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Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species
BACKGROUND: The BES1 gene family, an important class of plant-specific transcription factors, play key roles in the BR signal pathway in plants, regulating various development processes. Until now, there has been no comprehensive analysis of the BES1 gene family in Brassica napus, and a cross-genome...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5944053/ https://www.ncbi.nlm.nih.gov/pubmed/29743014 http://dx.doi.org/10.1186/s12864-018-4744-4 |
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author | Song, Xiaoming Ma, Xiao Li, Chunjin Hu, Jingjing Yang, Qihang Wang, Tong Wang, Li Wang, Jinpeng Guo, Di Ge, Weina Wang, Zhenyi Li, Miaomiao Wang, Qiumei Ren, Tianzeng Feng, Shuyan Wang, Lixia Zhang, Weimeng Wang, Xiyin |
author_facet | Song, Xiaoming Ma, Xiao Li, Chunjin Hu, Jingjing Yang, Qihang Wang, Tong Wang, Li Wang, Jinpeng Guo, Di Ge, Weina Wang, Zhenyi Li, Miaomiao Wang, Qiumei Ren, Tianzeng Feng, Shuyan Wang, Lixia Zhang, Weimeng Wang, Xiyin |
author_sort | Song, Xiaoming |
collection | PubMed |
description | BACKGROUND: The BES1 gene family, an important class of plant-specific transcription factors, play key roles in the BR signal pathway in plants, regulating various development processes. Until now, there has been no comprehensive analysis of the BES1 gene family in Brassica napus, and a cross-genome exploration of their origin, copy number changes, and functional innovation in plants was also not available. RESULTS: We identified 28 BES1 genes in B. napus from its two subgenomes (AA and CC). We found that 71.43% of them were duplicated in the tetraploidization, and their gene expression showed a prominent subgenome bias in the roots. Additionally, we identified 104 BES1 genes in another 18 representative angiosperms and performed a comparative analysis with B. napus, including evolutionary trajectory, gene duplication, positive selection, and expression pattern. Exploiting the available genome datasets, we performed a large-scale analysis across plants and algae suggested that the BES1 gene family could have originated from group F, expanding to form other groups (A to E) by duplicating or alternatively deleting some domains. We detected an additional domain containing M4 to M8 in exclusively groups F1 and F2. We found evidence that whole-genome duplication (WGD) contributed the most to the expansion of this gene family among examined dicots, while dispersed duplication contributed the most to expansion in certain monocots. Moreover, we inferred that positive selection might have occurred on major phylogenetic nodes during the evolution of plants. CONCLUSIONS: Grossly, a cross-genome comparative analysis of the BES1 genes in B. napus and other species sheds light on understanding its copy number expansion, natural selection, and functional innovation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4744-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5944053 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-59440532018-05-14 Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species Song, Xiaoming Ma, Xiao Li, Chunjin Hu, Jingjing Yang, Qihang Wang, Tong Wang, Li Wang, Jinpeng Guo, Di Ge, Weina Wang, Zhenyi Li, Miaomiao Wang, Qiumei Ren, Tianzeng Feng, Shuyan Wang, Lixia Zhang, Weimeng Wang, Xiyin BMC Genomics Research Article BACKGROUND: The BES1 gene family, an important class of plant-specific transcription factors, play key roles in the BR signal pathway in plants, regulating various development processes. Until now, there has been no comprehensive analysis of the BES1 gene family in Brassica napus, and a cross-genome exploration of their origin, copy number changes, and functional innovation in plants was also not available. RESULTS: We identified 28 BES1 genes in B. napus from its two subgenomes (AA and CC). We found that 71.43% of them were duplicated in the tetraploidization, and their gene expression showed a prominent subgenome bias in the roots. Additionally, we identified 104 BES1 genes in another 18 representative angiosperms and performed a comparative analysis with B. napus, including evolutionary trajectory, gene duplication, positive selection, and expression pattern. Exploiting the available genome datasets, we performed a large-scale analysis across plants and algae suggested that the BES1 gene family could have originated from group F, expanding to form other groups (A to E) by duplicating or alternatively deleting some domains. We detected an additional domain containing M4 to M8 in exclusively groups F1 and F2. We found evidence that whole-genome duplication (WGD) contributed the most to the expansion of this gene family among examined dicots, while dispersed duplication contributed the most to expansion in certain monocots. Moreover, we inferred that positive selection might have occurred on major phylogenetic nodes during the evolution of plants. CONCLUSIONS: Grossly, a cross-genome comparative analysis of the BES1 genes in B. napus and other species sheds light on understanding its copy number expansion, natural selection, and functional innovation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4744-4) contains supplementary material, which is available to authorized users. BioMed Central 2018-05-09 /pmc/articles/PMC5944053/ /pubmed/29743014 http://dx.doi.org/10.1186/s12864-018-4744-4 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 Song, Xiaoming Ma, Xiao Li, Chunjin Hu, Jingjing Yang, Qihang Wang, Tong Wang, Li Wang, Jinpeng Guo, Di Ge, Weina Wang, Zhenyi Li, Miaomiao Wang, Qiumei Ren, Tianzeng Feng, Shuyan Wang, Lixia Zhang, Weimeng Wang, Xiyin Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species |
title | Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species |
title_full | Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species |
title_fullStr | Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species |
title_full_unstemmed | Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species |
title_short | Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species |
title_sort | comprehensive analyses of the bes1 gene family in brassica napus and examination of their evolutionary pattern in representative species |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5944053/ https://www.ncbi.nlm.nih.gov/pubmed/29743014 http://dx.doi.org/10.1186/s12864-018-4744-4 |
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