Comparative Genomic Analysis of COMT Family Genes in Three <i>Vitis</i> Species Reveals Evolutionary Relationships and Functional Divergence
Caffeic acid-O-methyltransferase (COMT) is a key enzyme in lignin synthesis and secondary metabolism in plants, and it participates in the regulation of plant growth and development as well as plants’ stress response. To further investigate the function of COMT in grapevine, a total of 124 <i>...
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2025-07-01
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| author | Yashi Liu Zhiyuan Bian Shan Jiang Xiao Wang Lin Jiao Yun Shao Chengmei Ma Mingyu Chu |
| author_facet | Yashi Liu Zhiyuan Bian Shan Jiang Xiao Wang Lin Jiao Yun Shao Chengmei Ma Mingyu Chu |
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| description | Caffeic acid-O-methyltransferase (COMT) is a key enzyme in lignin synthesis and secondary metabolism in plants, and it participates in the regulation of plant growth and development as well as plants’ stress response. To further investigate the function of COMT in grapevine, a total of 124 <i>COMT</i> family genes were identified from three <i>Vitis</i> species in this study, namely Pinot noir (<i>Vitis vinifera</i> L.), <i>Vitis amurensis</i>, and <i>Vitis riparia</i>. The amino acid sequence encoded by these genes ranged from 55 to 1422 aa, and their molecular mass ranged from 6640.82 to 77,034.43 Da. Subcellular localization prediction inferred that they were mainly located in the plasma membrane and cytoplasm. The prediction of secondary structures showed that α-helix and irregular coiled-coil were primary structural elements. These genes were unevenly distributed across 10 different chromosomes, respectively. Phylogenetic tree analysis of the amino acid sequences of VvCOMT, VaCOMT, VrCOMT, and AtCOMT proteins showed that they were closely related and were divided into four subgroups. The motif distribution was similar among the cluster genes, and the gene sequence was notably conserved. The 124 members of the COMT gene family possessed a variable number of exons, ranging from 2 to 13. The promoter region of all of these <i>COMTs</i> genes contained multiple cis-acting elements related to hormones (e.g., ABA, IAA, MeJA, GA, and SA), growth and development (e.g., endosperm, circadian, meristem, light response), and various stress responses (e.g., drought, low temperature, wounding, anaerobic, defense, and stress). The intraspecies collinearity analysis suggested that there were one pair, three pairs, and six pairs of collinear genes in <i>Va</i>, Pinot noir, and <i>Vr</i>, respectively, and that tandem duplication contributed more to the expansion of these gene family members. In addition, interspecific collinearity revealed that the <i>VvCOMTs</i> had the strongest homology with the <i>VaCOMTs,</i> followed by the <i>VrCOMTs</i>, and the weakest homology with the <i>AtCOMTs</i>. The expression patterns of different tissues and organs at different developmental stages indicated that the <i>VvCOMT</i> genes had obvious tissue expression specificity. The majority of <i>VvCOMT</i> genes were only expressed at higher levels in certain tissues. Furthermore, we screened 13 <i>VvCOMT</i> genes to conduct qRT-PCR verification according to the transcriptome data of <i>VvCOMTs</i> under abiotic stresses (NaCl, PEG, and cold). The results confirmed that these genes were involved in the responses to NaCl, PEG, and cold stress. This study lays a foundation for the exploration of the function of the COMT genes, and is of great importance for the genetic improvement of abiotic stress resistance in grapes. |
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| spelling | doaj-art-249cbc15bb344c2792c9f97b5ffa4f8f2025-08-20T02:36:23ZengMDPI AGPlants2223-77472025-07-011413207910.3390/plants14132079Comparative Genomic Analysis of COMT Family Genes in Three <i>Vitis</i> Species Reveals Evolutionary Relationships and Functional DivergenceYashi Liu0Zhiyuan Bian1Shan Jiang2Xiao Wang3Lin Jiao4Yun Shao5Chengmei Ma6Mingyu Chu7College of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCollege of Horticulture, Gansu Agricultural University, Lanzhou 730070, ChinaCaffeic acid-O-methyltransferase (COMT) is a key enzyme in lignin synthesis and secondary metabolism in plants, and it participates in the regulation of plant growth and development as well as plants’ stress response. To further investigate the function of COMT in grapevine, a total of 124 <i>COMT</i> family genes were identified from three <i>Vitis</i> species in this study, namely Pinot noir (<i>Vitis vinifera</i> L.), <i>Vitis amurensis</i>, and <i>Vitis riparia</i>. The amino acid sequence encoded by these genes ranged from 55 to 1422 aa, and their molecular mass ranged from 6640.82 to 77,034.43 Da. Subcellular localization prediction inferred that they were mainly located in the plasma membrane and cytoplasm. The prediction of secondary structures showed that α-helix and irregular coiled-coil were primary structural elements. These genes were unevenly distributed across 10 different chromosomes, respectively. Phylogenetic tree analysis of the amino acid sequences of VvCOMT, VaCOMT, VrCOMT, and AtCOMT proteins showed that they were closely related and were divided into four subgroups. The motif distribution was similar among the cluster genes, and the gene sequence was notably conserved. The 124 members of the COMT gene family possessed a variable number of exons, ranging from 2 to 13. The promoter region of all of these <i>COMTs</i> genes contained multiple cis-acting elements related to hormones (e.g., ABA, IAA, MeJA, GA, and SA), growth and development (e.g., endosperm, circadian, meristem, light response), and various stress responses (e.g., drought, low temperature, wounding, anaerobic, defense, and stress). The intraspecies collinearity analysis suggested that there were one pair, three pairs, and six pairs of collinear genes in <i>Va</i>, Pinot noir, and <i>Vr</i>, respectively, and that tandem duplication contributed more to the expansion of these gene family members. In addition, interspecific collinearity revealed that the <i>VvCOMTs</i> had the strongest homology with the <i>VaCOMTs,</i> followed by the <i>VrCOMTs</i>, and the weakest homology with the <i>AtCOMTs</i>. The expression patterns of different tissues and organs at different developmental stages indicated that the <i>VvCOMT</i> genes had obvious tissue expression specificity. The majority of <i>VvCOMT</i> genes were only expressed at higher levels in certain tissues. Furthermore, we screened 13 <i>VvCOMT</i> genes to conduct qRT-PCR verification according to the transcriptome data of <i>VvCOMTs</i> under abiotic stresses (NaCl, PEG, and cold). The results confirmed that these genes were involved in the responses to NaCl, PEG, and cold stress. This study lays a foundation for the exploration of the function of the COMT genes, and is of great importance for the genetic improvement of abiotic stress resistance in grapes.https://www.mdpi.com/2223-7747/14/13/2079grapevinethree <i>Vitis</i> speciesCOMT gene familyabiotic stressexpression pattern |
| spellingShingle | Yashi Liu Zhiyuan Bian Shan Jiang Xiao Wang Lin Jiao Yun Shao Chengmei Ma Mingyu Chu Comparative Genomic Analysis of COMT Family Genes in Three <i>Vitis</i> Species Reveals Evolutionary Relationships and Functional Divergence Plants grapevine three <i>Vitis</i> species COMT gene family abiotic stress expression pattern |
| title | Comparative Genomic Analysis of COMT Family Genes in Three <i>Vitis</i> Species Reveals Evolutionary Relationships and Functional Divergence |
| title_full | Comparative Genomic Analysis of COMT Family Genes in Three <i>Vitis</i> Species Reveals Evolutionary Relationships and Functional Divergence |
| title_fullStr | Comparative Genomic Analysis of COMT Family Genes in Three <i>Vitis</i> Species Reveals Evolutionary Relationships and Functional Divergence |
| title_full_unstemmed | Comparative Genomic Analysis of COMT Family Genes in Three <i>Vitis</i> Species Reveals Evolutionary Relationships and Functional Divergence |
| title_short | Comparative Genomic Analysis of COMT Family Genes in Three <i>Vitis</i> Species Reveals Evolutionary Relationships and Functional Divergence |
| title_sort | comparative genomic analysis of comt family genes in three i vitis i species reveals evolutionary relationships and functional divergence |
| topic | grapevine three <i>Vitis</i> species COMT gene family abiotic stress expression pattern |
| url | https://www.mdpi.com/2223-7747/14/13/2079 |
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