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Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton

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:...

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Autores principales: Sun, Heng, Hu, Meiling, Li, Jianying, Chen, Lin, Li, Meng, Zhang, Shuqin, Zhang, Xianlong, Yang, Xiyan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057059/
https://www.ncbi.nlm.nih.gov/pubmed/30041622
http://dx.doi.org/10.1186/s12870-018-1367-5
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author Sun, Heng
Hu, Meiling
Li, Jianying
Chen, Lin
Li, Meng
Zhang, Shuqin
Zhang, Xianlong
Yang, Xiyan
author_facet Sun, Heng
Hu, Meiling
Li, Jianying
Chen, Lin
Li, Meng
Zhang, Shuqin
Zhang, Xianlong
Yang, Xiyan
author_sort Sun, Heng
collection PubMed
description 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-018-1367-5) contains supplementary material, which is available to authorized users.
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spelling pubmed-60570592018-07-30 Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton Sun, Heng Hu, Meiling Li, Jianying Chen, Lin Li, Meng Zhang, Shuqin Zhang, Xianlong Yang, Xiyan BMC Plant Biol Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-018-1367-5) contains supplementary material, which is available to authorized users. BioMed Central 2018-07-24 /pmc/articles/PMC6057059/ /pubmed/30041622 http://dx.doi.org/10.1186/s12870-018-1367-5 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Sun, Heng
Hu, Meiling
Li, Jianying
Chen, Lin
Li, Meng
Zhang, Shuqin
Zhang, Xianlong
Yang, Xiyan
Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton
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 Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6057059/
https://www.ncbi.nlm.nih.gov/pubmed/30041622
http://dx.doi.org/10.1186/s12870-018-1367-5
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