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Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton
Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177 SPL genes were identified, including 29, 30, 59 and 59 SPLs in Gossypium arboreum,...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768680/ https://www.ncbi.nlm.nih.gov/pubmed/29335584 http://dx.doi.org/10.1038/s41598-017-18673-4 |
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author | Cai, Caiping Guo, Wangzhen Zhang, Baohong |
author_facet | Cai, Caiping Guo, Wangzhen Zhang, Baohong |
author_sort | Cai, Caiping |
collection | PubMed |
description | Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177 SPL genes were identified, including 29, 30, 59 and 59 SPLs in Gossypium arboreum, G. raimondii, G. barbadense, and G. hirsutum, respectively. These SPL genes were classified into eight phylogenetical groups. The gene structure, conserved motif, and clustering were highly conserved within each orthologs. Two zinc finger-like structures (Cys3His and Cys2HisCys) and NLS segments were existed in all GrSPLs. Segmental duplications play important roles in SPL family expansion, with 20 genes involved in segmental duplications and 2 in tandem duplications, and ten ortholog pairs in syntenic regions between G. raimondii and A. thaliana. Several putative cis-elements, involved in light, stresses and phytohormones response, were found in the promoter regions of GhSPLs, suggesting that plant responses to those environmental changes may be induced through targeting SPL transcription factors. RNA-seq analysis shows that SPL genes were differentially expressed in cotton; some were highly expressed during fiber initiation and early development. Comparing with other plants, SPL genes show subfunctionalization, lost and/or gain functions in cotton during long-term domestication and evolution. |
format | Online Article Text |
id | pubmed-5768680 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-57686802018-01-25 Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton Cai, Caiping Guo, Wangzhen Zhang, Baohong Sci Rep Article Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177 SPL genes were identified, including 29, 30, 59 and 59 SPLs in Gossypium arboreum, G. raimondii, G. barbadense, and G. hirsutum, respectively. These SPL genes were classified into eight phylogenetical groups. The gene structure, conserved motif, and clustering were highly conserved within each orthologs. Two zinc finger-like structures (Cys3His and Cys2HisCys) and NLS segments were existed in all GrSPLs. Segmental duplications play important roles in SPL family expansion, with 20 genes involved in segmental duplications and 2 in tandem duplications, and ten ortholog pairs in syntenic regions between G. raimondii and A. thaliana. Several putative cis-elements, involved in light, stresses and phytohormones response, were found in the promoter regions of GhSPLs, suggesting that plant responses to those environmental changes may be induced through targeting SPL transcription factors. RNA-seq analysis shows that SPL genes were differentially expressed in cotton; some were highly expressed during fiber initiation and early development. Comparing with other plants, SPL genes show subfunctionalization, lost and/or gain functions in cotton during long-term domestication and evolution. Nature Publishing Group UK 2018-01-15 /pmc/articles/PMC5768680/ /pubmed/29335584 http://dx.doi.org/10.1038/s41598-017-18673-4 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Cai, Caiping Guo, Wangzhen Zhang, Baohong Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton |
title | Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton |
title_full | Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton |
title_fullStr | Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton |
title_full_unstemmed | Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton |
title_short | Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton |
title_sort | genome-wide identification and characterization of spl transcription factor family and their evolution and expression profiling analysis in cotton |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768680/ https://www.ncbi.nlm.nih.gov/pubmed/29335584 http://dx.doi.org/10.1038/s41598-017-18673-4 |
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