis of three FLOWERING LOCUS T ( FT ) homologous genes from Chinese Cymbidium . Int J Mol Sci. 2012;13(9):11385–98. Yang FX, Gao J, Wei YL, Ren R, Zhang GQ, Lu CQ, et al. The genome of Cymbidium sinense revealed the evolution of orchid traits. Plant Biotech J. 2021;19(12):2501–16. Ai Y, Li Z, Sun WH, Chen J, Zhang DY, Ma L, et al. The Cymbidium genome reveals the evolution of unique morphological traits. Hortic Res. 2021;8(1):255. Sun Y, Chen GZ, Huang J, Liu DK, Xue F, Chen XL, et al. The Cymbidium goeringii genome provides insight into organ development and adaptive evolution in orchids. Ornam Plant Res. 2021;1:10. Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, et al. OrchidBase: A collection of sequences of transcriptome derived from orchids. Plant Cell Physiol. 2011;52(2):238–43. Tsai WC, Fu CH, Hsiao YY, Huang YM, Chen LJ, Liu ZJ, et al. OrchidBase 2.0: Comprehensive collection of Orchidaceae floral transcriptomes. Plant Cell Physiol. 2013;54:e7. Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, et al. The genome sequence of the orchid Phalaenopsis equestris . Nat Genet. 2015;47(1):65–72. Zhang GQ, Xu Q, Bian C, Tsai WC, Yeh CM, Liu KW, et al. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, flower development and adaptive evolution. Sci Rep. 2016;6:19029. Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, et al. The Apostasia genome and the evolution of orchids. Nature. 2017;579(7672):379–83. Li MH, Liu KW, Li Z, Lu HC, Ye QL, Zhang D, et al. Genomes of leafy and leafless Platanthera orchids provide insights into the evolution of mycoheterotrophy. Nat Plants. 2022;8(4):373–88. Tsai WC, Fu CH, Hsiao YY, Wu WL, Zhang DY, Lan SR, et al. OrchidBase 3.0: a resource for studying gene function and genome evolution in orchids. J Fujian Agric Univ. 2019;48:440–6. Hsiao YY, Fu CH, Ho SY, Li CI, Chen YY, Wu WL, et al. OrchidBase 4.0: a database for orchid genomics and molecular biology. BMC Plant Biol. 2021;21:371. Chen YY, Li CI, Hsiao YY, Ho SY, Zhang ZB, Liao CC, et al. OrchidBase 5.0: updates to knowledge base of the orchid genomes. BMC Plant Biol. 2022;22:557. Su CL, Chao YT, Yen SH, Chen CY, Chen WC, Chang YCA, et al. Orchidstra: an integrated orchid functional genomics database. Plant Cell Physiol. 2013;54(2):e11. Chao YT, Yen SH, Yeh JH, Chen WC, Shih MC. Orchidstra 2.0 - A transcriptomics resource for the orchid family. Plant Cell Physiol. 2017;58(1):e9. Chao YT, Chen WC, Chen CY, Ho HY, Yeh CH, Kuo YT, et al. Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding. Plant Biotechnol J. 2018;16(12):2027–41. Chang YY, Chu YW, Chen CW, Leu WM, Hsu HF, Yang CH. Characterization of Oncidium ‘Gower Ramsey’ transcriptomes using 454 GS-FLX pyrosequencing and their application to the identification of genes associated with flowering time. Plant Cell Physiol. 2011;52(9):1532–45. Yuan Y, Jin X, Liu J, Zhao X, Zhou J, Wang X, et al. The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. Nat Commun. 2018;9(1):1615. Bae EK, An C, Kang MJ, Lee SA, Lee SJ, Kim KT et al. Chromosome-level genome assembly of the fully mycoheterotrophic orchid Gastrodia elata. G3 (Bethesda) 2022;12(3):jkab433. Yang J, Xiao Q, Xu J, Da L, Guo L, Huang L, et al. GelFAP: gene functional analysis platform for Gastrodia elata . Front Plant Sci. 2020;11:563237. Yang J, Li P, Li Y, Xiao Q. GelFAP v2.0: an improved platform for gene functional analysis in Gastrodia elata . BMC Genomics. 2023;24:164. Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36:338. Kel AE, Gossling E, Peuter I, Cheremushkin K, Kel-Margoulis OV, Wingerder E. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 2003;31:3576–9. Chow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH, et al. PlantPan3.0: a new and updated resource for reconstructing transcriptional regulatory networks from CHIP-seq experiments in plants. Nucleic Acids Res. 2019;47(D1):D1155–63. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402. Tsai WC, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Chen WH, et al. Molecular biology of orchid flower – with emphasis on Phalaenopsis . Adv Bot Res. 2008;47:99–145. Mondragón-Palomino M, Theissen G. MADS about the evolution of orchid flowers. Trends Plant Sci. 2008;13:51–9. Pan ZJ, Cheng CC, Tsai WC, Chung MC, Chen WH, Hu JM et al. The duplicated B-class MADS‐box genes display dualistic characters in orchid floral organ identity and growth. Plant Cell Physiol. 2011:52:1515–31. Hsu HF, Hsu WH, Lee YI, Mao WT, Yang CI, Li JY, et al. Model for perianth formation in orchids. Nat Plants. 2015;1:15046. Additional Declarations No competing interests reported. Supplementary Files SupplementaryTable1.docx Supplementary Table 1 Number of predicted transcription factors in each orchid genome, categorized by subfamily Cite Share Download PDF Status: Published Journal Publication published 02 Jan, 2025 Read the published version in BMC Plant Biology → Version 1 posted Editorial decision: Revision requested 13 Dec, 2024 Reviews received at journal 13 Dec, 2024 Reviews received at journal 11 Dec, 2024 Reviews received at journal 11 Dec, 2024 Reviewers agreed at journal 07 Dec, 2024 Reviews received at journal 04 Dec, 2024 Reviewers agreed at journal 03 Dec, 2024 Reviewers agreed at journal 02 Dec, 2024 Reviewers agreed at journal 02 Dec, 2024 Reviewers invited by journal 01 Dec, 2024 Editor invited by journal 29 Nov, 2024 Editor assigned by journal 20 Nov, 2024 Submission checks completed at journal 20 Nov, 2024 First submitted to journal 14 Nov, 2024 You are reading this latest preprint version 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-5454452","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":384949421,"identity":"44e1af0d-8ece-4dfb-90e3-12a490a23f5c","order_by":0,"name":"You-Yi Chen","email":"","orcid":"","institution":"National Chiayi University","correspondingAuthor":false,"prefix":"","firstName":"You-Yi","middleName":"","lastName":"Chen","suffix":""},{"id":384949422,"identity":"446e7120-8429-4bb0-8564-fe9f28770423","order_by":1,"name":"Ye Sun","email":"","orcid":"","institution":"Jiangsu Lixiahe District Institute of Agricultural Sciences","correspondingAuthor":false,"prefix":"","firstName":"Ye","middleName":"","lastName":"Sun","suffix":""},{"id":384949423,"identity":"e246f1f4-5a04-4f3e-9801-65e8133b5bf9","order_by":2,"name":"Chung-I Li","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Chung-I","middleName":"","lastName":"Li","suffix":""},{"id":384949424,"identity":"f29e953a-a030-46d7-8e88-8aa60cbf43ee","order_by":3,"name":"Shao-Ting Lin","email":"","orcid":"","institution":"National Cheng Kung University and Academia Sinica","correspondingAuthor":false,"prefix":"","firstName":"Shao-Ting","middleName":"","lastName":"Lin","suffix":""},{"id":384949425,"identity":"923b86cf-31b0-4490-8c3e-3875b1e12a80","order_by":4,"name":"Hao-Chen Zheng","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Hao-Chen","middleName":"","lastName":"Zheng","suffix":""},{"id":384949426,"identity":"111b74a5-33e5-4303-a192-e5f9266c5620","order_by":5,"name":"Zhe-Bin Zhang","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Zhe-Bin","middleName":"","lastName":"Zhang","suffix":""},{"id":384949427,"identity":"c42b0318-8913-423a-b013-fb86a6527d71","order_by":6,"name":"Bing-Ru Lee","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Bing-Ru","middleName":"","lastName":"Lee","suffix":""},{"id":384949428,"identity":"f7d2decc-73d6-454c-92b2-de325296c09b","order_by":7,"name":"Chun-Lin Hsieh","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Chun-Lin","middleName":"","lastName":"Hsieh","suffix":""},{"id":384949429,"identity":"884f1103-2719-4331-874a-ac0b40aa5c76","order_by":8,"name":"Yu-Yun Hsiao","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Yu-Yun","middleName":"","lastName":"Hsiao","suffix":""},{"id":384949430,"identity":"5ae1680c-0a56-4b59-8daa-83079926510f","order_by":9,"name":"Chi-Nga Chow","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Chi-Nga","middleName":"","lastName":"Chow","suffix":""},{"id":384949431,"identity":"c84d4a92-3ba3-42dc-89d1-6f8e943eaf73","order_by":10,"name":"Chien-Wen Yang","email":"","orcid":"","institution":"National Cheng Kung University and Academia Sinica","correspondingAuthor":false,"prefix":"","firstName":"Chien-Wen","middleName":"","lastName":"Yang","suffix":""},{"id":384949432,"identity":"31f77cd1-f9c5-48ea-98fa-66eef2f81e09","order_by":11,"name":"Wen-Chi Chang","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Wen-Chi","middleName":"","lastName":"Chang","suffix":""},{"id":384949433,"identity":"2cce4d21-77ec-4b3e-a12a-58887d0b8779","order_by":12,"name":"Heming Chen","email":"","orcid":"","institution":"Guangdong Academy of Agricultural","correspondingAuthor":false,"prefix":"","firstName":"Heming","middleName":"","lastName":"Chen","suffix":""},{"id":384949434,"identity":"115fa2d6-7ab9-4bac-833b-2aa3fe2140de","order_by":13,"name":"Feng-Xi Yang","email":"","orcid":"","institution":"Guangdong Academy of Agricultural","correspondingAuthor":false,"prefix":"","firstName":"Feng-Xi","middleName":"","lastName":"Yang","suffix":""},{"id":384949435,"identity":"17b4f590-20fb-43bc-8902-33b9ee8caaa6","order_by":14,"name":"Gen-Fa Zhu","email":"","orcid":"","institution":"Guangdong Academy of Agricultural","correspondingAuthor":false,"prefix":"","firstName":"Gen-Fa","middleName":"","lastName":"Zhu","suffix":""},{"id":384949436,"identity":"83ed3164-0285-4035-a3fa-a54c656e89ec","order_by":15,"name":"Qinyao Zheng","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Qinyao","middleName":"","lastName":"Zheng","suffix":""},{"id":384949438,"identity":"cd6763cd-380a-488a-ac85-a0fd2239deaf","order_by":16,"name":"Cheng-Yuan Zhou","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Cheng-Yuan","middleName":"","lastName":"Zhou","suffix":""},{"id":384949439,"identity":"5e738d52-1e02-4c50-806a-044e500ab710","order_by":17,"name":"Zhuang Zhao","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Zhuang","middleName":"","lastName":"Zhao","suffix":""},{"id":384949440,"identity":"3ada7af6-50c9-4857-8feb-e556b0a9525a","order_by":18,"name":"Ye Ai","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Ye","middleName":"","lastName":"Ai","suffix":""},{"id":384949442,"identity":"6ef360ab-ae6b-4986-aec4-66dbf20531cd","order_by":19,"name":"Lin-Ying Wang","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Lin-Ying","middleName":"","lastName":"Wang","suffix":""},{"id":384949444,"identity":"56851bf3-59e4-4a6d-80fa-626bbabb8373","order_by":20,"name":"Deqiang Chen","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Deqiang","middleName":"","lastName":"Chen","suffix":""},{"id":384949445,"identity":"4a83f3f4-0995-4490-a1b7-d259c0d67e7a","order_by":21,"name":"Xin He","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Xin","middleName":"","lastName":"He","suffix":""},{"id":384949446,"identity":"95aac322-7b87-43b7-af45-a4b9fb339454","order_by":22,"name":"Ming-Zhong Huang","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Ming-Zhong","middleName":"","lastName":"Huang","suffix":""},{"id":384949447,"identity":"6cee1b72-d26c-4fb9-940e-5eb95a1dcb9d","order_by":23,"name":"Dong-Hui Peng","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Dong-Hui","middleName":"","lastName":"Peng","suffix":""},{"id":384949448,"identity":"aacb8cb4-55e6-446d-9d0d-4b9d722856f5","order_by":24,"name":"Hao Yu","email":"","orcid":"","institution":"","correspondingAuthor":false,"prefix":"","firstName":"Hao","middleName":"","lastName":"Yu","suffix":""},{"id":384949449,"identity":"762e60d1-7f69-46f8-94c5-0c69afda2d74","order_by":25,"name":"Siren Lan","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Siren","middleName":"","lastName":"Lan","suffix":""},{"id":384949450,"identity":"d131c959-af05-470e-810f-91872ac5dbf7","order_by":26,"name":"Zhong-Jian Liu","email":"","orcid":"","institution":"Fujian Agriculture and Forestry University","correspondingAuthor":false,"prefix":"","firstName":"Zhong-Jian","middleName":"","lastName":"Liu","suffix":""},{"id":384949451,"identity":"d598b475-faf6-43c7-9989-703b94750fea","order_by":27,"name":"Wei-Sheng Wu","email":"","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":false,"prefix":"","firstName":"Wei-Sheng","middleName":"","lastName":"Wu","suffix":""},{"id":384949452,"identity":"0697739e-3f22-487c-80e4-6ff68b83a9d3","order_by":28,"name":"Wen-Chieh Tsai","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA7UlEQVRIiWNgGAWjYJCCAwwMNgwMzMwNQHYCSMAAr3IeiJY0oBZGZC0J+LUAwWEgJlaLPf/hh4d5as5H87czNjAX1KQlNrA3b5Ng/HEYty0SaQaHeY7dzp1xGKhlxrGcxAaeY2USDAn4tDAYHM5tuJ3bANLC21CR2CCRYwbUchu3Fv7jH4BazuXOh2uRf0NAC0MOyJYDuRsgWoAOk+AhoOVGTsHhP8eSczcCtQA9lWbcxpNWbJGQ9h+nFvb+45s/zqixy513/vDBxzw1ybL97Ic33vhgk4ZTCwo4ACLYQEQCcRpGwSgYBaNgFOAAAOTAVWE4HKmpAAAAAElFTkSuQmCC","orcid":"","institution":"National Cheng Kung University","correspondingAuthor":true,"prefix":"","firstName":"Wen-Chieh","middleName":"","lastName":"Tsai","suffix":""}],"badges":[],"createdAt":"2024-11-14 13:53:52","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5454452/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5454452/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1186/s12870-024-06024-1","type":"published","date":"2025-01-02T15:57:38+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":70451397,"identity":"42149361-343b-4cca-95b4-972bfd06c3dc","added_by":"auto","created_at":"2024-12-03 09:46:14","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":318475,"visible":true,"origin":"","legend":"\u003cp\u003eGenomic data from three \u003cem\u003eCymbidium\u003c/em\u003e species were added to OrchidBase 6.0. OrchidBase 6.0 includes genome information for eight orchid species. The pictures of the eight orchid species were from the authors.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/c3a370a55f64afb2464a8f31.png"},{"id":70452973,"identity":"fd1dfbf8-0ae2-419f-8c4a-ac8a7944c4a1","added_by":"auto","created_at":"2024-12-03 10:02:14","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":644090,"visible":true,"origin":"","legend":"\u003cp\u003eOverview of the OrchidBase 6.0 architecture.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/ed9b05eb83182b683f1ea024.png"},{"id":70451399,"identity":"39fa7f4e-8df8-4f50-afc4-1d5782bf7647","added_by":"auto","created_at":"2024-12-03 09:46:14","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1397060,"visible":true,"origin":"","legend":"\u003cp\u003eGenome page of OrchidBase 6.0. Three \u003cem\u003eCymbidium\u003c/em\u003e genomes were newly compiled in OrchidBase 6.0. Analytical tools such as a genome browser, gene annotation, metabolic pathways, synteny, gene order, miRNA, and regulation tools were developed.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/6a2085744756e5e5b2f6d49f.png"},{"id":70451401,"identity":"9cc00305-c01c-4cf1-9eaa-0f984d1c489b","added_by":"auto","created_at":"2024-12-03 09:46:14","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":1244988,"visible":true,"origin":"","legend":"\u003cp\u003eA step-by-step guide for using the “Regulation” tool.\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/d674b1be809da554fc98f55b.png"},{"id":70452974,"identity":"52d46e4a-4de5-4d06-abbc-5b370bf79038","added_by":"auto","created_at":"2024-12-03 10:02:14","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":1029394,"visible":true,"origin":"","legend":"\u003cp\u003eA step-by-step guide for using the updated “Transcriptome” tool.\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/f4396c5695f919eb2ca4694e.png"},{"id":70452975,"identity":"55b3b882-1806-4781-83e3-a4c3b309c74e","added_by":"auto","created_at":"2024-12-03 10:02:14","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":1095608,"visible":true,"origin":"","legend":"\u003cp\u003eA step-by-step guide for using the advanced “BLAST” tool.\u003c/p\u003e","description":"","filename":"6.png","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/3418acdae22bc8386111c696.png"},{"id":70452206,"identity":"7a42e118-3e1a-4824-9e82-2fef25e66188","added_by":"auto","created_at":"2024-12-03 09:54:14","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":909668,"visible":true,"origin":"","legend":"\u003cp\u003eA step-by-step guide for using the advanced “Domain Search” tool.\u003c/p\u003e","description":"","filename":"7.png","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/85211ae97da36f59714028a0.png"},{"id":70451403,"identity":"9509211c-1523-4b3f-afb5-0610eb854133","added_by":"auto","created_at":"2024-12-03 09:46:14","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":831659,"visible":true,"origin":"","legend":"\u003cp\u003eAn example showing the use of the “Regulation” tool for analyzing transcription factors and their binding sites in the promoter of the \u003cem\u003ePeMADS4\u003c/em\u003e-like gene in \u003cem\u003eC. sinense\u003c/em\u003e.\u003c/p\u003e","description":"","filename":"8.png","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/c7bf21787631bf66c03a94cb.png"},{"id":73093331,"identity":"e213e47a-63f2-4003-828d-9f9eb2643f83","added_by":"auto","created_at":"2025-01-06 16:13:51","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":8734690,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/31b68c5b-9eeb-41a5-b7a2-c3369840864a.pdf"},{"id":70452203,"identity":"411d6e78-bff1-4c0f-948b-d307dacba0fa","added_by":"auto","created_at":"2024-12-03 09:54:14","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":23341,"visible":true,"origin":"","legend":"\u003cp\u003eSupplementary Table 1 Number of predicted transcription factors in each orchid genome, categorized by subfamily\u003c/p\u003e","description":"","filename":"SupplementaryTable1.docx","url":"https://assets-eu.researchsquare.com/files/rs-5454452/v1/7a386a53b8e3f347248ffaec.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"OrchidBase 6.0: Increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis","fulltext":[{"header":"Introduction","content":"\u003cp\u003e \u003cem\u003eCymbidium\u003c/em\u003e contains approximately 80 species and belongs to the subfamily Epidendroideae of the family Orchidaceae. This genus is distributed in tropical and subtropical Asia (northern India, China, Japan, Malaysia, the Philippines, and Borneo) and further south in Papua New Guinea and Northern Australia [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. The cultivation of \u003cem\u003eCymbidium\u003c/em\u003e can be traced back to the time of Confucius, approximately 2,500 years ago (B.C. 500). Through the accumulation of cultural and scientific development over several thousand years, \u003cem\u003eCymbidium\u003c/em\u003e species and hybrids have become one of the most commercially important orchids, not only in the floriculture industry but also in medicinal applications globally. \u003cem\u003eCymbidium\u003c/em\u003e shows diversified lifestyles for adaptation to the environment, including epiphytic; lithophytic; terrestrial; and rarely, leafless mycoheterotrophy lifestyles [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. \u003cem\u003eC. goeringii\u003c/em\u003e, \u003cem\u003eC. ensifolium\u003c/em\u003e, and \u003cem\u003eC. sinense\u003c/em\u003e are terrestrial plants that are the most popular flowering ornamental orchids and are widely cultivated for their beauty and fragrance [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. Therefore, the genome sequences of these three \u003cem\u003eCymbidium\u003c/em\u003e species have been selected for decoding and used to explore the molecular mechanisms of flowering, floral shape morphogenesis, and flower odor biosynthesis [\u003cspan additionalcitationids=\"CR7\" citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eOrchidBase was created for the storage, management, and efficient usage of orchid genetic information. The data were primarily generated using first-generation sequencing technology. Sanger sequencing was performed on samples derived from \u003cem\u003ePhalaenopsis\u003c/em\u003e reproductive organs [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e]. OrchidBase 2.0 was constructed using transcriptomes derived from the floral buds of two species in each of the five subfamilies of Orchidaceae using next-generation sequencing (Solexa Illumina, San Diego, CA, USA) [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. With the advancement in sequencing technology, the cost of sequencing has reduced, and the sequence production speed has greatly increased. As a result, orchid whole-genome sequencing has been accomplished [\u003cspan additionalcitationids=\"CR7\" citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e, \u003cspan additionalcitationids=\"CR12 CR13\" citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. Based on these orchid genomes and their transcriptomic sequences, OrchidBase has been updated with new sequences and newly developed tools for mining information embedded in these sequences [\u003cspan additionalcitationids=\"CR16\" citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. In addition to OrchidBase, which provides orchid genomes and transcriptomes for analysis, several databases offer similar datasets and tools for mining specific orchid species, such as Orchidstra for \u003cem\u003eP. aphrodite\u003c/em\u003e [\u003cspan additionalcitationids=\"CR19\" citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e], OncidiumOrchidGenomeBase for \u003cem\u003eOncidium\u003c/em\u003e [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e], and GelFAP for \u003cem\u003eGastrodia elata\u003c/em\u003e [\u003cspan additionalcitationids=\"CR23 CR24\" citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn OrchidBase 6.0, the genomes of three \u003cem\u003eCymbidium\u003c/em\u003e species, namely, \u003cem\u003eC. sinense\u003c/em\u003e, \u003cem\u003eC, ensifolium\u003c/em\u003e, and \u003cem\u003eC. gorengii\u003c/em\u003e, belonging to the Epidendroideae family, and their relative transcriptomes derived from various floral developmental stages and tissues have been included (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Furthermore, new tools, including transcription regulation analysis (promoters, transcription factors, and downstream targets), advanced transcriptome analysis, and advanced BLAST tools, have been developed for the functional analysis of orchid genes. The content of the OrchidBase 6.0 is summarized in Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e. The information and tools launched in OrchidBase 6.0 are extensive and will be an excellent resource for orchid biology research.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eSummary of data and tools that could be browsed and used for the eight orchid species (Pha. equestris, D. catenatum, Apo. shenzhenica, P. zijinensis, P. guangdongensis, C. sinense, C. ensifolium and C. goeringii)\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"2\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTranscriptome\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGene ID, FPKM and TPM values in various tissues\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGenome browser\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eScaffold ID, Scaffold sequence, Gene model, miRNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGene annotation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGene ID, Gene sequence, BLAST top hit descriptions, KEGG pathway, GO terms, Interpro description, Swissprot description,\u003c/p\u003e \u003cp\u003eTrEMBL description, miRNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMetabolism pathway\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGene ID, Genes mapped to the KEGG pathways\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSynteny\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGene ID, Physical positions of genes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGene order\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGene ID, Physical positions of genes\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003emiRNA-targets information\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003emiRNA gene ID, Structure of miRNA, Target gene IDs of miRNA, Binding sites in the target genes of a miRNA\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRegulation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGene ID, Promoter binding site prediction\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTools\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eBLASTN, BLASTX, tBLASTX, BLASTP, tBLASTN, pfam ID, pfam description,\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Expanded database content","content":"\u003cp\u003e\u003cem\u003eC. sinense, C, ensifolium\u003c/em\u003e, and \u003cem\u003eC. gorengii\u003c/em\u003e each have a karyotype of 2N\u0026thinsp;=\u0026thinsp;2X\u0026thinsp;=\u0026thinsp;40. We generated 429 Gb of data using Nanopore technology [\u003cspan class=\"CitationRef\"\u003e26\u003c/span\u003e] and 670 Gb using Hi-C sequencing technology for \u003cem\u003eC. sinense\u003c/em\u003e; 351 Gb using PacBio technology and 349 Gb using Hi-C technology for \u003cem\u003eC. ensifolium\u003c/em\u003e; and 478 Gb using PacBio technology and 296 Gb using Hi-C technology for \u003cem\u003eC. gorengii\u003c/em\u003e. The genome assemblies were 3.45 Gb, with a contig N50 value of 1.11 Mb; 3.63 Gb, with a contig N50 value of 1.21 Mb; and 4.07 Gb, with a contig N50 value of 1.04 Mb for the \u003cem\u003eC. sinense\u003c/em\u003e, \u003cem\u003eC. ensifolium\u003c/em\u003e and \u003cem\u003eC. gorengii\u003c/em\u003e genomes, respectively (Table \u003cspan class=\"InternalRef\"\u003e2\u003c/span\u003e) [\u003cspan class=\"CitationRef\"\u003e6\u003c/span\u003e\u0026ndash;\u003cspan class=\"CitationRef\"\u003e8\u003c/span\u003e]. Twenty pseudochromosomes were constructed for each \u003cem\u003eCymbidium\u003c/em\u003e species based on the assembled sequences. The raw data and whole-genome-assembled scaffold sequences of \u003cem\u003eC. sinense\u003c/em\u003e and \u003cem\u003eC. gorengii\u003c/em\u003e were downloaded from BioProject PRJNA743748 and PRJNA749652, respectively, and deposited in the National Center for Biotechnology Information database. The corresponding data for \u003cem\u003eC. ensifolium\u003c/em\u003e (BioProject/GSA PRJCA005355/CRA004327) was downloaded from the National Genomics Data Center. The statistics for the added orchid genomes are presented in OrchidBase 6.0 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://cosbi.ee.ncku.edu.tw/orchibase6/\u003c/span\u003e\u003c/span\u003e). Based on these datasets, 29,638, 29,073, and 29,272 protein-coding genes were predicted for the genomes of \u003cem\u003eC. sinense\u003c/em\u003e, \u003cem\u003eC. ensifolium\u003c/em\u003e, and \u003cem\u003eC. gorengii\u003c/em\u003e, respectively. Furthermore, 200, 71, and 147 miRNA candidates have been identified in the \u003cem\u003eC. sinense, C. ensifolium\u003c/em\u003e, and \u003cem\u003eC. gorengii\u003c/em\u003e genomes, respectively [\u003cspan class=\"CitationRef\"\u003e6\u003c/span\u003e\u0026ndash;\u003cspan class=\"CitationRef\"\u003e8\u003c/span\u003e]. Each predicted gene and miRNA was assigned a specific ID. Specific genes or miRNAs can be selected to investigate their annotated functions associated with biological processes.\u003c/p\u003e\n\u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u003ctable id=\"Tab2\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eComparisons of the assembled genomes among eight orchid species in the OrchidBase 6.0\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"6\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eOrchid species\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eAssembled genome size\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eN50 length of Scaffold (Mb)\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eN50 length of contig size\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eNumber of predicted genes\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eReference\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePhalaenoipsis equestris\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.03 Gb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.22\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e45.8 Kb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e29,545\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eZhang \u003cem\u003eet al\u003c/em\u003e. 2017\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eDendrobium catenatum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.12 Gb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.06\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e51.7 Kb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e29,257\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eZhang \u003cem\u003eet al\u003c/em\u003e., 2017\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eApostasia shenzhenica\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e349 Mb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3.03\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e80.1 Kb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e21,841\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eZhang \u003cem\u003eet al\u003c/em\u003e., 2017\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePlatanthera zijinensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4.19 Gb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003end\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.77 Mb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e24,513\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLi \u003cem\u003eet al\u003c/em\u003e., 2022\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePlatanthera guangdongensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4.20 Gb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003end\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.57 Mb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e22,559\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eLi \u003cem\u003eet al\u003c/em\u003e., 2022\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eCymbidium sinense\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3.45\u0026thinsp;Gb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003end\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.11 Mb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e29,638\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eYang \u003cem\u003eet al\u003c/em\u003e., 2021\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eCymbidium ensifolium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e3.63\u0026thinsp;Gb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003end\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.21 Mb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e29,073\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eAi \u003cem\u003eet al\u003c/em\u003e., 2021\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eCymbidium goeringii\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e4.07 Gb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003end\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e1.04 Mb\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e29,272\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003eYe \u003cem\u003eet al\u003c/em\u003e., 2021\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003ctfoot\u003e\n \u003ctr\u003e\n \u003ctd colspan=\"6\"\u003end: not determined\u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tfoot\u003e\n \u003c/table\u003e\n\u003c/div\u003e\n\u003cp\u003eThe transcriptomic data derived from the three \u003cem\u003eCymbidium\u003c/em\u003e species were downloaded from BioProjects PRJNA743748 (\u003cem\u003eC. sinense\u003c/em\u003e), PRJNA749652 (\u003cem\u003eC. gorengii\u003c/em\u003e) and BioProject/GSA PRJCA005355/CRA004327 (\u003cem\u003eC. ensifolium\u003c/em\u003e). All RNA sequencing reads were mapped to the predicted genes and calculated as transcripts per million (TPM), fragments per kilobase of transcript per million mapped reads (FPKM), or raw counts for each gene in various tissues and at different developmental stages to provide the gene expression profiles. This biological information was integrated into the updated version of OrchidBase 6.0.\u003c/p\u003e\n\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e\n \u003ch2\u003eIdentification of transcription factor (TF) genes in the genomes of orchid species\u003c/h2\u003e\n \u003cp\u003eTo identify orchid genes encoding TFs, we retrieved the TF protein sequences of \u003cem\u003eArabidopsis thaliana\u003c/em\u003e and \u003cem\u003eOryza sativa\u003c/em\u003e subsp. \u003cem\u003ejaponica\u003c/em\u003e from PlantTFDB 5.0 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://planttfdb.gao-lab.org/index.php\u003c/span\u003e\u003c/span\u003e). In total, 2,296 and 2,408 TF sequences from \u003cem\u003eA. thaliana\u003c/em\u003e and \u003cem\u003eO. sativa\u003c/em\u003e subsp. \u003cem\u003ejaponica\u003c/em\u003e, respectively, were used as queries in BLASTP searches against each of the predicted proteomes of eight orchids, with an E value of 10\u003csup\u003e\u0026minus;\u0026thinsp;5\u003c/sup\u003e to obtain 13,169 putative orchid TF genes that could be categorized into different subfamilies (Supplementary Table 1). To predict TF binding sites, the region 2,000 bp upstream of the translation start site of each gene was annotated for each orchid species genome. These data were retrieved and searched using the Match\u0026trade; program [\u003cspan class=\"CitationRef\"\u003e27\u003c/span\u003e] based on the position weight matrices created in PlantPan 3.0 [\u003cspan class=\"CitationRef\"\u003e28\u003c/span\u003e]. In total, 1,786 and 420 TFmatrixIDs were predicted for each orchid species using \u003cem\u003eArabidopsis\u003c/em\u003e and rice model plants, respectively (Table \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e). Furthermore, approximately 37\u0026ndash;77 million TF binding sites in the orchid genomes were predicted using the \u003cem\u003eArabidopsis\u003c/em\u003e matrix, and 15\u0026ndash;28 million binding sites were predicted using the rice matrix (Table \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e\n \u003cdiv class=\"gridtable\"\u003e\u0026nbsp;\u003ctable id=\"Tab3\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 3\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eThe number of predicted TFmatrixID and TF binding site at the promoter of each orchid genome\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"4\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eOrchid species\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eCompared model plant species\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eNumber of hit TFmatrix ID and TF binding site at the promoter of each orchid species\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eNumber of TF binding sites at promoter\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAps. shenzhenica\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e45,452,473\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eP. zijinensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e51,027,954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eP. guangdongensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e37,226,223\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePha. equestris\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e51,218,142\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eD. catenatum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e53,846,987\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. sinense\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e65,068,952\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. ensifolium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e63,385,827\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. goeringii\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e76,868,231\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. shenzhenica\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e16,847,177\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eP. zijinensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e21,110,631\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eP. guangdongensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e15,589,098\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePha. equestris\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e19,206,180\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eD. catenatum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e19,977,158\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. sinense\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e23,942,903\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. ensifolium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e23,455,231\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. goeringii\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e28,271,112\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n \u003c/table\u003e\n \u003c/div\u003e\n \u003cdiv class=\"gridtable\"\u003e\n \u003cdiv align=\"char\" class=\"colspec\"\u003e\u003cbr\u003e\u003c/div\u003e\u0026nbsp;\u003ctable id=\"Tab4\" border=\"1\"\u003e\n \u003ccaption language=\"En\"\u003e\n \u003cdiv class=\"CaptionNumber\"\u003eTable 4\u003c/div\u003e\n \u003cdiv class=\"CaptionContent\"\u003e\n \u003cp\u003eThe number of predicted TFmatrixID and TF binding site at the promoter of each orchid genome.\u003c/p\u003e\n \u003c/div\u003e\n \u003c/caption\u003e\n \u003ccolgroup cols=\"4\"\u003e\u003c/colgroup\u003e\n \u003cthead\u003e\n \u003ctr\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eOrchid species\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eCompared model plant species\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eNumber of hit TFmatrix ID and TF binding site at the promoter of each orchid species\u003c/p\u003e\n \u003c/th\u003e\n \u003cth align=\"left\"\u003e\n \u003cp\u003eNumber of TF binding sites at promoter\u003c/p\u003e\n \u003c/th\u003e\n \u003c/tr\u003e\n \u003c/thead\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eAps. shenzhenica\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e45,452,473\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eP. zijinensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e51,027,954\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eP. guangdongensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e37,226,223\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePha. equestris\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e51,218,142\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eD. catenatum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e53,846,987\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. sinense\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e65,068,952\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. ensifolium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e63,385,827\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. goeringii\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e1,786\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e76,868,231\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eA. shenzhenica\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e16,847,177\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eP. zijinensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e21,110,631\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eP. guangdongensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e15,589,098\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003ePha. equestris\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e19,206,180\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eD. catenatum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e19,977,158\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. sinense\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e23,942,903\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. ensifolium\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e23,455,231\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eC. goeringii\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"left\"\u003e\n \u003cp\u003e\u003cem\u003eO. sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e420\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd align=\"char\"\u003e\n \u003cp\u003e28,271,112\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\u003e\u003cstrong\u003eSearching the genome information for the three species of\u003c/strong\u003e \u003cstrong\u003eCymbidium\u003c/strong\u003e \u003cstrong\u003ein the database\u003c/strong\u003e\u003c/p\u003e\n \u003cp\u003eThe genome information for the three \u003cem\u003eCymbidium\u003c/em\u003e species in OrchidBase 6.0 can be accessed using the assembled pseudochromosomes and predicted genes. Through the web interface, the newly added orchid genome information in OrchidBase 6.0 can be freely obtained. The information can be linked via the \u0026ldquo;Orchid Genome\u0026rdquo; icon (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Step 1). Using this interface, users are able to select one of the five existing orchid genomes (\u003cem\u003ePha. equestris\u003c/em\u003e, \u003cem\u003eD. catenatum\u003c/em\u003e, \u003cem\u003eAps. shenzhenica\u003c/em\u003e, \u003cem\u003eP. zijinensis\u003c/em\u003e, and \u003cem\u003eP. guangdongensis\u003c/em\u003e), and from the three newly added \u003cem\u003eCymbidium\u003c/em\u003e genomes (\u003cem\u003eC. sinense, C. ensifolium, and C. gorengii\u003c/em\u003e) (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Step 2). Users can then access the genome browser (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Step 3) and obtain information about gene annotation (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Step 4), metabolic pathways (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Step 5), synteny (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, step 6), gene order (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Step 7), miRNAs (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Step 8), and regulation (Fig. \u003cspan class=\"InternalRef\"\u003e3\u003c/span\u003e, Step 9) by searching the orchid genome. Comparative analysis can then be performed using the selected orchid genomes. The genome browser and gene annotation, metabolic pathway, synteny, gene order, and miRNA information were introduced in the previous versions of OrchidBase [\u003cspan class=\"CitationRef\"\u003e16\u003c/span\u003e, \u003cspan class=\"CitationRef\"\u003e17\u003c/span\u003e]. In the following sections, we explain in detail the new \u0026ldquo;Regulation\u0026rdquo; function, the updated transcriptome information, and advanced BLAST and Domain searches, which can be found in the Tools menu.\u003c/p\u003e\n\u003c/div\u003e"},{"header":"Data content and “Regulation” web interface","content":"\u003cp\u003eThe OrchidBase 6.0 database update provides a \u0026ldquo;Regulation\u0026rdquo; function for each orchid genome. This function allows users to predict genes that may be regulated by different types of TFs and the binding sites at which the corresponding TFs bind to the promoters. Regulation analysis provides a graphical interface for displaying the relationships between genes, the binding sites and sequences at their individual promoters, and the corresponding TFs (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e). To use the Regulation Analysis page, users can click on the orchid genome (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 1) and choose one of the orchid species (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 2). They will then be navigated to the main function page for genome analysis and enter the \u0026ldquo;Regulation\u0026rdquo; page (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 3). On the \u0026ldquo;Regulation\u0026rdquo; page, users can select one of the TF reference libraries (\u003cem\u003eA. thaliana\u003c/em\u003e or \u003cem\u003eO. sativa\u003c/em\u003e) (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 4), which means that the identified TFs in each of the orchid genomes were based on orthologs in \u003cem\u003eArabidopsis\u003c/em\u003e or rice. One orchid species (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 5) can be chosen or maintained, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 2. If users are interested in gene ID analysis, they can fill in the \u0026ldquo;Search\u0026rdquo; box (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 6). In this study, the gene ID \u003cem\u003ecymsin_Mol016808\u003c/em\u003e, a gene encoding \u003cem\u003eSEPTALLA\u003c/em\u003e (\u003cem\u003eSEP\u003c/em\u003e)-like MADS-box protein, was used as an example. The results for the example showed that 274 TFs could bind to the promoter of \u003cem\u003ecymsin_Mol016808\u003c/em\u003e. By clicking on these 274 TFs (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 7), users can observe a table characterizing different TF families and the number of corresponding members that potentially regulate the expression of \u003cem\u003ecymsin_Mol016808\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Steps 8 and 9). Users can choose any of the TF families, and AP2, ERF, and ERF (3) can be selected (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 10). On the same page, a new table under the TF families table shows the IDs of three genes encoding AP2, ERF, and ERF TFs that bind to specific sequences in the \u003cem\u003ecymsin_Mol016808\u003c/em\u003e promoter, and the IDs of their ortholog genes in \u003cem\u003eArabidopsis\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Step 11). Clicking on the binding site directs users to PlantPAN 3.0, where they can see the TFmatrixID logo and access additional information related to the binding sites (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Steps 12 and 13). Under the TF table, users can further visualize a graph of the binding positions and sequences of the TF (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e, Steps 14\u0026ndash;16). Different TFs are shown in different colors.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Updated transcriptome","content":"\u003cp\u003eThe previous version of the transcriptome in OrchidBase only provided the FPKM of each gene in each sequenced orchid genome [\u003cspan additionalcitationids=\"CR16\" citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. In the current version, we provide the TPM and raw counts for the expression of each gene as well as different presentation styles for the gene expression data. The user can navigate to the transcriptome and choose one of the orchids (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 1). This page shows the expression of each gene in different tissues and organs. Users can select the data type with the contig (raw count), TPM, or FPKM (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 2), and then click \u0026ldquo;Search\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 3). Alternatively, they can enter the gene ID, if they know it, in the \u0026ldquo;Search\u0026rdquo; box (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 4). The subsequent page then shows the expression patterns that the users would like to see (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 5). Users can further click \u0026ldquo;Gene ID\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 6) to hyperlink to the gene annotation (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, step 7). They can even type several Gene IDs or keywords in the \u0026ldquo;Search\u0026rdquo; box to explore multiple gene expression patterns (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 8). After clicking \u0026ldquo;View/Search\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 9), users can obtain the transcriptome of assigned genes listed in the table under the \u0026ldquo;Search\u0026rdquo; box (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 10). Users can choose the values used to measure the expression levels (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 11) and further select items from various tissues or organs (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 12) to investigate their expression patterns. The button under the table is designed to \u0026ldquo;Refresh or Reset\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 13). In addition to the table describing the expression patterns of the assigned genes, we designed several graphic modes to visualize the transcripts of the genes, including a heatmap (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Steps 14 and 15), bar chart (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Steps 16 and 17), principal component analysis (PCA) results (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Steps 18 and 19), and hierarchical clustering (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Steps 20 and 21). Overall, this page provides an interface for users to explore gene expression patterns using TPM, FPKM, or raw counts, and users can obtain gene annotations using the gene ID.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Advanced BLAST","content":"\u003cp\u003eBLAST is one of the most popular pairwise alignment tools to search for similar sequences stored in databases [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. However, scientists would like to know the expression patterns of hit sequences to further infer their functions. Here, we combined the BLAST tool with different expression patterns to display tools that simultaneously reveal the biological significance of the genes. Users can visit \u0026ldquo;Tools\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 1), and select one of the sequenced orchid genomes. Here, we selected \u003cem\u003eC. ensifolium\u003c/em\u003e using nucleotide BLAST as an example (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 2). Based on the nucleotide BLAST search (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 3), users can select one of the nucleotide BLAST programs (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 4), paste the nucleotide sequence (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 5), and click BLAST (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, step 6). In the BLAST results page (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 7), users would click the hit \u0026ldquo;Gene ID\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 8) to link to the gene annotation (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 9), or click the \u0026ldquo;View Detail\u0026rdquo; icon to obtain the sequence alignment (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Steps 10 and 11). Additionally, users can tick any one of the hit gene IDs (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 12) and click \u0026ldquo;Show Expression Profile\u0026rdquo; at the bottom of the table (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Step 13). The subsequent page provides various graphic presentations of the updated transcriptomes described above (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e, Steps 14\u0026ndash;26). In summary, this tool not only contributes to pairwise alignment results, but also provides additional gene annotation and expression profiles of the hit sequences.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Domain search","content":"\u003cp\u003eProtein domains are fundamental units of protein structure, folding, function, evolution, and design. They are considered homologous sequences encoded in different gene contexts that have remained intact at the sequence level throughout evolution. Based on these concepts, we designed the tool \u0026ldquo;Domain Search\u0026rdquo; to characterize the protein-coding sequences based on the Pfam and InterPro classifications. For example, with the \u0026ldquo;Domain Research\u0026rdquo; tool, users can click on \u0026ldquo;Tools\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 1) and choose one of the orchid species in the panel of Tools_Domain Search (InterProScan or Pfam) (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 2). Protein sequences can be pasted in the box (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 3), and Pfam or Interproscan can be chosen. After clicking \u0026ldquo;Submit\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 4), the page shows an additional table presenting the hit sequence ID in the genome of the selected species (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 5). The page also allows users to choose either the Jaccard, intersection, or union method (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 6) for similarity comparison and to determine how the domains are screened for the inclusion of the query. The unique design of this tool includes the \u0026ldquo;Domain Search\u0026rdquo; and the expression patterns of the hit sequences (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 7). Users can further click \u0026ldquo;Show Similar Gene\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 8), tick the genes of interest (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 9), and click \u0026ldquo;Show Expression Profile\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Step 10). The additional table page provides various graphical presentations of the expression pattern, such as the updated transcriptome described above (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e, Steps 11\u0026ndash;23).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eA case study\u003c/h2\u003e \u003cp\u003eOne of the most well-known orchid characteristics is their delicate floral organ labellum, which attracts pollinators for precision pollination and humans for art appreciation. Several models have been described for the MADS-box genes involved in labellum development, such as the Orchid Tepal Model [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e], Orchid Code [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e], the HOT (Homeotic Orchid Tepal) model [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e], and P (perianth)-code [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. One of the B-class MADS-box genes, \u003cem\u003ePeMADS4\u003c/em\u003e in \u003cem\u003ePhalaenopsis\u003c/em\u003e, has been proposed as a candidate labellum identity gene that is not excluded from the models. However, the genes that regulate the expression of \u003cem\u003ePeMADS4\u003c/em\u003e orthologs in the labellum of orchids remain unclear. In this study, we screened for TFs that could bind to the promoters of \u003cem\u003ePeMADS4\u003c/em\u003e orthologs in \u003cem\u003eC. sinense\u003c/em\u003e. First, we clicked \u0026ldquo;Orchid Genome\u0026rdquo;, chose one of the orchid species, \u003cem\u003eC. sinense\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 1), and clicked \u0026ldquo;Regulation\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 2). The ortholog ID (\u003cem\u003ecymsin_Mol018952\u003c/em\u003e) of \u003cem\u003ePeMADS4\u003c/em\u003e in \u003cem\u003eC. sinense\u003c/em\u003e was identified using BLAST (data not shown). We then selected the \u0026ldquo;TF Reference Library\u0026rdquo; as \u003cem\u003eA. thaliana\u003c/em\u003e and selected the library as \u003cem\u003eC. sinense\u003c/em\u003e, or directly entered \u003cem\u003ecymsin_Mol018952\u003c/em\u003e as the gene ID in the \u0026ldquo;Search\u0026rdquo; box (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 3). This page shows the annotation of \u003cem\u003ecymsin_Mol018952\u003c/em\u003e and the number (242) of TFs that are possible regulators of \u003cem\u003ecymsin_Mol018952\u003c/em\u003e expression. We clicked the 242 TFs (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 4), and then \u0026ldquo;MADS box, MIKC(8)\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 5), because a previous study reported that MADS-box genes also have the ability to regulate the expression of self- or other MADS-box genes [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. After choosing the second \u003cem\u003eCymbidium\u003c/em\u003e MADS-box gene \u003cem\u003ecymsin_Mol006225\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 6), and clicking the third matrix ID \u0026ldquo;TFmatrixID_0508\u0026rdquo; (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, Step 7), we could see the page linked to PlantPan 3.0 showing the binding logo and \u003cem\u003eArabidopsis\u003c/em\u003e TFs binding to it.\u003c/p\u003e \u003c/div\u003e"},{"header":"Conclusions and future directions","content":"\u003cp\u003eWe added the whole-genome sequences of the \u003cem\u003eCymbidium\u003c/em\u003e species, \u003cem\u003eC. sinense\u003c/em\u003e, \u003cem\u003eC. ensifolium\u003c/em\u003e, and \u003cem\u003eC. goeringii\u003c/em\u003e, and their transcriptomes to OrchidBase 6.0. Additionally, two functions for genome comparisons and miRNA characterization were developed in this study. These additions increased the number of \u003cem\u003eCymbidium\u003c/em\u003e genomes in OrchidBase and has provided tools for exploring the knowledge embedded in nucleotide sequences, providing the opportunity for users to obtain novel insights into the conservation and diversification of orchid genomes. We will continue to increase the number of orchid whole-genome sequences in OrchidBase and add omics analysis tools for use by plant scientists.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics declarations\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe raw data and whole genome-assembled scaffold sequences of the \u003cem\u003eC. sinense\u003c/em\u003e and \u003cem\u003eC. goeringii\u003c/em\u003e (PRJNA743748 and PRJNA749652) were downloaded from the National Center for Biotechnology Information (NCBI) database. The related genomic data of \u003cem\u003eC. ensifolium\u003c/em\u003e (BioProject/GSA PRJCA005355/CRA004327) was retrieved from the National Genomics Data Center (NGDC). The transcriptomics data derived from the three \u003cem\u003eCymbidium\u003c/em\u003e species were also downloaded from BioProjects PRJNA743748, PRJNA749652, and BioProject/GSA PRJCA005355/CRA004327.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData availability\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll data generated or analyzed during this study are included in this published article.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;Authors declare that they have no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was funded by the Ministry of Science and Technology, Taiwan, (MOST 110-2313-B-006-002-MY3, 110-2221-E-006-198-MY3, 110-2622-B-006-009-, 111-2313-B-006-003, NSTC 112-2313-B-006-003-, and 113-2313-B-006-003-), National Cheng Kung University, Taiwan (D113-F1738), and National Key R\u0026amp;D Program of China (Grant No.2019YFD1000400) and the National Natural Science Foundation of China [no. 31870199].\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026apos; contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSL, ZJL, WSW, and WCT conceived the project idea, directed the project, generated analyzing ideas and wrote the paper. YYC and YS analyzed the data and wrote the paper. CIL, YYH, STL, and HY contributed to the project idea and did the transcriptomic analysis. HCZ, ZBZ, BRL and CLH established the platform for data analyzed and provided the required hardware. CNC and WCC contributed TFmatrix and TF binding site statistical analyses, HC, FXY, GFZ, QZ, CYZ, ZZ, YA, LYW, DC, XH, MZH and DHP collected the data and contributed the project idea. The author(s) read and approved the final manuscript.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAcknowledgement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis research was also supported in part by Higher Education Sprout Project, Ministry of Education to the Headquarters of University Advancement at National Cheng Kung University, Taiwan.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eLiu Z, Chen S, Ru Z. The genus Cymbidium in China. Beijing, China: Science Press. pp.1\u0026thinsp;\u0026ndash;\u0026thinsp;342; 2006.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDu Puy D, Cribb P. The genus Cymbidium. London and Portland, Oregon: Christopher Helm and Timber Press. pp.1\u0026thinsp;\u0026ndash;\u0026thinsp;236; 1988.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eThakur S, Dutt HC. \u003cem\u003eCymbidium macrorhizon\u003c/em\u003e lindl. (Orchidaceae): a new record for flora of jammu and Kashmir, India. Natl Acad Sci Lett. 2021;44:271\u0026ndash;74.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBidartondo MI. The evolutionary ecology of mycoheterotrophy. New Phytol. 2005;167:335\u0026ndash;52.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHuang WT, Fang ZM, Zeng SJ, Zhang JX, Wu KL, Chen ZL, et al. Molecular cloning and functional analysis of three \u003cem\u003eFLOWERING LOCUS T\u003c/em\u003e (\u003cem\u003eFT\u003c/em\u003e) homologous genes from Chinese \u003cem\u003eCymbidium\u003c/em\u003e. Int J Mol Sci. 2012;13(9):11385\u0026ndash;98.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYang FX, Gao J, Wei YL, Ren R, Zhang GQ, Lu CQ, et al. The genome of \u003cem\u003eCymbidium sinense\u003c/em\u003e revealed the evolution of orchid traits. Plant Biotech J. 2021;19(12):2501\u0026ndash;16.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAi Y, Li Z, Sun WH, Chen J, Zhang DY, Ma L, et al. The \u003cem\u003eCymbidium\u003c/em\u003e genome reveals the evolution of unique morphological traits. Hortic Res. 2021;8(1):255.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSun Y, Chen GZ, Huang J, Liu DK, Xue F, Chen XL, et al. The \u003cem\u003eCymbidium goeringii\u003c/em\u003e genome provides insight into organ development and adaptive evolution in orchids. Ornam Plant Res. 2021;1:10.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, et al. OrchidBase: A collection of sequences of transcriptome derived from orchids. Plant Cell Physiol. 2011;52(2):238\u0026ndash;43.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTsai WC, Fu CH, Hsiao YY, Huang YM, Chen LJ, Liu ZJ, et al. OrchidBase 2.0: Comprehensive collection of Orchidaceae floral transcriptomes. Plant Cell Physiol. 2013;54:e7.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW, et al. The genome sequence of the orchid \u003cem\u003ePhalaenopsis equestris\u003c/em\u003e. Nat Genet. 2015;47(1):65\u0026ndash;72.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang GQ, Xu Q, Bian C, Tsai WC, Yeh CM, Liu KW, et al. The \u003cem\u003eDendrobium catenatum\u003c/em\u003e Lindl. genome sequence provides insights into polysaccharide synthase, flower development and adaptive evolution. Sci Rep. 2016;6:19029.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, et al. The \u003cem\u003eApostasia\u003c/em\u003e genome and the evolution of orchids. Nature. 2017;579(7672):379\u0026ndash;83.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi MH, Liu KW, Li Z, Lu HC, Ye QL, Zhang D, et al. Genomes of leafy and leafless \u003cem\u003ePlatanthera\u003c/em\u003e orchids provide insights into the evolution of mycoheterotrophy. Nat Plants. 2022;8(4):373\u0026ndash;88.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTsai WC, Fu CH, Hsiao YY, Wu WL, Zhang DY, Lan SR, et al. OrchidBase 3.0: a resource for studying gene function and genome evolution in orchids. J Fujian Agric Univ. 2019;48:440\u0026ndash;6.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHsiao YY, Fu CH, Ho SY, Li CI, Chen YY, Wu WL, et al. OrchidBase 4.0: a database for orchid genomics and molecular biology. BMC Plant Biol. 2021;21:371.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChen YY, Li CI, Hsiao YY, Ho SY, Zhang ZB, Liao CC, et al. OrchidBase 5.0: updates to knowledge base of the orchid genomes. BMC Plant Biol. 2022;22:557.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSu CL, Chao YT, Yen SH, Chen CY, Chen WC, Chang YCA, et al. Orchidstra: an integrated orchid functional genomics database. Plant Cell Physiol. 2013;54(2):e11.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChao YT, Yen SH, Yeh JH, Chen WC, Shih MC. Orchidstra 2.0 - A transcriptomics resource for the orchid family. Plant Cell Physiol. 2017;58(1):e9.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChao YT, Chen WC, Chen CY, Ho HY, Yeh CH, Kuo YT, et al. Chromosome-level assembly, genetic and physical mapping of \u003cem\u003ePhalaenopsis aphrodite\u003c/em\u003e genome provides new insights into species adaptation and resources for orchid breeding. Plant Biotechnol J. 2018;16(12):2027\u0026ndash;41.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChang YY, Chu YW, Chen CW, Leu WM, Hsu HF, Yang CH. Characterization of \u003cem\u003eOncidium\u003c/em\u003e \u0026lsquo;Gower Ramsey\u0026rsquo; transcriptomes using 454 GS-FLX pyrosequencing and their application to the identification of genes associated with flowering time. Plant Cell Physiol. 2011;52(9):1532\u0026ndash;45.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYuan Y, Jin X, Liu J, Zhao X, Zhou J, Wang X, et al. The \u003cem\u003eGastrodia elata\u003c/em\u003e genome provides insights into plant adaptation to heterotrophy. Nat Commun. 2018;9(1):1615.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBae EK, An C, Kang MJ, Lee SA, Lee SJ, Kim KT et al. Chromosome-level genome assembly of the fully mycoheterotrophic orchid \u003cem\u003eGastrodia elata.\u003c/em\u003e G3 (Bethesda) 2022;12(3):jkab433.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYang J, Xiao Q, Xu J, Da L, Guo L, Huang L, et al. GelFAP: gene functional analysis platform for \u003cem\u003eGastrodia elata\u003c/em\u003e. Front Plant Sci. 2020;11:563237.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYang J, Li P, Li Y, Xiao Q. GelFAP v2.0: an improved platform for gene functional analysis in \u003cem\u003eGastrodia elata\u003c/em\u003e. BMC Genomics. 2023;24:164.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eJain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36:338.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKel AE, Gossling E, Peuter I, Cheremushkin K, Kel-Margoulis OV, Wingerder E. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 2003;31:3576\u0026ndash;9.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChow CN, Lee TY, Hung YC, Li GZ, Tseng KC, Liu YH, et al. PlantPan3.0: a new and updated resource for reconstructing transcriptional regulatory networks from CHIP-seq experiments in plants. Nucleic Acids Res. 2019;47(D1):D1155\u0026ndash;63.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAltschul SF, Madden TL, Sch\u0026auml;ffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389\u0026ndash;402.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTsai WC, Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Chen WH, et al. Molecular biology of orchid flower \u0026ndash; with emphasis on \u003cem\u003ePhalaenopsis\u003c/em\u003e. Adv Bot Res. 2008;47:99\u0026ndash;145.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMondrag\u0026oacute;n-Palomino M, Theissen G. MADS about the evolution of orchid flowers. Trends Plant Sci. 2008;13:51\u0026ndash;9.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePan ZJ, Cheng CC, Tsai WC, Chung MC, Chen WH, Hu JM et al. The duplicated B-class MADS‐box genes display dualistic characters in orchid floral organ identity and growth. Plant Cell Physiol. 2011:52:1515\u0026ndash;31.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHsu HF, Hsu WH, Lee YI, Mao WT, Yang CI, Li JY, et al. Model for perianth formation in orchids. Nat Plants. 2015;1:15046.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-5454452/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5454452/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u003c/strong\u003e Containing the largest number of species, the orchid family provides not only material for studying plant evolution and environmental adaptation, but also economically and culturally important ornamental plants for the human society. Previously, we collected genomic and transcriptomic information on \u003cem\u003eApostasia shenzhenica\u003c/em\u003e, \u003cem\u003eDendrobium catenatum\u003c/em\u003e, \u003cem\u003ePhalaenopsis equestris\u003c/em\u003e,\u003cem\u003e \u003c/em\u003eand two species of \u003cem\u003ePlatanthera\u003c/em\u003e that belong to three different subfamilies of Orchidaceae, and developed user-friendly tools to explore orchid genetic sequences in OrchidBase. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDescription: \u003c/strong\u003eRecently, three whole-genome sequences of the Epidendroideae species, \u003cem\u003eCymbidium sinense\u003c/em\u003e, \u003cem\u003eC. ensifolium \u003c/em\u003eand\u003cem\u003e C. goeringii\u003c/em\u003e, were sequenced \u003cem\u003ede novo\u003c/em\u003e, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusion: \u003c/strong\u003eOrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.\u003c/p\u003e","manuscriptTitle":"OrchidBase 6.0: Increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-12-03 09:46:09","doi":"10.21203/rs.3.rs-5454452/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2024-12-13T17:37:52+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-12-13T09:39:56+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-12-12T01:15:01+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-12-11T08:26:06+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"25061398736404853059179498981639812523","date":"2024-12-07T05:00:01+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2024-12-05T02:15:38+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"186813884586738465537228018280651780310","date":"2024-12-03T11:18:35+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"21734275208400769384856710257380489872","date":"2024-12-03T02:30:11+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"237224728782526500403014929565204183846","date":"2024-12-02T05:55:05+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2024-12-01T16:44:26+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2024-11-29T14:35:06+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2024-11-20T13:59:31+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2024-11-20T13:57:56+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2024-11-14T13:46:50+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"bmc-plant-biology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pbio","sideBox":"Learn more about [BMC Plant Biology](http://bmcplantbiol.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/pbio/default.aspx","title":"BMC Plant Biology","twitterHandle":"BMC_series","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"em","reportingPortfolio":"BMC Series","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"fddd190a-9c96-4d3c-bcb1-03a7ca4ce082","owner":[],"postedDate":"December 3rd, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-01-06T16:02:28+00:00","versionOfRecord":{"articleIdentity":"rs-5454452","link":"https://doi.org/10.1186/s12870-024-06024-1","journal":{"identity":"bmc-plant-biology","isVorOnly":false,"title":"BMC Plant Biology"},"publishedOn":"2025-01-02 15:57:38","publishedOnDateReadable":"January 2nd, 2025"},"versionCreatedAt":"2024-12-03 09:46:09","video":"","vorDoi":"10.1186/s12870-024-06024-1","vorDoiUrl":"https://doi.org/10.1186/s12870-024-06024-1","workflowStages":[]},"version":"v1","identity":"rs-5454452","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5454452","identity":"rs-5454452","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}