Cargando…

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,...

Descripción completa

Detalles Bibliográficos
Autores principales: Cai, Caiping, Guo, Wangzhen, Zhang, Baohong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
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
_version_ 1783292747973656576
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
work_keys_str_mv AT caicaiping genomewideidentificationandcharacterizationofspltranscriptionfactorfamilyandtheirevolutionandexpressionprofilinganalysisincotton
AT guowangzhen genomewideidentificationandcharacterizationofspltranscriptionfactorfamilyandtheirevolutionandexpressionprofilinganalysisincotton
AT zhangbaohong genomewideidentificationandcharacterizationofspltranscriptionfactorfamilyandtheirevolutionandexpressionprofilinganalysisincotton