Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton
Abstract Background Transcription factors operate as important switches of transcription networks, and NAC (NAM, ATAF, and CUC) transcription factors are a plant-specific family involved in multiple biological processes. However, this gene family has not been systematically characterized in cotton....
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-07-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-018-1367-5 |
| _version_ | 1819019412191051776 |
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| author | Heng Sun Meiling Hu Jianying Li Lin Chen Meng Li Shuqin Zhang Xianlong Zhang Xiyan Yang |
| author_facet | Heng Sun Meiling Hu Jianying Li Lin Chen Meng Li Shuqin Zhang Xianlong Zhang Xiyan Yang |
| author_sort | Heng Sun |
| collection | DOAJ |
| description | Abstract Background Transcription factors operate as important switches of transcription networks, and NAC (NAM, ATAF, and CUC) transcription factors are a plant-specific family involved in multiple biological processes. However, this gene family has not been systematically characterized in cotton. Results Here we identify a large number of genes with conservative NAC domains in four cotton species, with 147 found in Gossypium arboreum, 149 in G. raimondii, 267 in G. barbadense and 283 in G. hirsutum. Predicted membrane-bound NAC genes were also identified. Phylogenetic analysis showed that cotton NAC proteins clustered into seven subfamilies and homologous protein pairs showed similar characteristics. Evolutionary property analysis revealed that purifying selection of NAC genes occurred between diploid and polyploid cotton species, and variation analysis showed GhNAC genes may have been subjected to selection and domestication. NAC proteins showed extensive transactivation and this was dependent on the C-terminus. Some development and stress related cis-elements were enriched in the promoters of GhNAC genes. Comprehensive expression analysis indicated that 38 GhNAC genes were candidates for involvement in fiber development, and 120 in stress responses. Gene co-expression network analysis revealed relationships between fiber-associated NAC genes and secondary cell wall (SCW) biosynthesis genes. Conclusions NAC genes were identified in diploid and tetraploid cotton, revealing new insights into their evolution, variation and homology relationships. Transcriptome analysis and co-expression network indicated roles for GhNAC genes in cotton fiber development and stress response, and NAC genes may prove useful in molecular breeding programmes. |
| first_indexed | 2024-12-21T03:34:54Z |
| format | Article |
| id | doaj.art-87b11ee5b32c4dab9ce3bd569313f6fa |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-21T03:34:54Z |
| publishDate | 2018-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-87b11ee5b32c4dab9ce3bd569313f6fa2022-12-21T19:17:22ZengBMCBMC Plant Biology1471-22292018-07-0118111510.1186/s12870-018-1367-5Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cottonHeng Sun0Meiling Hu1Jianying Li2Lin Chen3Meng Li4Shuqin Zhang5Xianlong Zhang6Xiyan Yang7National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityAbstract Background Transcription factors operate as important switches of transcription networks, and NAC (NAM, ATAF, and CUC) transcription factors are a plant-specific family involved in multiple biological processes. However, this gene family has not been systematically characterized in cotton. Results Here we identify a large number of genes with conservative NAC domains in four cotton species, with 147 found in Gossypium arboreum, 149 in G. raimondii, 267 in G. barbadense and 283 in G. hirsutum. Predicted membrane-bound NAC genes were also identified. Phylogenetic analysis showed that cotton NAC proteins clustered into seven subfamilies and homologous protein pairs showed similar characteristics. Evolutionary property analysis revealed that purifying selection of NAC genes occurred between diploid and polyploid cotton species, and variation analysis showed GhNAC genes may have been subjected to selection and domestication. NAC proteins showed extensive transactivation and this was dependent on the C-terminus. Some development and stress related cis-elements were enriched in the promoters of GhNAC genes. Comprehensive expression analysis indicated that 38 GhNAC genes were candidates for involvement in fiber development, and 120 in stress responses. Gene co-expression network analysis revealed relationships between fiber-associated NAC genes and secondary cell wall (SCW) biosynthesis genes. Conclusions NAC genes were identified in diploid and tetraploid cotton, revealing new insights into their evolution, variation and homology relationships. Transcriptome analysis and co-expression network indicated roles for GhNAC genes in cotton fiber development and stress response, and NAC genes may prove useful in molecular breeding programmes.http://link.springer.com/article/10.1186/s12870-018-1367-5CottonNACEvolutionary analysisTransactivationFiber developmentStress response |
| spellingShingle | Heng Sun Meiling Hu Jianying Li Lin Chen Meng Li Shuqin Zhang Xianlong Zhang Xiyan Yang Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton BMC Plant Biology Cotton NAC Evolutionary analysis Transactivation Fiber development Stress response |
| title | Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton |
| title_full | Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton |
| title_fullStr | Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton |
| title_full_unstemmed | Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton |
| title_short | Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton |
| title_sort | comprehensive analysis of nac transcription factors uncovers their roles during fiber development and stress response in cotton |
| topic | Cotton NAC Evolutionary analysis Transactivation Fiber development Stress response |
| url | http://link.springer.com/article/10.1186/s12870-018-1367-5 |
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