Parallel Genome-Wide Identification and Analysis of the COMT Gene Family in Potato (Solanum tuberosum L.) and Arabidopsis ( Arabidopsis thaliana (L.) Heynh.)

Parallel Genome-Wide Identification and Analysis of the COMT Gene Family in Potato (Solanum tuberosum L.) and Arabidopsis ( Arabidopsis thaliana (L.) 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Heynh.) Huaiwen Du, Lijia Liu, Jiayu Yuan, Na Wu, Yuxin Wei, Lili Jiang This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7918038/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 19 You are reading this latest preprint version Abstract Lignin and melatonin play crucial roles in plant stress resistance, and COMT (Caffeic acid O-methyltransferase) genes are key regulators in their biosynthesis, contributing significantly to plant adaptation under adverse conditions.Although COMT genes have been characterized in multiple plant species, research in potato has so far been limited to individual genes. In this study, we present the first genome-wide identification and systematic analysis of the COMT gene family in potato. A total of 12 StCOMT members were identified and comparatively analyzed with 10 Arabidopsis counterparts. These genes were predominantly distributed on one chromosome, with additional members scattered across other chromosomes.Phylogenetic analysis revealed that COMT genes are evolutionarily conserved and can be classified into five subfamilies.Partial members exhibited syntenic relationships.The encoded proteins typically displayed acidic and hydrophobic properties, formed stable dimeric structures, and were primarily localized to the chloroplast.Promoter analysis identified numerous light- and hormone-responsive elements.Expression profiling demonstrated both tissue-specific and stress-induced patterns among members.These findings indicate that COMT genes play a critical role in potato stress resistance and provide valuable genetic resources and a theoretical basis for stress-tolerant potato breeding.Further functional validation through biological experiments will be essential. Potato COMT Plant Stress Resistance Parallel Analysis Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Introduction Caffeic acid O-methyltransferase (COMT), an S-adenosyl-L-methionine (SAM)-dependent O-methyltransferase, modulates diverse physiological processes in plants through the phenylpropanoid metabolic pathway (see Fig. 1 for its role in melatonin biosynthesis)[1]. This enzyme catalyzes melatonin synthesis to enhance stress resistance [2], promotes lignin biosynthesis to improve lodging resistance [3], and facilitates the production of pharmacologically active compounds such as ferulic acid and flavonoids in medicinal plants [4]. Additionally, COMT mediates the biosynthesis of vanillin in aromatic plants [5], highlighting its significance as an integral component of plant metabolic systems. Melatonin, a crucial phytohormone, plays a pivotal role in mitigating both biotic and abiotic stresses, including extreme temperatures and salinity [6-8]. Substantial evidence indicates that COMT-catalyzed melatonin biosynthesis significantly enhances plant resilience to these adversities [9-10]. Lignin, a fundamental component of the plant cell wall, is essential for long-distance transport of water and nutrients, mechanical support, and stress defense [11-13]. COMT also fulfills several key functions in the lignin biosynthesis pathway [14-15]. The catalysis of melatonin and lignin synthesis represents two central functions of COMT, thereby regulating plant growth, promoting stress resistance, and enhancing lodging tolerance. Potato (Solanum tuberosum L.) holds a critical position as a major global food crop [16]. Despite the characterization of COMT genes in key Solanaceous species—including tomato (Solanum lycopersicum), pepper (Capsicum annuum), and American black nightshade (Solanum americanum) [17-19]—and the examination of specific StCOMT genes in potato itself [20], a systematic understanding of the entire gene family is still lacking. The present study bridges this gap by conducting a genome-wide characterization of StCOMT genes, leveraging comparative analysis with the Arabidopsis COMT family. This work establishes a basis for future breeding programs targeting enhanced stress tolerance in potato. Materials and Methods 2.1 Genome Data Retrieval and Gene Family Member Identification Genomic data for the 15 selected species were acquired from public repositories. The eggplant (Solanum melongena) genome was retrieved from the Sol Genomics Network, whereas genomic resources for all other species were downloaded from the Ensembl Plants database. The Hidden Markov Model (HMM) profiles for the COMT (PF00891) and ASMT (PF08100) domains were obtained from the Pfam database. These HMM profiles were employed to screen the respective proteomes using the "Simple HMM Search" function in TBtools, with an E-value≤-5.A subsequent curation process involved filtering redundant COMT/ASMT members, visualizing their chromosomal positions, and merging tandem repeats, leading to the final identification of the COMT gene family members. 2.2 Characterization of COMT Protein Physicochemical Properties and Subcellular Localization Prediction The physicochemical properties of the identified members were analyzed using the "Protein Parameter Calculate" function in TBtools.Protein secondary structures were predicted with the NPS@online server, while tertiary structures were modeled using SWISS-MODEL. Subcellular localizations were forecasted employing the Cell-PLoc 2.0 web server. 2.3Synteny Analysis and Phylogenetic Reconstruction for the COMT Gene Family Intra-genomic synteny analysis of COMT genes in potato and Arabidopsis was performed separately using the "Advanced Circos" tool in TBtools. For inter-species synteny assessment, the "Multiple Synteny Plot" function was employed to analyze the relationships among potato, Arabidopsis, and Nicotiana tabacum, with the results visualized accordingly. A phylogenetic tree was constructed from the protein sequences of potato and Arabidopsis COMT genes using the "One Step Build a ML Tree" feature in TBtools. The maximum likelihood method was applied with the UltraFast BootStrap algorithm, and the bootstrap replication number was set to 5000. The resulting tree was subsequently annotated and visualized using the iTOL online platform. 2.4 Gene and Protein Structure Analysis of the COMT Gene Family Conserved domains in COMT proteins were analyzed with the Batch CD-Search tool. Protein motifs were predicted using the MEME suite, configured to identify up to 10 distinct motifs. Gene structures (exon-intron organization) were determined from genome annotations and displayed with TBtools "Visualize Gene Structure". Promoter sequences spanning 2000 bp upstream of each COMT gene's transcription start site were examined for cis-acting regulatory elements using the PlantCARE database. These analyses were collectively visualized through the "Gene Structure View (Advanced)" function in TBtools. 2.5 Analysis of Tissue-Specific and Stress-Responsive Expression of COMT Gene Family Members Expression profiles of COMT gene family members in potato and Arabidopsis, encompassing various tissues and stress conditions, were extracted from the ePlant database, and the results were visualized using the HeatMap function in TBtools. Table 1 The websites and software used Name Use Website link Sol Genomics Network Data download https://solgenomics.net/ ensembl Data download https://plants.ensembl.org/ ePlant Data download https://bar.utoronto.ca/ NPS@ Secondary structure prediction https://npsa.lyon.inserm.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html SWISS-MODEL Three-level structure prediction https://swissmodel.expasy.org/interactive Cell-PLoc 2.0 Subcellular localization prediction http://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc-2/ Batch CD-Search Domain prediction https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi MEME Motif sequence prediction https://meme-suite.org/meme/tools/meme iTOL Evolutionary tree beautification https://itol.embl.de/ ChiPlot Chart beautification https://www.chiplot.online/ HiPlot Chart beautification https://hiplot.cn/ TBtools Main functions https://github.com/CJ-Chen/TBtools Results 3.1 Identification of COMT Gene Family Members and Analysis of Protein Physicochemical Properties Comprehensive analysis identified 12 StCOMT genes in potato and 10 AtCOMT genes in Arabidopsis. The encoded proteins displayed generally uniform molecular characteristics, with most molecular weights clustering between 39–42 kDa and amino acid lengths ranging from 350 to 380 residues. Notable exceptions included StCOMT1 , StCOMT4 , StCOMT6 , and StCOMT9 , which fell outside these ranges. Theoretical pI analysis revealed that the majority of COMT proteins are acidic, with pI values spanning 4.8–6.3, except for the basic StCOMT5 (pI = 9.26). Evaluation of protein stability indicated that 21 out of the 29 COMT members exhibited an Instability Index below 40, suggesting high structural stability. Hydrophobicity assessment using the Grand Average of Hydropathicity showed positive values for 20 members, supporting their classification as hydrophobic proteins. Furthermore, 26 COMT proteins possessed an Aliphatic Index exceeding 90, consistent with enhanced thermostability and structural compactness. Table 2 Physicochemical Analysis and Predicted location of StCOMT Genes Sequence ID Number of Amino Acid Molecular Weight Theoretical pI Instability Index Aliphatic Index Grand Average of Hydropathicity Predicted location(s) StCOMT1 642 71607.79 9.26 53.87 77.46 -0.524 Nucleus. StCOMT2 337 36532.27 6.05 30.28 97.57 0.117 Chloroplast. StCOMT3 353 39712.06 5.66 34.1 89.75 -0.047 Chloroplast. Cytoplasm. Mitochondrion. Nucleus. StCOMT4 266 29597.06 5.5 28.95 95.71 -0.02 Chloroplast. StCOMT5 363 39694.75 5.6 31.91 86.25 -0.046 Chloroplast. StCOMT6 265 29217.62 5.29 36.91 101.09 0.08 Chloroplast. Mitochondrion. StCOMT7 348 39189.41 5.67 34.79 94.63 -0.026 Chloroplast. StCOMT8 364 40964.26 5.36 29.89 98.63 -0.085 Chloroplast. StCOMT9 226 24744.59 6.05 37.11 99.65 0.134 Chloroplast. Nucleus. StCOMT10 359 39927.88 5.13 34.33 101.87 0.008 Chloroplast. StCOMT11 356 39960.31 6.22 39.72 98.03 -0.041 Chloroplast. StCOMT12 351 39880.91 5.46 40.25 90.54 -0.126 Chloroplast. Cytoplasm. StCOMT13 363 40221.31 5.48 31.2 89.61 -0.055 Chloroplast. StCOMT14 365 40916.42 5.67 36.84 98.25 0.03 Chloroplast. Mitochondrion. StCOMT15 360 40556.55 5.8 37.89 84.72 -0.282 Chloroplast. StCOMT16 355 40184 4.82 37.24 85.1 -0.177 Chloroplast. StCOMT17 359 40027.99 5.35 32.06 94.71 0.006 Chloroplast. StCOMT18 394 43966.59 6.33 26.75 92.11 -0.116 Chloroplast. Table 3 Physicochemical Analysis and Predicted location of AtCOMT Genes Sequence ID Number of Amino Acid Molecular Weight Theoretical pI Instability Index Aliphatic Index Grand Average of Hydropathicity Predicted location(s) AtCOMT1 373 40747.86 5.01 28.06 92.01 0.083 Chloroplast. AtCOMT2 352 38967.6 5.58 38.49 88.84 -0.006 Chloroplast. AtCOMT3 363 40408.86 5.66 34.71 95.12 -0.121 Chloroplast. AtCOMT4 288 32100.06 5.6 29.68 94.1 -0.024 Chloroplast. AtCOMT5 367 40222.38 5 24.09 102.53 0.103 Chloroplast. AtCOMT6 381 42326.12 5.29 37.29 97.72 0.031 Chloroplast. AtCOMT7 359 39688.48 5.28 48.19 88.02 -0.096 Chloroplast. AtCOMT8 382 42614.17 5.32 41.78 90.31 -0.099 Chloroplast. Mitochondrion. Nucleus. AtCOMT9 378 41944.63 5.33 29.94 98.52 0.078 Chloroplast. AtCOMT10 363 39617.93 5.62 33.38 92.4 -0.026 Chloroplast. 3.2 Analysis of COMT Protein Structure Secondary structure prediction via the NPS@ tool revealed that COMT proteins from both potato and Arabidopsis are primarily composed of alpha helices (Hh), extended strands (Ee), and random coils (Cc). Among these, alpha helices constituted the largest proportion (averaging 47.72% in StCOMTs and 47.12% in AtCOMTs), followed by extended strands (38.77% in StCOMTs and 39.65% in AtCOMTs), and random coils (13.51% in StCOMTs and 13.23% in AtCOMTs). The consistent compositional profiles across most family members reflect considerable conservation in secondary architecture. Tertiary structure modeling performed with SWISS-MODEL further indicated that proteins within the same subfamily share similar folding patterns, consistent with the secondary structure predictions. All COMT proteins were predicted to adopt homodimeric quaternary structures. 3.3 Prediction of Subcellular Localization of COMT Proteins Subcellular localization predictions generated by Cell-PLoc 2.0 indicated that most COMT proteins in both potato and Arabidopsis are predominantly localized to the chloroplast. Additional localizations were detected for specific members: AtCOMT8 was found in both the nucleus and mitochondria; StCOMT1, StCOMT12, and StCOMT13 showed nuclear localization; while StCOMT3, StCOMT6, and StCOMT14 were predicted to localize to mitochondria.A few members, including StCOMT3 and StCOMT12, also exhibited cytoplasmic presence.Based on these findings, we propose that chloroplasts serve as the primary functional site for COMT proteins. 3.4 Chromosomal Localization of the COMT Gene Family Chromosomal localization visualization revealed an uneven genomic distribution of COMT gene family members in both potato and Arabidopsis thaliana. In the potato genome, COMT genes were predominantly clustered on chromosome 6 (harboring three members), with two members localized to chromosomes 10 and 3 respectively. Chromosomes 1, 2, 8, and 12 each contained only a single member, whereas no COMT genes were detectable on chromosomes 4, 5, or 7. In Arabidopsis, COMT genes exhibited significant clustering on chromosome 1 (containing six members). Chromosome 15 harbored two members, while chromosomes 3 and 4 showed minimal representation with one member each. Notably, chromosome 2 lacked detectable COMT homologs. 3.5 Synteny Analysis of the COMT Gene Family To analyse the evolutionary trajectory of the COMT gene family, a comprehensive synteny analysis was conducted across potato, arabidopsis thaliana, and narrowleaf tobacco. This investigation encompassed both interspecific synteny assessments and intraspecific synteny evaluation within potato and arabidopsis thaliana. Following stringent filtration of tandem duplicates, key findings emerged: Two orthologous COMT gene pairs were identified between potato and arabidopsis thaliana, whereas three orthologous pairs were detected between potato and its con-familial species narrowleaf tobacco. These results demonstrate pronounced evolutionary and functional conservation of the COMT family within Solanaceae species, alongside considerable conservation of synteny blocks across divergent plant families. Intraspecific analysis further revealed the presence of one paralogous COMT gene pair within each of the potato and arabidopsis thaliana genomes. Notably, both paralogous pairs localized to genomic loci exhibiting the highest COMT gene density in their respective species (chromosome 6 in potato; chromosome 1 in A. thaliana), suggesting localized gene duplication events as a potential mechanism for COMT gene family expansion. Despite potential evolutionary divergence, these paralogs maintained significant sequence homology and retention of functional homology. 3.6 Phylogenetic Analysis of the COMT Gene Family Table 4 Species Used for Phylogenetic Tree Construction Serial Number Plant Scientific name Gene Name Number of Identified genes 1 Arabidopsis Arabidopsis thaliana AtCOMT 10 2 Narrow leaved tobacco Nicotiana attenuata NaCOMT 7 3 Tomato Solanum lycopersicum SlCOMT 15 4 Chili Capsicum annuum CaCOMT 18 5 Potato Solanum tuberosum StCOMT 18 6 Soybean Glycine max GmCOMT 26 7 Millet Setaria italica SiCOMT 27 8 Eggplant Solanum melongena SmCOMT 15 9 Corn Zea mays ZmCOMT 21 10 Rice plant Oryza sativa OsCOMT 19 11 Apple Malus domestica MdCOMT 20 12 Sunflower Helianthus annuus HaCOMT 20 13 American Cotton Gossypium raimondii GrCOMT 17 14 Wild carrot Daucus carota DcCOMT 8 15 Chinese rose Rosa chinensis RcCOMT 23 A phylogenetic tree was constructed using 264 COMT protein sequences from 15 plant species.The evolutionary analysis revealed that COMT could be classified into five distinct subfamilies. Potato StCOMT were distributed across all subfamilies except subfamily I, with specific distribution as follows: two in subfamily V, eight in subfamily II, one in subfamily III, and seven in subfamily IV. Subsequently, a separate phylogenetic tree containing 29 COMT members from potato and Arabidopsis resolved them into four subfamilies. Further species-specific phylogenetic analyses demonstrated that potato COMT members clustered into four subfamilies , while Arabidopsis COMT members grouped into three subfamilies. 3.7 Comprehensive Analysis of COMT Gene Structure A comprehensive analysis was performed on 18 potato and 10 Arabidopsis COMT sequences, encompassing conserved motifs, gene structure, protein domains and promoter regions . 3.7.1 Conserved Motif Analysis of the COMT Gene Family Analysis of conserved motifs revealed high conservation in both distribution patterns and motif numbers among COMT family members. The number of motifs ranged from 8 to 10. Although some proteins lacked specific motifs, the overall arrangement remained largely consistent across the gene family, suggesting possible evolutionary loss or acquisition of particular motifs. 3.7.2 Gene Structure Analysis of the COMT Gene Family Gene structure prediction showed that COMT gene sequences exhibited similar organizational patterns in CDS-UTR distribution. All COMT genes consisted of coding sequences (CDS) and untranslated regions (UTR). As shown in the corresponding figure, most members within the same group shared identical CDS numbers and distribution patterns, with CDS counts ranging from 1 to 2 and UTR counts varying between 2 and 4. 3.7.5 Protein Domain Analysis of the COMT Gene Family Domain prediction analysis indicated that the COMT gene family primarily contains two structural domains: AdoMet_MTases superfamily and dimerization2 superfamily. With few exceptions— StCOMT1 contains an additional SANT domain, and StCOMT15 lacks one AdoMet_MTases domain—all StCOMT and AtCOMT genes possess one AdoMet_MTases domain and one Dimerization2 domain, further supporting the evolutionary conservation within this gene family. 3.7.4 Promoter Analysis of the COMT Gene Family Promoter prediction analysis classified the cis-acting elements in COMT genes into four categories: light response (including circadian and light-related elements), plant growth and development (endosperm, meristem, seed, palisade mesophyll cells, and zein), stress response (anaerobic, anoxic, low-temperature, wound, mixed stress, elicitor, and MYB binding site), and phytohormone response (abscisic acid, auxin, gibberellin, MeJA, and salicylic acid). The distribution patterns of these promoter elements were similar in both potato and Arabidopsis COMT genes, with light- and hormone-related elements being predominant, along with several elements associated with growth regulation. These results suggest that COMT genes may primarily function in light signal perception and transduction, as well as in phytohormone-mediated pathways. 3.8 Analysis of Tissue-Specific Expression of the COMT Gene Family Expression profiling across 13 potato organs revealed distinct tissue-specific patterns among StCOMT genes. Transcript accumulation of StCOMT1 was most pronounced in the stem apex, whereas StCOMT5 displayed specific enrichment in stem tissues. Four genes— StCOMT4 , StCOMT8 , StCOMT12 , and StCOMT15 —were observed to be co-expressed in both stem and stem apex tissues. Preferential expression in stamens was recorded for StCOMT3 and StCOMT10 . Root-specific transcript accumulation characterized StCOMT6 , StCOMT9 , and StCOMT17 . Stolons showed marked enrichment of StCOMT13 , StCOMT14 , and StCOMT18 , while young tubers demonstrated activated expression of StCOMT1 , StCOMT2 , and StCOMT18 . Notably, StCOMT7 , StCOMT11 , and StCOMT16 maintained minimal expression levels across all examined organs. In Arabidopsis, examination of 18 developmental stages and organs uncovered specialized expression patterns. AtCOMT1 transcription was restricted to cotyledons, while AtCOMT2 accumulation was predominant in senescing leaves. Mature pollen exhibited specific high expression of AtCOMT3 .Multiple family members— AtCOMT4 , AtCOMT6 , and AtCOMT8 —showed significant upregulation during seed developmental stages.Elevated transcript levels of AtCOMT5 were detected in 24-hour imbibed seeds, along with hypocotyl and root tissues. AtCOMT6 displayed upregulation in both root tissues and seed developmental stages, whereas AtCOMT7 and AtCOMT9 expression peaked during full bloom. Dry seeds showed increased AtCOMT8 accumulation, and AtCOMT10 demonstrated specific enrichment in the second internode of stems. 3.9 Analysis of Stress-Specific Expression of the COMT Gene Family Evaluation of stress-responsive expression demonstrated specialized activation patterns among COMT members.In potato, significant induction of StCOMT3 and StCOMT10 occurred under biotic stress conditions.High temperature treatment specifically triggered StCOMT14 and StCOMT18 transcription.Gibberellin application regulated four genes—StCOMT5, StCOMT6 , StCOMT9 , and StCOMT17 . Mechanical wounding strongly activated StCOMT4, StCOMT8 , StCOMT10 , StCOMT12 , and StCOMT15 .Combined salt-mannitol stress elevated transcript levels of StCOMT6 , StCOMT13 , and StCOMT18 .In contrast, StCOMT2 , StCOMT7 , StCOMT11 , and StCOMT16 remained uninduced across all stress treatments. Arabidopsis COMT genes displayed complex stress response profiles.Seven members— AtCOMT3 , AtCOMT4 , AtCOMT6 , AtCOMT7 , AtCOMT8 , AtCOMT9 , and AtCOMT10 —showed elevated expression under various abiotic stresses compared to control conditions. Heat stress specifically induced upregulation of AtCOMT3 , AtCOMT4 , AtCOMT7 , AtCOMT9 , and AtCOMT10 . Drought treatment enhanced transcription of AtCOMT5 , AtCOMT6 , AtCOMT7 , and AtCOMT8 . Wounding response involved upregulation of AtCOMT5 , AtCOMT6 , AtCOMT8 , and AtCOMT9 . Unique stress activation patterns included UV radiation specifically inducing AtCOMT1 and AtCOMT2 , osmotic stress activating AtCOMT1 and AtCOMT10 , and low temperature upregulating AtCOMT1 , AtCOMT5 , and AtCOMT8 .Notably, oxidative stress resulted in comprehensive downregulation across the entire AtCOMT family. Discussion COMT proteins in both potato and Arabidopsis exhibit similar physicochemical properties, with molecular weights ranging from 39-42 kDa and lengths of 350-380 amino acids. They are characterized as stable, structurally compact, thermostable, acidic, and hydrophobic proteins. These characteristics are intrinsically linked to their function [1, 24, 25]. For an enzyme catalyzing the methylation of diverse, often hydrophobic substrates—such as caffeic acid, 5-hydroxyferulic acid, and 5-hydroxyconiferaldehyde, which belong to methylated phenylpropanoids, flavonoids, and terpenoids [26-28]—hydrophobicity facilitates better substrate binding. Furthermore, a compact structure provides a tight hydrophobic environment conducive to efficient catalysis. Structurally, COMT proteins are primarily composed of alpha-helices (Hh), extended strands (Ee), and random coils (Cc) at the secondary level and universally form homodimers at the tertiary level, indicating significant structural conservation. Predominantly localized to the chloroplasts, with additional presence in other cellular compartments, this localization pattern is conserved across species. For instance, melatonin synthesis in tea plant (Camellia sinensis) is closely associated with light conditions [25], and the ZmCOMT family in maize is functionally implicated in light response [29]. This evidence strongly suggests that the chloroplastic localization of COMT is likely linked to photosynthesis or light signal transduction, while its presence in other organelles hints at additional, specialized functions. The evolutionary classification of the COMT gene family varies among studies. Some researchers, for example in soybean (Glycine max) [28], propose a two-class system, while others advocate for a more refined classification into four or more groups, as seen in Vitis species [30] and kenaf (Hibiscus cannabinus L.) [27]. Our analysis supports the latter, more detailed view. A multi-category classification better reflects the complex evolutionary history involving gene duplication, segmental duplication, and whole-genome duplication events specific to different lineages. We classified COMT members from 15 species into five distinct clades based on phylogenetic relationships. The distribution of potato StCOMT members across these clades demonstrates considerable evolutionary divergence. Intra-species synteny analysis, after excluding tandem duplicates, revealed conserved syntenic relationships among COMT genes, underscoring the high evolutionary conservation of this family [23, 30]. Inter-species comparative analysis identified conserved syntenic blocks between potato and its con-familial species (Nicotiana attenuata) as well as the distantly related model plant Arabidopsis. This aligns with established findings of close evolutionary relationships between Solanum species (including potato and tomato) and Nicotiana [31, 32]. Integrating sequence and functional homology evidence, we hypothesize that local gene duplication events have been a key mechanism in the expansion of the COMT family, with paralogous genes retaining strong functional constraints—a pattern also observed in the evolution of the TCP transcription factor family [36]. Gene structure analysis revealed high conservation within the potato StCOMT family, with members typically containing 8-10 motifs and 2-4 introns [23, 30]. The identified conserved domains are directly linked to their molecular functions: the AdoMet_MTases domain confers methyltransferase activity, Dimerization2 facilitates protein dimerization, and the SANT domain may act as an adapter in chromatin complexes. These structural features are integral to the canonical roles of COMT genes in catalyzing the synthesis of melatonin and lignin [23, 30, 37-39], thereby enhancing plant stress resistance. This high degree of structural similarity and functional adaptation among family members is consistent with findings in other crops like maize, kenaf, and grape [29, 30, 40]. Analysis of cis-regulatory elements in the promoters indicated that StCOMT genes possess elements responsive to all four major categories: light, plant hormones, development, and stress. This finding is corroborated by existing research. In tomato, COMT expression is regulated by red light, influencing melatonin synthesis in fruits [41]. In maize, COMT is light-regulated and affects lignin biosynthesis [29]. Furthermore, COMT overexpression enhances thermotolerance in rose [42] and salt tolerance in poplar [43]. Collectively, these studies confirm that COMT gene family members participate in various aspects of plant growth and development, albeit with potential functional specializations [44]. Expression profiling reveals that COMT genes exhibit distinct, tissue-specific expression patterns and demonstrate differential relative expression levels under various stress treatments. This observed regulatory complexity, when integrated with established evidence—including transcriptomic and metabolomic studies linking COMT to combined drought-alkaline salt stress in potato [45], reported enhanced resistance to early blight in potato COMT -overexpressing lines [46], its fundamental role in mediating melatonin and lignin biosynthesis pathways, and the abundance of stress-responsive cis-acting elements identified in its promoters—leads us to conclude that the COMT gene family constitutes a pivotal gene family conferring resistance to both biotic and abiotic stresses in potato. However, it is important to acknowledge that relying solely on bioinformatic predictions to assign definitive functions to StCOMT family members provides an incomplete perspective. Therefore, we propose that future research should build directly upon our findings. Subsequent investigations ought to employ a combined approach, integrating more advanced bioinformatics tools with experimental validation to systematically elucidate the specific biological functions of StCOMT genes, particularly their roles in mediating responses to biotic/abiotic stresses, as well as potential involvement in photomorphogenesis and photosynthetic processes. Conclusion This investigation conducted a comprehensive genomic identification and functional characterization of the COMT gene family in potato, revealing 12 StCOMT genes. A parallel examination with the Arabidopsis COMT family was performed, indicating non-random chromosomal distribution of these genes. Phylogenetic assessment supported their categorization into five distinct subfamilies. The encoded proteins were characterized by acidic and hydrophobic properties, featured alpha-helix dominated secondary structures, and shared a conserved homodimeric tertiary conformation. Subcellular localization predictions strongly favored chloroplast targeting. In-depth promoter scanning identified numerous cis-regulatory elements associated with light responsiveness, hormone signaling, and stress activation. Expression profiling demonstrated clear tissue-specific patterns among StCOMT members, along with differentiated induction profiles under diverse biotic and abiotic stress conditions. Collectively, these findings imply that the StCOMT gene family contributes to potato stress adaptation, potentially through modulating the biosynthesis of key metabolites like lignin and melatonin. This work establishes a foundation for subsequent functional studies and identifies promising genetic targets for enhancing stress resilience in potato breeding programs. Declarations Author Contributions: Author Contributions: H.D. (Huaiwen Du): Led the experimental design and execution, conducted the majority of the data analysis, and wrote the initial manuscript draft. L.L. (Lijia Liu): Developed specific methodologies, performed bioinformatics analyses, and contributed to data curation and manuscript revision. J.Y. (Jiayu Yuan): Assisted in data analysis, conducted statistical validation, and prepared the figures and tables. W.N. (Wu Na): Contributed to data validation and formal analysis. Y.W. (Yuxin Wei): Assisted in data curation and visualization. L.J. (Lili Jiang): Provided the conceptual framework, supervised the entire research project, and critically reviewed and edited the manuscript. All authors have read and agreed to the published version of the manuscript. Funding : This research was supported by The Construction Project of Double First-Class Initiative in Heilongjiang Province "Green and Low-Carbon of Grain Crops" (LJGXCG2022-107) and the Heilongjiang Provincial National College Students' Innovation and Entrepreneurship Training Program Project (202510223155), entitled "Study on the Association Mechanism of COMT Gene-mediated Melatonin Synthesis and Tuber Formation in Potato under the Background of Photoperiod Response Differences". Data Availability Statement: The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request. Conflicts of Interest: The authors declare no relevant financial or non-financial interests to disclose. Ethics, Consent to Participate, and Consent to Publish declarations Ethics, Consent to Participate, and Consent to Publish declarations: not applicable. References Feng, X.; Wu ,X.;Hong, J.; Guo, Z.; Khan, Y.; Wei,D.; Fan,H.; Cai, Y. 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13:57:23","extension":"xml","order_by":22,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":185360,"visible":true,"origin":"","legend":"","description":"","filename":"367492615d224afd94be88a5673388d81structuring.xml","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/a9d1bba86a53df4ca66f2b5d.xml"},{"id":95553551,"identity":"b97e1a65-c7cd-408d-9667-c38b679fcfa9","added_by":"auto","created_at":"2025-11-10 13:57:23","extension":"html","order_by":23,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":203432,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/c9be524a877b2a275fc48aff.html"},{"id":95553522,"identity":"f0b27171-5705-4cd9-a89a-5dced19efbd6","added_by":"auto","created_at":"2025-11-10 13:57:22","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":62110,"visible":true,"origin":"","legend":"\u003cp\u003eCOMT is involved in a key melatonin biosynthetic step.\u003c/p\u003e","description":"","filename":"Figure1.png","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/f329a51d13e29f46bf1c51d4.png"},{"id":95553526,"identity":"892273b0-e4d5-4b69-a5a2-e171e1b42205","added_by":"auto","created_at":"2025-11-10 13:57:22","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":2669157,"visible":true,"origin":"","legend":"\u003cp\u003eThe tertiary structure of COMT protein\u003c/p\u003e\n\u003cp\u003eA. The tertiary structure of StCOMT protein\u003c/p\u003e\n\u003cp\u003eB. The tertiary structure of AtCOMT protein\u003c/p\u003e","description":"","filename":"Figure2.png","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/ec8f93e7efa7a81151b2669b.png"},{"id":95654326,"identity":"df57566a-aa03-4cc2-8916-073abe099efe","added_by":"auto","created_at":"2025-11-11 16:11:05","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1832263,"visible":true,"origin":"","legend":"\u003cp\u003eChromosome location and distribution analysis of COMTs genes\u003c/p\u003e\n\u003cp\u003eA Localization of \u003cem\u003eCOMTs \u003c/em\u003egenes in potato chromosome\u003c/p\u003e\n\u003cp\u003eB Localization of \u003cem\u003eCOMTs \u003c/em\u003egenes in Arabidopsis chromosome\u003c/p\u003e\n\u003cp\u003eC Distribution of \u003cem\u003eCOMTs \u003c/em\u003egenes in potato chromosome\u003c/p\u003e\n\u003cp\u003eD Distribution of \u003cem\u003eCOMTs \u003c/em\u003egenes in Arabidopsis chromosome\u003c/p\u003e","description":"","filename":"Figure3.png","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/10b751e05d5553c423fb38e1.png"},{"id":95553529,"identity":"3fd249e4-a94c-409d-98a8-69bbea769643","added_by":"auto","created_at":"2025-11-10 13:57:22","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":3272134,"visible":true,"origin":"","legend":"\u003cp\u003eCOMTs gene family collinearity analysis\u003c/p\u003e\n\u003cp\u003eA Collinearity of COMTs gene family within potato\u003c/p\u003e\n\u003cp\u003eB Collinearity of COMTs gene family within Arabidopsis thaliana\u003c/p\u003e\n\u003cp\u003eC Collinearity of COMTs gene family between\u003c/p\u003e\n\u003cp\u003ePotato,Arabidopsis thaliana and Narrowleaf Tobacco\u003c/p\u003e","description":"","filename":"Figure4.png","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/0085f399d719e11405b3caa0.png"},{"id":95553532,"identity":"8d0f21b1-5f57-4251-a907-df22e6dce491","added_by":"auto","created_at":"2025-11-10 13:57:22","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":5511744,"visible":true,"origin":"","legend":"\u003cp\u003eCOMT Protein Phylogenetic Tree\u003c/p\u003e\n\u003cp\u003eA. COMT Protein Phylogenetic Tree Composed of 15 Species\u003c/p\u003e\n\u003cp\u003eB. COMT Protein Phylogenetic Tree Composed of Potato and Arabidopsis\u003c/p\u003e\n\u003cp\u003eC. Arabidopsis COMT Protein Phylogenetic Tree\u003c/p\u003e\n\u003cp\u003eD. Potato COMT Protein Phylogenetic Tree\u003c/p\u003e","description":"","filename":"Figure5.png","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/6507c72fc606f9b5d1590206.png"},{"id":95553535,"identity":"bc88ada7-954f-4914-89bf-dae60c4057f8","added_by":"auto","created_at":"2025-11-10 13:57:22","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":12295333,"visible":true,"origin":"","legend":"\u003cp\u003eComprehensive Analysis of \u003cem\u003eCOMT \u003c/em\u003eGene Structure\u003c/p\u003e\n\u003cp\u003eA: Comprehensive analysis of 18 \u003cem\u003eStCOMT \u003c/em\u003egenes. From left to right, the panels display the distribution of conserved protein motifs, gene structure (CDS and UTR), and the types and distribution of cis-acting elements in the promoter regions.\u003c/p\u003e\n\u003cp\u003eB:Comprehensive analysis of 10 \u003cem\u003eAtCOMT \u003c/em\u003egenes. From left to right, the panels display the distribution of conserved protein motifs, gene structure (CDS and UTR), and the types and distribution of cis-acting elements in the promoter regions.\u003c/p\u003e","description":"","filename":"Figure6.png","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/27d67e0bc5565d98c0b01b7b.png"},{"id":95655299,"identity":"bfbcdf22-f1b2-472a-aeaa-63e748276f47","added_by":"auto","created_at":"2025-11-11 16:15:14","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":1759379,"visible":true,"origin":"","legend":"\u003cp\u003eTissue-Specific Expression Heatmap of the \u003cem\u003eCOMT \u003c/em\u003eGene Family\u003c/p\u003e\n\u003cp\u003eA:Tissue-Specific Expression Analysis of the \u003cem\u003eStCOMT \u003c/em\u003eGene Family\u003c/p\u003e\n\u003cp\u003eB:Tissue-Specific Expression Analysis of the \u003cem\u003eAtCOMT \u003c/em\u003eGene Family\u003c/p\u003e","description":"","filename":"Figure7.png","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/90d976e139bab92aaf240e20.png"},{"id":95654829,"identity":"9478322c-61c9-4bab-af92-2977b80ea3b1","added_by":"auto","created_at":"2025-11-11 16:13:17","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":1141607,"visible":true,"origin":"","legend":"\u003cp\u003eStress-Specific Expression Heatmap of the \u003cem\u003eCOMT \u003c/em\u003eGene Family\u003c/p\u003e\n\u003cp\u003eA:Stress-Specific Expression Analysis of the \u003cem\u003eStCOMT \u003c/em\u003eGene Family\u003c/p\u003e\n\u003cp\u003eB:Stress-Specific Expression Analysis of the \u003cem\u003eAtCOMT \u003c/em\u003eGene Family\u003c/p\u003e","description":"","filename":"Figure8.png","url":"https://assets-eu.researchsquare.com/files/rs-7918038/v1/18301b5ee01bafa7c40313ca.png"}],"financialInterests":"No competing interests reported.","formattedTitle":"Parallel Genome-Wide Identification and Analysis of the COMT Gene Family in Potato (Solanum tuberosum L.) and Arabidopsis ( Arabidopsis thaliana (L.) Heynh.)","fulltext":[{"header":"Introduction","content":"\u003cp\u003eCaffeic acid O-methyltransferase (COMT), an S-adenosyl-L-methionine (SAM)-dependent O-methyltransferase, modulates diverse physiological processes in plants through the phenylpropanoid metabolic pathway (see Fig. 1 for its role in melatonin biosynthesis)[1]. This enzyme catalyzes melatonin synthesis to enhance stress resistance [2], promotes lignin biosynthesis to improve lodging resistance [3], and facilitates the production of pharmacologically active compounds such as ferulic acid and flavonoids in medicinal plants [4]. Additionally, COMT mediates the biosynthesis of vanillin in aromatic plants [5], highlighting its significance as an integral component of plant metabolic systems.\u003c/p\u003e\n\u003cp\u003eMelatonin, a crucial phytohormone, plays a pivotal role in mitigating both biotic and abiotic stresses, including extreme temperatures and salinity [6-8]. Substantial evidence indicates that COMT-catalyzed melatonin biosynthesis significantly enhances plant resilience to these adversities [9-10]. Lignin, a fundamental component of the plant cell wall, is essential for long-distance transport of water and nutrients, mechanical support, and stress defense [11-13]. COMT also fulfills several key functions in the lignin biosynthesis pathway [14-15]. The catalysis of melatonin and lignin synthesis represents two central functions of COMT, thereby regulating plant growth, promoting stress resistance, and enhancing lodging tolerance.\u003c/p\u003e\n\u003cp\u003ePotato (Solanum tuberosum L.) holds a critical position as a major global food crop [16]. \u0026nbsp;Despite the characterization of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egenes in key Solanaceous species\u0026mdash;including tomato (Solanum lycopersicum), pepper (Capsicum annuum), and American black nightshade (Solanum americanum) [17-19]\u0026mdash;and the examination of specific \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003egenes in potato itself [20], a systematic understanding of the entire gene family is still lacking. \u0026nbsp;The present study bridges this gap by conducting a genome-wide characterization of \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003egenes, leveraging comparative analysis with the Arabidopsis \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003efamily. \u0026nbsp;This work establishes a basis for future breeding programs targeting enhanced stress tolerance in potato.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cp\u003e\u003cstrong\u003e2.1 Genome Data Retrieval and Gene Family Member Identification\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eGenomic data for the 15 selected species were acquired from public repositories. The eggplant (Solanum melongena) genome was retrieved from the Sol Genomics Network, whereas genomic resources for all other species were downloaded from the Ensembl Plants database. The Hidden Markov Model (HMM) profiles for the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003e(PF00891) and \u003cem\u003eASMT\u0026nbsp;\u003c/em\u003e(PF08100) domains were obtained from the Pfam database. These HMM profiles were employed to screen the respective proteomes using the \u0026quot;Simple HMM Search\u0026quot; function in TBtools, with an E-value\u0026le;-5.A subsequent curation process involved filtering redundant \u003cem\u003eCOMT/ASMT\u003c/em\u003e members, visualizing their chromosomal positions, and merging tandem repeats, leading to the final identification of the \u0026nbsp;\u003cem\u003eCOMT\u003c/em\u003e gene family members.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.2 Characterization of COMT Protein Physicochemical Properties and Subcellular Localization Prediction\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe physicochemical properties of the identified members were analyzed using the \u0026quot;Protein Parameter Calculate\u0026quot; function in TBtools.Protein secondary structures were predicted with the NPS@online server, while tertiary structures were modeled using SWISS-MODEL. Subcellular localizations were forecasted employing the Cell-PLoc 2.0 web server.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.3Synteny Analysis and Phylogenetic Reconstruction for the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eIntra-genomic synteny analysis of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egenes in potato and Arabidopsis was performed separately using the \u0026quot;Advanced Circos\u0026quot; tool in TBtools. \u0026nbsp;For inter-species synteny assessment, the \u0026quot;Multiple Synteny Plot\u0026quot; function was employed to analyze the relationships among potato, Arabidopsis, and Nicotiana tabacum, with the results visualized accordingly.\u003c/p\u003e\n\u003cp\u003eA phylogenetic tree was constructed from the protein sequences of potato and Arabidopsis COMT genes using the \u0026quot;One Step Build a ML Tree\u0026quot; feature in TBtools. The maximum likelihood method was applied with the UltraFast BootStrap algorithm, and the bootstrap replication number was set to 5000. The resulting tree was subsequently annotated and visualized using the iTOL online platform.\u003ca href=\"https://plants.ensembl.org/\"\u003e\u003cbr\u003e\u0026nbsp;\u003c/a\u003e\u003cstrong\u003e2.4 Gene and Protein Structure Analysis of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eConserved domains in COMT proteins were analyzed with the Batch CD-Search tool. \u0026nbsp;Protein motifs were predicted using the MEME suite, configured to identify up to 10 distinct motifs. Gene structures (exon-intron organization) were determined from genome annotations and displayed with TBtools \u0026quot;Visualize Gene Structure\u0026quot;. Promoter sequences spanning 2000 bp upstream of each \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene\u0026apos;s transcription start site were examined for cis-acting regulatory elements using the PlantCARE database. \u0026nbsp;These analyses were collectively visualized through the \u0026quot;Gene Structure View (Advanced)\u0026quot; function in TBtools.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e2.5 Analysis of Tissue-Specific and Stress-Responsive Expression of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family Members\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eExpression profiles of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene family members in potato and Arabidopsis, encompassing various tissues and stress conditions, were extracted from the ePlant database, and the results were visualized using the HeatMap function in TBtools.\u003c/p\u003e\n\u003cp\u003eTable 1 The websites and software used\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"586\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd valign=\"top\" style=\"width: 158px;\"\u003e\n \u003cp\u003eName\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 163px;\"\u003e\n \u003cp\u003eUse\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd valign=\"top\" style=\"width: 266px;\"\u003e\n \u003cp\u003eWebsite link\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eSol Genomics Network\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eData download\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://solgenomics.net/\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eensembl\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eData download\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://plants.ensembl.org/\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eePlant\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eData download\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://bar.utoronto.ca/\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eNPS@\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eSecondary structure prediction\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://npsa.lyon.inserm.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eSWISS-MODEL\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eThree-level structure prediction\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://swissmodel.expasy.org/interactive\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eCell-PLoc 2.0\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eSubcellular localization prediction\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttp://www.csbio.sjtu.edu.cn/bioinf/Cell-PLoc-2/\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eBatch CD-Search\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eDomain prediction\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eMEME\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eMotif sequence prediction\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://meme-suite.org/meme/tools/meme\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eiTOL\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eEvolutionary tree beautification\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://itol.embl.de/\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eChiPlot\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eChart beautification\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://www.chiplot.online/\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eHiPlot\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eChart beautification\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://hiplot.cn/\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 158px;\"\u003e\n \u003cp\u003eTBtools\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 163px;\"\u003e\n \u003cp\u003eMain functions\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 266px;\"\u003e\n \u003cp\u003ehttps://github.com/CJ-Chen/TBtools\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e"},{"header":"Results","content":"\u003cp\u003e\u003cstrong\u003e3.1\u0026nbsp;\u003c/strong\u003e\u003cstrong\u003eIdentification of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family Members and Analysis of Protein Physicochemical Properties\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eComprehensive analysis identified 12 \u003cem\u003eStCOMT\u003c/em\u003e genes in potato and 10 \u003cem\u003eAtCOMT\u0026nbsp;\u003c/em\u003egenes in Arabidopsis. The encoded proteins displayed generally uniform molecular characteristics, with most molecular weights clustering between 39\u0026ndash;42 kDa and amino acid lengths ranging from 350 to 380 residues. Notable exceptions included \u003cem\u003eStCOMT1\u003c/em\u003e, \u003cem\u003eStCOMT4\u003c/em\u003e, \u003cem\u003eStCOMT6\u003c/em\u003e, and \u003cem\u003eStCOMT9\u003c/em\u003e, which fell outside these ranges. Theoretical pI analysis revealed that the majority of COMT proteins are acidic, with pI values spanning 4.8\u0026ndash;6.3, except for the basic StCOMT5 (pI = 9.26). Evaluation of protein stability indicated that 21 out of the 29 \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003emembers exhibited an Instability Index below 40, suggesting high structural stability. Hydrophobicity assessment using the Grand Average of Hydropathicity showed positive values for 20 members, supporting their classification as hydrophobic proteins. Furthermore, 26 \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eproteins possessed an Aliphatic Index exceeding 90, consistent with enhanced thermostability and structural compactness.\u003c/p\u003e\n\u003cp\u003eTable 2 Physicochemical Analysis and Predicted location of \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003eGenes\u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"627\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" style=\"width: 79px;\"\u003e\n \u003cp\u003eSequence ID\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 81px;\"\u003e\n \u003cp\u003eNumber of Amino Acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 78px;\"\u003e\n \u003cp\u003eMolecular Weight\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 62px;\"\u003e\n \u003cp\u003eTheoretical pI\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 65px;\"\u003e\n \u003cp\u003eInstability Index\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 65px;\"\u003e\n \u003cp\u003eAliphatic Index\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 107px;\"\u003e\n \u003cp\u003eGrand Average of Hydropathicity\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 90px;\"\u003e\n \u003cp\u003ePredicted location(s)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"21\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd height=\"21\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT1\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e642\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e71607.79\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e9.26\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e53.87\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e77.46\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.524\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eNucleus.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT2\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e337\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e36532.27\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e6.05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e30.28\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e97.57\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e0.117\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT3\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e353\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e39712.06\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.66\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e34.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e89.75\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.047\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast. Cytoplasm. Mitochondrion. Nucleus.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT4\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e266\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e29597.06\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e28.95\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e95.71\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.02\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT5\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e363\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e39694.75\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e31.91\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e86.25\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.046\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT6\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e265\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e29217.62\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.29\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e36.91\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e101.09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e0.08\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast. Mitochondrion.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT7\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e348\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e39189.41\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.67\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e34.79\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e94.63\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.026\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT8\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e364\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e40964.26\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.36\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e29.89\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e98.63\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.085\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT9\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e226\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e24744.59\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e6.05\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e37.11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e99.65\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e0.134\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast. Nucleus.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT10\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e359\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e39927.88\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e34.33\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e101.87\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e0.008\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT11\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e356\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e39960.31\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e6.22\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e39.72\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e98.03\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.041\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT12\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e351\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e39880.91\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.46\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e40.25\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e90.54\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.126\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast. Cytoplasm.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT13\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e363\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e40221.31\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.48\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e31.2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e89.61\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.055\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT14\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e365\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e40916.42\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.67\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e36.84\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e98.25\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e0.03\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast. Mitochondrion.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT15\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e360\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e40556.55\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e37.89\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e84.72\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.282\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT16\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e355\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e40184\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e4.82\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e37.24\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e85.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.177\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT17\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e359\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e40027.99\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.35\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e32.06\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e94.71\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e0.006\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 79px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT18\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 81px;\"\u003e\n \u003cp\u003e394\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 78px;\"\u003e\n \u003cp\u003e43966.59\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e6.33\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e26.75\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 65px;\"\u003e\n \u003cp\u003e92.11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 107px;\"\u003e\n \u003cp\u003e-0.116\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 90px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"19\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003eTable 3 Physicochemical Analysis and Predicted location of \u003cem\u003eAtCOMT\u0026nbsp;\u003c/em\u003eGenes\u0026nbsp;\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"627\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd rowspan=\"2\" style=\"width: 74px;\"\u003e\n \u003cp\u003eSequence ID\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 75px;\"\u003e\n \u003cp\u003eNumber of Amino Acid\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 89px;\"\u003e\n \u003cp\u003eMolecular Weight\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 62px;\"\u003e\n \u003cp\u003eTheoretical pI\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 63px;\"\u003e\n \u003cp\u003eInstability Index\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 66px;\"\u003e\n \u003cp\u003eAliphatic Index\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 108px;\"\u003e\n \u003cp\u003eGrand Average of Hydropathicity\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd rowspan=\"2\" style=\"width: 89px;\"\u003e\n \u003cp\u003ePredicted location(s)\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"21\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd height=\"21\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT1\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e373\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e40747.86\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.01\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e28.06\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e92.01\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0.083\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT2\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e352\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e38967.6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.58\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e38.49\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e88.84\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e-0.006\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT3\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e363\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e40408.86\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.66\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e34.71\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e95.12\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e-0.121\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT4\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e288\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e32100.06\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e29.68\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e94.1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e-0.024\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT5\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e367\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e40222.38\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e24.09\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e102.53\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0.103\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT6\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e381\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e42326.12\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.29\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e37.29\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e97.72\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0.031\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT7\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e359\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e39688.48\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.28\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e48.19\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e88.02\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e-0.096\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT8\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e382\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e42614.17\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.32\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e41.78\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e90.31\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e-0.099\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast. Mitochondrion. Nucleus.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"37\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT9\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e378\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e41944.63\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.33\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e29.94\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e98.52\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e0.078\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 74px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT10\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 75px;\"\u003e\n \u003cp\u003e363\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003e39617.93\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 62px;\"\u003e\n \u003cp\u003e5.62\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 63px;\"\u003e\n \u003cp\u003e33.38\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 66px;\"\u003e\n \u003cp\u003e92.4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 108px;\"\u003e\n \u003cp\u003e-0.026\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 89px;\"\u003e\n \u003cp\u003eChloroplast.\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd height=\"24\" style=\"width: 0px;\"\u003e\u003cbr\u003e\u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e\u003cstrong\u003e3.2 Analysis of COMT Protein Structure\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSecondary structure prediction via the NPS@ tool revealed that COMT proteins from both potato and Arabidopsis are primarily composed of alpha helices (Hh), extended strands (Ee), and random coils (Cc). Among these, alpha helices constituted the largest proportion (averaging 47.72% in StCOMTs and 47.12% in AtCOMTs), followed by extended strands (38.77% in StCOMTs and 39.65% in AtCOMTs), and random coils (13.51% in StCOMTs and 13.23% in AtCOMTs). The consistent compositional profiles across most family members reflect considerable conservation in secondary architecture. Tertiary structure modeling performed with SWISS-MODEL further indicated that proteins within the same subfamily share similar folding patterns, consistent with the secondary structure predictions. All COMT proteins were predicted to adopt homodimeric quaternary structures.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.3 Prediction of Subcellular Localization of COMT Proteins\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSubcellular localization predictions generated by Cell-PLoc 2.0 indicated that most COMT proteins in both potato and Arabidopsis are predominantly localized to the chloroplast. \u0026nbsp;Additional localizations were detected for specific members: AtCOMT8 was found in both the nucleus and mitochondria; StCOMT1, StCOMT12, and StCOMT13 showed nuclear localization; \u0026nbsp;while StCOMT3, StCOMT6, and StCOMT14 were predicted to localize to mitochondria.A few members, including StCOMT3 and StCOMT12, also exhibited cytoplasmic presence.Based on these findings, we propose that chloroplasts serve as the primary functional site for COMT proteins.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.4 Chromosomal Localization of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eChromosomal localization visualization revealed an uneven genomic distribution of \u003cem\u003eCOMT\u003c/em\u003e gene family members in both potato and Arabidopsis thaliana. In the potato genome, \u003cem\u003eCOMT\u003c/em\u003e genes were predominantly clustered on chromosome 6 (harboring three members), with two members localized to chromosomes 10 and 3 respectively. Chromosomes 1, 2, 8, and 12 each contained only a single member, whereas no \u003cem\u003eCOMT\u003c/em\u003e genes were detectable on chromosomes 4, 5, or 7. In Arabidopsis, \u003cem\u003eCOMT\u003c/em\u003e genes exhibited significant clustering on chromosome 1 (containing six members). Chromosome 15 harbored two members, while chromosomes 3 and 4 showed minimal representation with one member each. Notably, chromosome 2 lacked detectable \u003cem\u003eCOMT\u003c/em\u003e homologs.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.5 Synteny Analysis of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTo analyse the evolutionary trajectory of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene family, a comprehensive synteny analysis was conducted across potato, arabidopsis thaliana, and narrowleaf tobacco. This investigation encompassed both interspecific synteny assessments and intraspecific synteny evaluation within potato and arabidopsis thaliana. Following stringent filtration of tandem duplicates, key findings emerged: Two orthologous \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene pairs were identified between potato and arabidopsis thaliana, whereas three orthologous pairs were detected between potato and its con-familial species narrowleaf tobacco. These results demonstrate pronounced evolutionary and functional conservation of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003efamily within Solanaceae species, alongside considerable conservation of synteny blocks across divergent plant families. Intraspecific analysis further revealed the presence of one paralogous \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene pair within each of the potato and arabidopsis thaliana genomes. Notably, both paralogous pairs localized to genomic loci exhibiting the highest \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene density in their respective species (chromosome 6 in potato; chromosome 1 in A. thaliana), suggesting localized gene duplication events as a potential mechanism for COMT gene family expansion. Despite potential evolutionary divergence, these paralogs maintained significant sequence homology and retention of functional homology.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.6 Phylogenetic Analysis of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTable 4 Species Used for Phylogenetic Tree Construction\u003c/p\u003e\n\u003ctable border=\"0\" cellspacing=\"0\" cellpadding=\"0\" width=\"101%\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003eSerial Number\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003ePlant\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003eScientific name\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u0026nbsp;Gene Name\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003eNumber of Identified genes\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e1\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eArabidopsis\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eArabidopsis thaliana\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eAtCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e10\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e2\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eNarrow leaved tobacco\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eNicotiana attenuata\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eNaCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e7\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e3\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eTomato\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eSolanum lycopersicum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eSlCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e15\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e4\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eChili\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eCapsicum annuum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eCaCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e5\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003ePotato\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eSolanum tuberosum\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eStCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e18\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e6\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eSoybean\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eGlycine max\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eGmCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e26\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e7\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eMillet\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eSetaria italica\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eSiCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e27\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e8\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eEggplant\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eSolanum melongena\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eSmCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e15\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e9\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eCorn\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eZea mays\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eZmCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e21\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e10\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eRice plant\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eOryza sativa\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eOsCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e19\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e11\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eApple\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eMalus domestica\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eMdCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e20\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e12\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eSunflower\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eHelianthus annuus\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eHaCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e20\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e13\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eAmerican Cotton\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eGossypium raimondii\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eGrCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e17\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e14\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eWild carrot\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eDaucus carota\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eDcCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e8\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd style=\"width: 10px;\"\u003e\n \u003cp\u003e15\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 20px;\"\u003e\n \u003cp\u003eChinese rose\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 30px;\"\u003e\n \u003cp\u003e\u003cem\u003eRosa chinensis\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 17px;\"\u003e\n \u003cp\u003e\u003cem\u003eRcCOMT\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd style=\"width: 19px;\"\u003e\n \u003cp\u003e23\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003eA phylogenetic tree was constructed using 264 COMT protein sequences from 15 plant species.The evolutionary analysis revealed that COMT could be classified into five distinct subfamilies. Potato StCOMT were distributed across all subfamilies except subfamily I, with specific distribution as follows: two in subfamily V, eight in subfamily II, one in subfamily III, and seven in subfamily IV. Subsequently, a separate phylogenetic tree containing 29 COMT members from potato and Arabidopsis resolved them into four subfamilies. Further species-specific phylogenetic analyses demonstrated that potato COMT members clustered into four subfamilies , while Arabidopsis COMT members grouped into three subfamilies.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.7 Comprehensive Analysis of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Structure\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eA comprehensive analysis was performed on 18 potato and 10 Arabidopsis COMT sequences, encompassing conserved motifs, gene structure, protein domains and promoter regions .\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.7.1 Conserved Motif Analysis of the COMT Gene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAnalysis of conserved motifs revealed high conservation in both distribution patterns and motif numbers among COMT family members. \u0026nbsp;The number of motifs ranged from 8 to 10. \u0026nbsp; Although some proteins lacked specific motifs, the overall arrangement remained largely consistent across the gene family, suggesting possible evolutionary loss or acquisition of particular motifs.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.7.2 Gene Structure Analysis of the COMT Gene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eGene structure prediction showed that COMT gene sequences exhibited similar organizational patterns in CDS-UTR distribution. \u0026nbsp;All COMT genes consisted of coding sequences (CDS) and untranslated regions (UTR). \u0026nbsp;As shown in the corresponding figure, most members within the same group shared identical CDS numbers and distribution patterns, with CDS counts ranging from 1 to 2 and UTR counts varying between 2 and 4.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.7.5 Protein Domain Analysis of the COMT Gene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDomain prediction analysis indicated that the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene family primarily contains two structural domains: AdoMet_MTases superfamily and dimerization2 superfamily. \u0026nbsp;With few exceptions\u0026mdash;\u003cem\u003eStCOMT1\u0026nbsp;\u003c/em\u003econtains an additional SANT domain, and \u003cem\u003eStCOMT15\u0026nbsp;\u003c/em\u003elacks one AdoMet_MTases domain\u0026mdash;all \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003eand \u003cem\u003eAtCOMT\u0026nbsp;\u003c/em\u003egenes possess one AdoMet_MTases domain and one Dimerization2 domain, further supporting the evolutionary conservation within this gene family.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.7.4 Promoter Analysis of the COMT Gene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003ePromoter prediction analysis classified the cis-acting elements in \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egenes into four categories: light response (including circadian and light-related elements), plant growth and development (endosperm, meristem, seed, palisade mesophyll cells, and zein), stress response (anaerobic, anoxic, low-temperature, wound, mixed stress, elicitor, and MYB binding site), and phytohormone response (abscisic acid, auxin, gibberellin, MeJA, and salicylic acid). \u0026nbsp;The distribution patterns of these promoter elements were similar in both potato and Arabidopsis \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egenes, with light- and hormone-related elements being predominant, along with several elements associated with growth regulation. \u0026nbsp; These results suggest that COMT genes may primarily function in light signal perception and transduction, as well as in phytohormone-mediated pathways.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.8 Analysis of Tissue-Specific Expression of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eExpression profiling across 13 potato organs revealed distinct tissue-specific patterns among \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003egenes. \u0026nbsp;Transcript accumulation of \u003cem\u003eStCOMT1\u0026nbsp;\u003c/em\u003ewas most pronounced in the stem apex, whereas \u003cem\u003eStCOMT5\u0026nbsp;\u003c/em\u003edisplayed specific enrichment in stem tissues. \u0026nbsp;Four genes\u0026mdash;\u003cem\u003eStCOMT4\u003c/em\u003e, \u003cem\u003eStCOMT8\u003c/em\u003e, \u003cem\u003eStCOMT12\u003c/em\u003e, and \u003cem\u003eStCOMT15\u003c/em\u003e\u0026mdash;were observed to be co-expressed in both stem and stem apex tissues. \u0026nbsp;Preferential expression in stamens was recorded for \u003cem\u003eStCOMT3\u0026nbsp;\u003c/em\u003eand \u003cem\u003eStCOMT10\u003c/em\u003e. \u0026nbsp;Root-specific transcript accumulation characterized \u003cem\u003eStCOMT6\u003c/em\u003e, \u003cem\u003eStCOMT9\u003c/em\u003e, and \u003cem\u003eStCOMT17\u003c/em\u003e. \u0026nbsp;Stolons showed marked enrichment of \u003cem\u003eStCOMT13\u003c/em\u003e, \u003cem\u003eStCOMT14\u003c/em\u003e, and \u003cem\u003eStCOMT18\u003c/em\u003e, while young tubers demonstrated activated expression of \u003cem\u003eStCOMT1\u003c/em\u003e, \u003cem\u003eStCOMT2\u003c/em\u003e, and \u003cem\u003eStCOMT18\u003c/em\u003e. \u0026nbsp;Notably, \u003cem\u003eStCOMT7\u003c/em\u003e, \u003cem\u003eStCOMT11\u003c/em\u003e, and \u003cem\u003eStCOMT16\u0026nbsp;\u003c/em\u003emaintained minimal expression levels across all examined organs.\u003c/p\u003e\n\u003cp\u003eIn Arabidopsis, examination of 18 developmental stages and organs uncovered specialized expression patterns.\u003cem\u003eAtCOMT1\u0026nbsp;\u003c/em\u003etranscription was restricted to cotyledons, while \u003cem\u003eAtCOMT2\u0026nbsp;\u003c/em\u003eaccumulation was predominant in senescing leaves. \u0026nbsp;Mature pollen exhibited specific high expression of \u003cem\u003eAtCOMT3\u003c/em\u003e.Multiple family members\u0026mdash;\u003cem\u003eAtCOMT4\u003c/em\u003e, \u003cem\u003eAtCOMT6\u003c/em\u003e, and \u003cem\u003eAtCOMT8\u003c/em\u003e\u0026mdash;showed significant upregulation during seed developmental stages.Elevated transcript levels of \u003cem\u003eAtCOMT5\u0026nbsp;\u003c/em\u003ewere detected in 24-hour imbibed seeds, along with hypocotyl and root tissues.\u003cem\u003eAtCOMT6\u0026nbsp;\u003c/em\u003edisplayed upregulation in both root tissues and seed developmental stages, whereas \u003cem\u003eAtCOMT7\u0026nbsp;\u003c/em\u003eand \u003cem\u003eAtCOMT9\u0026nbsp;\u003c/em\u003eexpression peaked during full bloom. \u0026nbsp;Dry seeds showed increased \u003cem\u003eAtCOMT8\u0026nbsp;\u003c/em\u003eaccumulation, and \u003cem\u003eAtCOMT10\u0026nbsp;\u003c/em\u003edemonstrated specific enrichment in the second internode of stems.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e3.9 Analysis of Stress-Specific Expression of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene Family\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eEvaluation of stress-responsive expression demonstrated specialized activation patterns among COMT members.In potato, significant induction of \u003cem\u003eStCOMT3\u0026nbsp;\u003c/em\u003eand \u003cem\u003eStCOMT10\u0026nbsp;\u003c/em\u003eoccurred under biotic stress conditions.High temperature treatment specifically triggered StCOMT14 and \u003cem\u003eStCOMT18\u0026nbsp;\u003c/em\u003etranscription.Gibberellin application regulated four genes\u0026mdash;StCOMT5, \u003cem\u003eStCOMT6\u003c/em\u003e, \u003cem\u003eStCOMT9\u003c/em\u003e, and \u003cem\u003eStCOMT17\u003c/em\u003e. \u0026nbsp; Mechanical wounding strongly activated StCOMT4, \u003cem\u003eStCOMT8\u003c/em\u003e, \u003cem\u003eStCOMT10\u003c/em\u003e, \u003cem\u003eStCOMT12\u003c/em\u003e, and \u003cem\u003eStCOMT15\u003c/em\u003e.Combined salt-mannitol stress elevated transcript levels of \u003cem\u003eStCOMT6\u003c/em\u003e, \u003cem\u003eStCOMT13\u003c/em\u003e, and \u003cem\u003eStCOMT18\u003c/em\u003e.In contrast, \u003cem\u003eStCOMT2\u003c/em\u003e, \u003cem\u003eStCOMT7\u003c/em\u003e, \u003cem\u003eStCOMT11\u003c/em\u003e, and \u003cem\u003eStCOMT16\u0026nbsp;\u003c/em\u003eremained uninduced across all stress treatments.\u003c/p\u003e\n\u003cp\u003eArabidopsis COMT genes displayed complex stress response profiles.Seven members\u0026mdash;\u003cem\u003eAtCOMT3\u003c/em\u003e, \u003cem\u003eAtCOMT4\u003c/em\u003e, \u003cem\u003eAtCOMT6\u003c/em\u003e, \u003cem\u003eAtCOMT7\u003c/em\u003e, \u003cem\u003eAtCOMT8\u003c/em\u003e, \u003cem\u003eAtCOMT9\u003c/em\u003e, and \u003cem\u003eAtCOMT10\u003c/em\u003e\u0026mdash;showed elevated expression under various abiotic stresses compared to control conditions. \u0026nbsp;Heat stress specifically induced upregulation of \u003cem\u003eAtCOMT3\u003c/em\u003e, \u003cem\u003eAtCOMT4\u003c/em\u003e, \u003cem\u003eAtCOMT7\u003c/em\u003e, \u003cem\u003eAtCOMT9\u003c/em\u003e, and \u003cem\u003eAtCOMT10\u003c/em\u003e. Drought treatment enhanced transcription of \u003cem\u003eAtCOMT5\u003c/em\u003e, \u003cem\u003eAtCOMT6\u003c/em\u003e, \u003cem\u003eAtCOMT7\u003c/em\u003e, and \u003cem\u003eAtCOMT8\u003c/em\u003e. Wounding response involved upregulation of \u003cem\u003eAtCOMT5\u003c/em\u003e, \u003cem\u003eAtCOMT6\u003c/em\u003e, \u003cem\u003eAtCOMT8\u003c/em\u003e, and \u003cem\u003eAtCOMT9\u003c/em\u003e. Unique stress activation patterns included UV radiation specifically inducing \u003cem\u003eAtCOMT1\u0026nbsp;\u003c/em\u003eand \u003cem\u003eAtCOMT2\u003c/em\u003e, osmotic stress activating \u003cem\u003eAtCOMT1\u0026nbsp;\u003c/em\u003eand \u003cem\u003eAtCOMT10\u003c/em\u003e, and low temperature upregulating \u003cem\u003eAtCOMT1\u003c/em\u003e, \u003cem\u003eAtCOMT5\u003c/em\u003e, and \u003cem\u003eAtCOMT8\u003c/em\u003e.Notably, oxidative stress resulted in comprehensive downregulation across the entire \u003cem\u003eAtCOMT\u0026nbsp;\u003c/em\u003efamily.\u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eCOMT proteins in both potato and Arabidopsis exhibit similar physicochemical properties, with molecular weights ranging from 39-42 kDa and lengths of 350-380 amino acids. They are characterized as stable, structurally compact, thermostable, acidic, and hydrophobic proteins. These characteristics are intrinsically linked to their function [1, 24, 25]. For an enzyme catalyzing the methylation of diverse, often hydrophobic substrates\u0026mdash;such as caffeic acid, 5-hydroxyferulic acid, and 5-hydroxyconiferaldehyde, which belong to methylated phenylpropanoids, flavonoids, and terpenoids [26-28]\u0026mdash;hydrophobicity facilitates better substrate binding. Furthermore, a compact structure provides a tight hydrophobic environment conducive to efficient catalysis.\u003c/p\u003e\n\u003cp\u003eStructurally, COMT proteins are primarily composed of alpha-helices (Hh), extended strands (Ee), and random coils (Cc) at the secondary level and universally form homodimers at the tertiary level, indicating significant structural conservation. Predominantly localized to the chloroplasts, with additional presence in other cellular compartments, this localization pattern is conserved across species. For instance, melatonin synthesis in tea plant (Camellia sinensis) is closely associated with light conditions [25], and the \u003cem\u003eZmCOMT\u0026nbsp;\u003c/em\u003efamily in maize is functionally implicated in light response [29]. This evidence strongly suggests that the chloroplastic localization of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eis likely linked to photosynthesis or light signal transduction, while its presence in other organelles hints at additional, specialized functions.\u003c/p\u003e\n\u003cp\u003eThe evolutionary classification of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene family varies among studies. Some researchers, for example in soybean (Glycine max) [28], propose a two-class system, while others advocate for a more refined classification into four or more groups, as seen in Vitis species [30] and kenaf (Hibiscus cannabinus L.) [27]. Our analysis supports the latter, more detailed view. A multi-category classification better reflects the complex evolutionary history involving gene duplication, segmental duplication, and whole-genome duplication events specific to different lineages. We classified \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003emembers from 15 species into five distinct clades based on phylogenetic relationships. The distribution of potato \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003emembers across these clades demonstrates considerable evolutionary divergence.\u003c/p\u003e\n\u003cp\u003eIntra-species synteny analysis, after excluding tandem duplicates, revealed conserved syntenic relationships among \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egenes, underscoring the high evolutionary conservation of this family [23, 30]. Inter-species comparative analysis identified conserved syntenic blocks between potato and its con-familial species (Nicotiana attenuata) as well as the distantly related model plant Arabidopsis. This aligns with established findings of close evolutionary relationships between Solanum species (including potato and tomato) and Nicotiana [31, 32]. Integrating sequence and functional homology evidence, we hypothesize that local gene duplication events have been a key mechanism in the expansion of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003efamily, with paralogous genes retaining strong functional constraints\u0026mdash;a pattern also observed in the evolution of the TCP transcription factor family [36].\u003c/p\u003e\n\u003cp\u003eGene structure analysis revealed high conservation within the potato \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003efamily, with members typically containing 8-10 motifs and 2-4 introns [23, 30]. The identified conserved domains are directly linked to their molecular functions: the AdoMet_MTases domain confers methyltransferase activity, Dimerization2 facilitates protein dimerization, and the \u003cem\u003eSANT\u0026nbsp;\u003c/em\u003edomain may act as an adapter in chromatin complexes. These structural features are integral to the canonical roles of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egenes in catalyzing the synthesis of melatonin and lignin [23, 30, 37-39], thereby enhancing plant stress resistance. This high degree of structural similarity and functional adaptation among family members is consistent with findings in other crops like maize, kenaf, and grape [29, 30, 40].\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eAnalysis of cis-regulatory elements in the promoters indicated that \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003egenes possess elements responsive to all four major categories: light, plant hormones, development, and stress. This finding is corroborated by existing research. In tomato, \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eexpression is regulated by red light, influencing melatonin synthesis in fruits [41]. In maize, COMT is light-regulated and affects lignin biosynthesis [29]. Furthermore, \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eoverexpression enhances thermotolerance in rose [42] and salt tolerance in poplar [43]. Collectively, these studies confirm that \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene family members participate in various aspects of plant growth and development, albeit with potential functional specializations [44].\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eExpression profiling reveals that \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egenes exhibit distinct, tissue-specific expression patterns and demonstrate differential relative expression levels under various stress treatments. This observed regulatory complexity, when integrated with established evidence\u0026mdash;including transcriptomic and metabolomic studies linking \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eto combined drought-alkaline salt stress in potato [45], reported enhanced resistance to early blight in potato \u003cem\u003eCOMT\u003c/em\u003e-overexpressing lines [46], its fundamental role in mediating melatonin and lignin biosynthesis pathways, and the abundance of stress-responsive cis-acting elements identified in its promoters\u0026mdash;leads us to conclude that the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene family constitutes a pivotal gene family conferring resistance to both biotic and abiotic stresses in potato.\u003c/p\u003e\n\u003cp\u003eHowever, it is important to acknowledge that relying solely on bioinformatic predictions to assign definitive functions to \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003efamily members provides an incomplete perspective. Therefore, we propose that future research should build directly upon our findings. Subsequent investigations ought to employ a combined approach, integrating more advanced bioinformatics tools with experimental validation to systematically elucidate the specific biological functions of \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003egenes, particularly their roles in mediating responses to biotic/abiotic stresses, as well as potential involvement in photomorphogenesis and photosynthetic processes.\u003c/p\u003e"},{"header":"Conclusion","content":"\u003cp\u003eThis investigation conducted a comprehensive genomic identification and functional characterization of the \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003egene family in potato, revealing 12 \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003egenes. A parallel examination with the Arabidopsis \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003efamily was performed, indicating non-random chromosomal distribution of these genes. Phylogenetic assessment supported their categorization into five distinct subfamilies. The encoded proteins were characterized by acidic and hydrophobic properties, featured alpha-helix dominated secondary structures, and shared a conserved homodimeric tertiary conformation. Subcellular localization predictions strongly favored chloroplast targeting. In-depth promoter scanning identified numerous cis-regulatory elements associated with light responsiveness, hormone signaling, and stress activation. Expression profiling demonstrated clear tissue-specific patterns among \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003emembers, along with differentiated induction profiles under diverse biotic and abiotic stress conditions. Collectively, these findings imply that the \u003cem\u003eStCOMT\u0026nbsp;\u003c/em\u003egene family contributes to potato stress adaptation, potentially through modulating the biosynthesis of key metabolites like lignin and melatonin. This work establishes a foundation for subsequent functional studies and identifies promising genetic targets for enhancing stress resilience in potato breeding programs.\u003c/p\u003e\n\u003cp\u003e\u003cbr\u003e\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAuthor Contributions:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAuthor Contributions: H.D. (Huaiwen Du): Led the experimental design and execution, conducted the majority of the data analysis, and wrote the initial manuscript draft. L.L. (Lijia Liu): Developed specific methodologies, performed bioinformatics analyses, and contributed to data curation and manuscript revision. J.Y. (Jiayu Yuan): Assisted in data analysis, conducted statistical validation, and prepared the figures and tables. W.N. (Wu Na): Contributed to data validation and formal analysis. Y.W. (Yuxin Wei): Assisted in data curation and visualization. L.J. (Lili Jiang): Provided the conceptual framework, supervised the entire research project, and critically reviewed and edited the manuscript.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eAll authors have read and agreed to the published version of the manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e:\u003c/p\u003e\n\u003cp\u003eThis research was supported by The Construction Project of Double First-Class Initiative in Heilongjiang Province \u0026quot;Green and Low-Carbon of Grain Crops\u0026quot; (LJGXCG2022-107) and the Heilongjiang Provincial National College Students\u0026apos; Innovation and Entrepreneurship Training Program Project (202510223155), entitled \u0026quot;Study on the Association Mechanism of \u003cem\u003eCOMT\u0026nbsp;\u003c/em\u003eGene-mediated Melatonin Synthesis and Tuber Formation in Potato under the Background of Photoperiod Response Differences\u0026quot;.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData Availability Statement:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflicts of Interest:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare no relevant financial or non-financial interests to disclose.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics, Consent to Participate, and Consent to Publish declarations\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eEthics, Consent to Participate, and Consent to Publish declarations: not applicable.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003eFeng, X.; Wu ,X.;Hong, J.; Guo, Z.; Khan, Y.; Wei,D.; Fan,H.; Cai, Y. 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Genome-wide analysis of the COMT gene family in \u003cem\u003eAvena sativa\u003c/em\u003e: insights into lignin biosynthesis and disease defense mechanisms. Front Plant Sci. 2025 Jun 19:16:1609698.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eChen, H.; Wang, H.; Zhao, Z.; Pan, J.; Yao, Y.; Wang, Y.; Luo, K.; Song, Q. The Fiber Cell-Specific Overexpression of \u003cem\u003eCOMT2\u003c/em\u003e Modulates Secondary Cell Wall Biosynthesis in Poplar. Plants (Basel). 2025 Jun 6;14(12):1739.\u003c/li\u003e\n \u003cli\u003eWei, L.; Zhao, X.; Gu, X.; Peng, J.; Song, W. Deng, B.; Cao, Y.; Hu, S. Genome-Wide Identification and Expression Analysis of \u003cem\u003eDendrocalamus f\u003c/em\u003earinosus CCoAOMT Gene Family and the Role of DfCCoAOMT14 Involved in Lignin Synthesis. Int J Mol Sci. 2023 May 18;24(10):8965.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eZhang, Z.; Zhang, P.; Ding, Y.; Wang, Z.; Ma, Z..Ancient hybridization underlies tuberization and radiation of the potato lineage.Cell. 2025 Sep 18;188(19):5249-5265.e15.\u003c/li\u003e\n \u003cli\u003eShan, Q.; Zhao, D.; Cao, B.; Zhu, X.; Wang, C.; Deng, L.; Li, C.; Zhang, Y.; Shi, Q.; Gong, B.;Jasmonic acid and nitric oxide orchestrate a hierarchical melatonin cascade for Botrytis cinerea resistance in tomato. Plant Physiol. 2025 Mar 1;197(3):kiaf078.\u003c/li\u003e\n \u003cli\u003eLi, S.; Cai, Y.; Ma, H,; Chen, S.; Yang, R.; Zheng, J.; Zhou, X.; He, J.; Wu, D.; Liu, Y.; Chen, G.; Chen, C.; Zhu, Z. A comprehensive analysis of the O-methyltransferase gene family in the chili pepper (Capsicum annuum) identifies COMT36 involved in capsaicinoids biosynthesis. Int J Biol Macromol. 2025 Jun;312:144247.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eZhou, J.; Zhu, JG.; Xiao, P.; Wang, KL.; Xu, Q.; Wu, MX.; Pan, YZ. Physiological and Multi-Omics Analysis in Leaves of \u003cem\u003eSolanum americanum\u003c/em\u003e in Response to Cd Toxicity. Plants (Basel). 2025 Jul 10;14(14):2131.\u003c/li\u003e\n \u003cli\u003eZhang, R.; Wang, Y.; Kang, Y.; Du, Y.; Wang, X.; Jiao, S.; Yang, X.; Liu, Y.; Qin, S.; Zhang, W. Transcriptomics-proteomics analysis reveals StCOMT1 regulates drought, alkali and combined stresses in potato. Plant Cell Rep. 2025 Apr 29;44(5):109.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eL, Li.; J L, Popko.; T, Umezawa.; V L, Chiang.5-Hydroxyconiferyl Aldehyde Modulates Enzymatic Methylation for Syringyl Monolignol Formation, a New View of Monolignol Biosynthesis in Angiosperms. J Biol Chem. 2000 Mar 3;275(9):6537-45.\u003c/li\u003e\n \u003cli\u003eCai,C. ; Ye, S.;Liu, J.;Wang,N.; Tu, T.Functional insights into 4-coumarate-CoA ligase and caffeic acid O-methyltransferase genes involved in lignin biosynthesis in Chinese fir (Cunninghamia lanceolata) .Int J Biol Macromol. 2025 Sep;322(Pt 4):146909.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eGao, Y.; Wang, X.; Hou, X.;Evolution and Analysis of Caffeic Acid Transferase (COMT) in Seed Plants.\u0026nbsp;Biochem Genet. 2024 Jun;62(3):1953-1976.\u003c/li\u003e\n \u003cli\u003eLu, N.; Ma, W.; Han, D.; Liu, Y.; Wang, Z.; Wang, N.; Yang, G.; Qu, G.; Wang, Q.; Zhao, K.;Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood. PeerJ. 2019 Mar 14:7:e6520.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003ePham, T H.; Tian, X.; Zhao, H.; Li, T. \u0026amp; Lu, L. (2024). Genome-wide characterization of COMT family and regulatory role of CsCOMT19 in melatonin synthesis in Camellia sinensis.\u0026nbsp;BMC Plant Biol. 2024 Jan 16;24(1):51.\u003c/li\u003e\n \u003cli\u003eXu, J.; Liu, T.; Lin, H.; Huang, R.; Chen, M.; Fang, P.; \u0026amp; Niu, X. (2025). Comprehensive analysis of the Caffeic acid O-methyltransferase (COMT) gene family in kenaf (Hibiscus cannabinus L.) and their expression characteristics in response to salinity stress. Plant Sci.Volume 16 - 2025.\u003c/li\u003e\n \u003cli\u003eLei, D.; Chen, Y.; Li, Y.; Hu, Y.; Zhang, J.; \u0026amp; Wang, L. (2024). Genome-Wide Identification of COMT Gene Family in Maize and its Function in Response to Light. \u0026nbsp;Biochem Genet. 2025 Oct;63(5):4547-4565.\u003c/li\u003e\n \u003cli\u003eZhang, X.; Chen, B.; Wang, L.; Ali, S.; Guo, Y.; Liu, J.; Wang, J.; Xie, L.; \u0026amp; Zhang, Q. (2021). Genome-Wide Identification and Characterization of Caffeic Acid O-Methyltransferase Gene Family in Soybean. Plants (Basel). 2021 Dec 20;10(12):2816.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eLei, D.; Chen, Y.; Li, Y.; Hu, Y.; Zhang, J.; \u0026amp; Wang, L. (2024). Genome-Wide Identification of COMT Gene Family in Maize and its Function in Response to Light. Biochemical Genetics.Biochem Genet. 2025 Oct;63(5):4547-4565.\u003c/li\u003e\n \u003cli\u003eLiu, Y.; Bian, Z.; Jiang, S.; Wang, X.; Jiao, L.; Shao, Y.; Ma, C.; \u0026amp; Chu, M. (2025). Comparative Genomic Analysis of COMT Family Genes in Three Vitis Species Reveals Evolutionary Relationships and Functional Divergence.Plants (Basel). 2025 Jul 7;14(13):2079.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eLiao, Z.; Hod\u0026eacute;n, K. P.; Singh, R. K.; \u0026amp; Dixelius, C. (2020). Genome-wide identification of Argonautes in Solanaceae with emphasis on potato. Sci Rep. 2020 Nov 25;10(1):20577.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eVarr\u0026eacute;, J.-S.; D\u0026rsquo;Agostino, N.; Touzet, P.; Gallina, S.; Tamburino, R.; Cantarella, C.; Ubrig, E.; Cardi, T.; Drouard, L.; Gualberto, J. M.; \u0026amp; Scotti, N. (2019). Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome. Int J Mol Sci. 2019 Sep 26;20(19):4788.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eLiu, M.-M.; Wang, M.-M.; Yang, J.; Wen, J.; Guo, P.-C.; Wu, Y.-W.; Ke, Y.-Z.; Li, P.-F.；Li, J.-N.；\u0026nbsp;\u0026amp; Du, H. (2019). Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. Comparative Study Int J Mol Sci. 2019 Jul 23;20(14):3591.\u003c/li\u003e\n \u003cli\u003eMAGADUM, S.；BANERJEE, U.；\u0026nbsp;MURUGAN, P.；\u0026nbsp;GANGAPUR, D.；\u0026nbsp;\u0026amp; RAVIKESAVAN, R. (2013). Gene duplication as a major force in evolution. Journal of Genetics. Review J Genet. 2013 Apr;92(1):155-61.\u003c/li\u003e\n \u003cli\u003ePanchy, N.；\u0026nbsp;Lehti-Shiu, M.；\u0026nbsp;\u0026amp; Shiu, S.-H. (2016). Evolution of Gene Duplication in Plants. Plant PhysiologyReview. Plant Physiol. 2016 Aug;171(4):2294-316.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eLiu, M.-M.； Wang, M.-M.; Yang, J.; Wen, J.； Guo, P.-C.,；Wu, Y.-W.,；Ke, Y.-Z.； Li, P.-F.； Li, J.-N.；\u0026amp; Du, H. (2019). Evolutionary and Comparative Expression Analyses of TCP Transcription Factor Gene Family in Land Plants. \u0026nbsp;Int J Mol Sci. 2019 Jul 23;20(14):3591.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eChang, J.；Guo, Y.; Yan, J.;Zhang,Z.; Yuan,L .The role of watermelon caffeic acid O-methyltransferase (ClCOMT1) in melatonin biosynthesis and abiotic stress tolerance.Hortic Res. 2021 Oct 1;8(1):210.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eLi, Y.; Sun, Y.;Cui, H.; Li, M.; Yang, G.; Wang, Z.; \u0026amp; Zhang, K. (2022). Carex rigescens caffeic acid O-methyltransferase gene CrCOMT confer melatonin-mediated drought tolerance in transgenic tobacco. Frontiers in Plant Science.Front Plant Sci. 2022 Aug 10:13:971431.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eZhang, M.; Chen, X.; Wang, N.; Guan, L.; Wang, L.; Chen, X.; Yang, Z.; Sun, Y.; Fan, Y.; Meng, Y.; Liu, M.; Chen, W.; Wu, F.; Song, R.; Wang, S.; Lu, X.; Wang, J.; Guo, L.; Zhao, L. \u0026hellip; Ye, W. GhCOMT33D modulates melatonin synthesis, impacting plant response to Cd\u003csup\u003e2+\u003c/sup\u003e in cotton via ROS.Physiol Plant. 2024 Nov-Dec;176(6):e14647.\u003c/li\u003e\n \u003cli\u003eZhao, C.; Li G.; Che, H.Overexpression of COMT enhances thermotolerance by regulating lignin biosynthesis in rose. [J]Grassland and Turf.2024-03-25.2025,45(03):90-99.DOI:10.13817/j.cnki.cyycp.2025.03.010.\u003c/li\u003e\n \u003cli\u003eArnao, M.B.; et al. .Melatonin biosynthesis by tomato fruits is enhanced by red light.Journal of Pineal Research(2021)\u0026nbsp;71(3): e12743.\u003c/li\u003e\n \u003cli\u003eChen, Y.; et al. .Overexpression of COMT enhances thermotolerance by regulating lignin biosynthesis in rose. Horticulture Research(2022) 9: uhac056.\u003c/li\u003e\n \u003cli\u003eZhang, J., et al. .COMT1 overexpression enhances salt stress tolerance by promoting lignin deposition in poplar.Tree Physiology (2020)40(5): 675-690.\u003c/li\u003e\n \u003cli\u003eLiu, Q. et al. .Functional diversification of the caffeic acid O-methyltransferase gene family in plant metabolism.Trends in Plant Science (2018)23(9): 779-788.\u003c/li\u003e\n \u003cli\u003eZhang, R.; Wang, Y.; Kang, Y.; Du, Y.; Wang, X.Transcriptomics-proteomics analysis reveals StCOMT1 regulates drought, alkali and combined stresses in potato.Plant Cell Rep. 2025 Apr 29;44(5):109.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eRichard, W. Jones .Melatonin Effects on Potato Yield and Disease Resistance Assessed Through Exogenous Application and Endogenous Modification.Potato Research.29 April 2025\u003c/li\u003e\n\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":false,"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":"Potato, COMT, Plant Stress Resistance, Parallel Analysis","lastPublishedDoi":"10.21203/rs.3.rs-7918038/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7918038/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eLignin and melatonin play crucial roles in plant stress resistance, and \u003cem\u003eCOMT\u003c/em\u003e (Caffeic acid O-methyltransferase) genes are key regulators in their biosynthesis, contributing significantly to plant adaptation under adverse conditions.Although \u003cem\u003eCOMT\u003c/em\u003e genes have been characterized in multiple plant species, research in potato has so far been limited to individual genes. In this study, we present the first genome-wide identification and systematic analysis of the \u003cem\u003eCOMT\u003c/em\u003e gene family in potato. A total of 12 \u003cem\u003eStCOMT\u003c/em\u003e members were identified and comparatively analyzed with 10 Arabidopsis counterparts. These genes were predominantly distributed on one chromosome, with additional members scattered across other chromosomes.Phylogenetic analysis revealed that \u003cem\u003eCOMT\u003c/em\u003e genes are evolutionarily conserved and can be classified into five subfamilies.Partial members exhibited syntenic relationships.The encoded proteins typically displayed acidic and hydrophobic properties, formed stable dimeric structures, and were primarily localized to the chloroplast.Promoter analysis identified numerous light- and hormone-responsive elements.Expression profiling demonstrated both tissue-specific and stress-induced patterns among members.These findings indicate that \u003cem\u003eCOMT\u003c/em\u003e genes play a critical role in potato stress resistance and provide valuable genetic resources and a theoretical basis for stress-tolerant potato breeding.Further functional validation through biological experiments will be essential.\u003c/p\u003e","manuscriptTitle":"Parallel Genome-Wide Identification and Analysis of the COMT Gene Family in Potato (Solanum tuberosum L.) and Arabidopsis ( Arabidopsis thaliana (L.) Heynh.)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-11-10 13:57:17","doi":"10.21203/rs.3.rs-7918038/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-12-16T09:48:01+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-12-07T09:23:07+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"85724068674743181369466227049340193073","date":"2025-12-05T02:10:10+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"39558535614263051903939791816663959038","date":"2025-12-01T06:10:59+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-30T17:19:47+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"38698996461727829405609837789475565697","date":"2025-11-30T10:48:05+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"67984574449825989522146450854546739696","date":"2025-11-30T09:06:31+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-30T07:39:59+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"270593203705010993589051549058322440009","date":"2025-11-30T02:32:59+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"115228380280719291427565492997395290657","date":"2025-11-10T16:39:19+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-11-09T11:45:16+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"112051774210581414396615488358367886729","date":"2025-11-08T16:54:15+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"254850717911892484953987850148685634692","date":"2025-11-08T11:21:36+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"11205446844792123727945656027304606496","date":"2025-10-29T17:20:54+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-10-29T12:49:03+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-10-27T10:18:49+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-10-25T03:15:04+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-10-25T03:14:38+00:00","index":"","fulltext":""},{"type":"submitted","content":"BMC Plant Biology","date":"2025-10-21T14:11:46+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":"61ad593e-e31b-4c36-8b76-c0c261fc01b0","owner":[],"postedDate":"November 10th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-04-13T05:55:20+00:00","versionOfRecord":[],"versionCreatedAt":"2025-11-10 13:57:17","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7918038","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7918038","identity":"rs-7918038","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}