Genome-Wide Identification and Characterization of <i>TCP</i> Gene Family Members in <i>Melastoma candidum</i>
It has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (<i>TCP</i>) gene family plays a pivotal role during plant growth and development. <i>M. candidum</i> is a native ornamental species and has a wide range of pharmacodynamic effects. Howe...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-12-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/27/24/9036 |
| _version_ | 1827637570256764928 |
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| author | Hui Li Xiaoxia Wen Xiong Huang Mingke Wei Hongpeng Chen Yixun Yu Seping Dai |
| author_facet | Hui Li Xiaoxia Wen Xiong Huang Mingke Wei Hongpeng Chen Yixun Yu Seping Dai |
| author_sort | Hui Li |
| collection | DOAJ |
| description | It has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (<i>TCP</i>) gene family plays a pivotal role during plant growth and development. <i>M. candidum</i> is a native ornamental species and has a wide range of pharmacodynamic effects. However, there is still a lack of research on <i>TCP</i>’s role in controlling <i>M</i>. <i>candidum</i>’s development, abiotic stress responses and hormone metabolism. A comprehensive description of the <i>TCP</i> gene family in <i>M</i>. <i>candidum</i> is urgently needed. In this study, we used the HMMER search method in conjunction with the BLASTp method to identify the members of the <i>TCP</i> gene family, and a total of 35 <i>TCP</i> genes were identified. A domain analysis further confirmed that all 35 TCPs contained a TCP superfamily, a characteristic involved in dimerization and DNA binding that can be found in most genes from this gene family, suggesting that our identification was effective. As a result of the domain conservation analysis, the 35 <i>TCP</i> genes could be classified into two classes, TCP-P and TCP-C, based on the conservative regions of 55 and 59 amino acids, respectively. Gene-duplication analysis revealed that most <i>TCP</i> genes were present in duplication events that eventually led to <i>TCP</i> gene expansion in <i>M. candidum</i>. All the detected gene pairs had a Ka/Ks value of less than one, suggesting that purification selection is the most important factor that influences the evolution of <i>TCP</i> genes. Phylogenetic analysis of three species displayed the evolutionary relationship of <i>TCP</i> genes across different species and further confirmed our results. The real-time quantitative PCR (qRT-PCR) results showed that <i>McTCP2a</i>, <i>McTCP7a</i>, <i>McTCP10</i>, <i>McTCP11</i>, <i>McTCP12a</i>, <i>McTCP13</i>, <i>McTCP16</i>, <i>McTCP17</i>, <i>McTCP18</i>, <i>McTCP20</i> and <i>McTCP21</i> may be involved in leaf development; <i>McTCP4a</i>, <i>McTCP1</i>, <i>McTCP14</i>, <i>McTCP17</i>, <i>McTCP18</i>, <i>McTCP20, McTCP22</i> and <i>McTCP24</i> may be involved in flower development; and <i>McTCP2a</i>, <i>McTCP3</i>, <i>McTCP5a</i>, <i>McTCP6</i>, <i>McTCP7a</i>, <i>McTCP9</i>, <i>McTCP11</i>, <i>McTCP14</i> and <i>McTCP16</i> may be involved in seed development. Our results dissect the <i>TCP</i> gene family across the genome of <i>M</i>. <i>candidum</i> and provide valuable information for exploring <i>TCP</i> genes to promote molecular breeding and property improvement of <i>M</i>. <i>candidum</i> in the future. |
| first_indexed | 2024-03-09T16:02:47Z |
| format | Article |
| id | doaj.art-f478d053c8ea4529a3f654fa2c072fc8 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T16:02:47Z |
| publishDate | 2022-12-01 |
| publisher | MDPI AG |
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| series | Molecules |
| spelling | doaj.art-f478d053c8ea4529a3f654fa2c072fc82023-11-24T17:01:43ZengMDPI AGMolecules1420-30492022-12-012724903610.3390/molecules27249036Genome-Wide Identification and Characterization of <i>TCP</i> Gene Family Members in <i>Melastoma candidum</i>Hui Li0Xiaoxia Wen1Xiong Huang2Mingke Wei3Hongpeng Chen4Yixun Yu5Seping Dai6Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, ChinaFaculty of Electronic Information Engineering, Guangdong Baiyun University, Guangzhou 510450, ChinaCollege of Forestry, Sichuan Agricultural University, Chengdu 611130, ChinaState Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, ChinaSchool of Traditional Chinese Medicinal Resources, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaCollege of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaGuangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, ChinaIt has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (<i>TCP</i>) gene family plays a pivotal role during plant growth and development. <i>M. candidum</i> is a native ornamental species and has a wide range of pharmacodynamic effects. However, there is still a lack of research on <i>TCP</i>’s role in controlling <i>M</i>. <i>candidum</i>’s development, abiotic stress responses and hormone metabolism. A comprehensive description of the <i>TCP</i> gene family in <i>M</i>. <i>candidum</i> is urgently needed. In this study, we used the HMMER search method in conjunction with the BLASTp method to identify the members of the <i>TCP</i> gene family, and a total of 35 <i>TCP</i> genes were identified. A domain analysis further confirmed that all 35 TCPs contained a TCP superfamily, a characteristic involved in dimerization and DNA binding that can be found in most genes from this gene family, suggesting that our identification was effective. As a result of the domain conservation analysis, the 35 <i>TCP</i> genes could be classified into two classes, TCP-P and TCP-C, based on the conservative regions of 55 and 59 amino acids, respectively. Gene-duplication analysis revealed that most <i>TCP</i> genes were present in duplication events that eventually led to <i>TCP</i> gene expansion in <i>M. candidum</i>. All the detected gene pairs had a Ka/Ks value of less than one, suggesting that purification selection is the most important factor that influences the evolution of <i>TCP</i> genes. Phylogenetic analysis of three species displayed the evolutionary relationship of <i>TCP</i> genes across different species and further confirmed our results. The real-time quantitative PCR (qRT-PCR) results showed that <i>McTCP2a</i>, <i>McTCP7a</i>, <i>McTCP10</i>, <i>McTCP11</i>, <i>McTCP12a</i>, <i>McTCP13</i>, <i>McTCP16</i>, <i>McTCP17</i>, <i>McTCP18</i>, <i>McTCP20</i> and <i>McTCP21</i> may be involved in leaf development; <i>McTCP4a</i>, <i>McTCP1</i>, <i>McTCP14</i>, <i>McTCP17</i>, <i>McTCP18</i>, <i>McTCP20, McTCP22</i> and <i>McTCP24</i> may be involved in flower development; and <i>McTCP2a</i>, <i>McTCP3</i>, <i>McTCP5a</i>, <i>McTCP6</i>, <i>McTCP7a</i>, <i>McTCP9</i>, <i>McTCP11</i>, <i>McTCP14</i> and <i>McTCP16</i> may be involved in seed development. Our results dissect the <i>TCP</i> gene family across the genome of <i>M</i>. <i>candidum</i> and provide valuable information for exploring <i>TCP</i> genes to promote molecular breeding and property improvement of <i>M</i>. <i>candidum</i> in the future.https://www.mdpi.com/1420-3049/27/24/9036<i>TCP</i> gene familyphylogenetic analysiscollinearity analysisgene pairs<i>Melastoma candidum</i> |
| spellingShingle | Hui Li Xiaoxia Wen Xiong Huang Mingke Wei Hongpeng Chen Yixun Yu Seping Dai Genome-Wide Identification and Characterization of <i>TCP</i> Gene Family Members in <i>Melastoma candidum</i> Molecules <i>TCP</i> gene family phylogenetic analysis collinearity analysis gene pairs <i>Melastoma candidum</i> |
| title | Genome-Wide Identification and Characterization of <i>TCP</i> Gene Family Members in <i>Melastoma candidum</i> |
| title_full | Genome-Wide Identification and Characterization of <i>TCP</i> Gene Family Members in <i>Melastoma candidum</i> |
| title_fullStr | Genome-Wide Identification and Characterization of <i>TCP</i> Gene Family Members in <i>Melastoma candidum</i> |
| title_full_unstemmed | Genome-Wide Identification and Characterization of <i>TCP</i> Gene Family Members in <i>Melastoma candidum</i> |
| title_short | Genome-Wide Identification and Characterization of <i>TCP</i> Gene Family Members in <i>Melastoma candidum</i> |
| title_sort | genome wide identification and characterization of i tcp i gene family members in i melastoma candidum i |
| topic | <i>TCP</i> gene family phylogenetic analysis collinearity analysis gene pairs <i>Melastoma candidum</i> |
| url | https://www.mdpi.com/1420-3049/27/24/9036 |
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