Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood
Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuab...
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| Format: | Article |
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PeerJ Inc.
2019-03-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/6520.pdf |
| _version_ | 1827606078995562496 |
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| author | Nan Lu Wenjun Ma Donghua Han Ying Liu Zhi Wang Nan Wang Guijuan Yang Guanzheng Qu Qiuxia Wang Kun Zhao Junhui Wang |
| author_facet | Nan Lu Wenjun Ma Donghua Han Ying Liu Zhi Wang Nan Wang Guijuan Yang Guanzheng Qu Qiuxia Wang Kun Zhao Junhui Wang |
| author_sort | Nan Lu |
| collection | DOAJ |
| description | Caffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research. |
| first_indexed | 2024-03-09T06:32:59Z |
| format | Article |
| id | doaj.art-653383cfd8c94b18a441e85944b87a24 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:32:59Z |
| publishDate | 2019-03-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj.art-653383cfd8c94b18a441e85944b87a242023-12-03T11:03:03ZengPeerJ Inc.PeerJ2167-83592019-03-017e652010.7717/peerj.6520Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite woodNan Lu0Wenjun Ma1Donghua Han2Ying Liu3Zhi Wang4Nan Wang5Guijuan Yang6Guanzheng Qu7Qiuxia Wang8Kun Zhao9Junhui Wang10State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaCollege of Landscape Architecture, Nanjing Forestry University, Nanjing, ChinaCollege of Forestry, Northwest A&F University, Yangling, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, ChinaNanyang Research Institute of Forestry, Nanyang, ChinaLuoyang Academy of Agriculture and Forestry, Luoyang, ChinaState Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaCaffeic acid O-methyltransferase (COMT) is an important protein that participates in lignin synthesis and is associated with the ratio of G-/S-type lignin in plants. COMTs are associated with the wood properties of forest trees; however, little known about the COMT family in Catalpa bungei, a valuable timber tree species in China . We performed a comprehensive analysis of COMT genes in the C. bungei genome by describing the gene structure and phylogenetic relationships of each family member using bioinformatics-based methods. A total of 23 putative COMT genes were identified using the conserved domain sequences and amino acid sequences of COMTs from Arabidopsis thaliana and Populus trichocarpa as probes. Phylogenetic analysis showed that 23 CbuCOMTs can be divided into three groups based on their structural characteristics; five conserved domains were found in the COMT family. Promoter analysis indicated that the CbuCOMT promoters included various cis-acting elements related to growth and development. Real-time quantitative polymerase chain reaction (PCR) analysis showed differential expression among CbuCOMTs. CbuCOMT2, 7, 8, 9, 10, 12, 13, 14, 21, and 23 were mainly expressed in xylem. Only CbuCOMT23 was significantly downregulated in tension wood and upregulated in opposite wood compared to normal wood. Our study provides new information about the CbuCOMT gene family and will facilitate functional characterisation in further research.https://peerj.com/articles/6520.pdfTension woodCatalpa bungeiGenome-wideCOMTs |
| spellingShingle | Nan Lu Wenjun Ma Donghua Han Ying Liu Zhi Wang Nan Wang Guijuan Yang Guanzheng Qu Qiuxia Wang Kun Zhao Junhui Wang 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 Tension wood Catalpa bungei Genome-wide COMTs |
| title | Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood |
| title_full | Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood |
| title_fullStr | Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood |
| title_full_unstemmed | Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood |
| title_short | Genome-wide analysis of the Catalpa bungei caffeic acid O-methyltransferase (COMT) gene family: identification and expression profiles in normal, tension, and opposite wood |
| title_sort | genome wide analysis of the catalpa bungei caffeic acid o methyltransferase comt gene family identification and expression profiles in normal tension and opposite wood |
| topic | Tension wood Catalpa bungei Genome-wide COMTs |
| url | https://peerj.com/articles/6520.pdf |
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