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Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.)
BACKGROUND: Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738175/ https://www.ncbi.nlm.nih.gov/pubmed/29258434 http://dx.doi.org/10.1186/s12864-017-4377-z |
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author | Wang, Jinglei Qiu, Yang Cheng, Feng Chen, Xiaohua Zhang, Xiaohui Wang, Haiping Song, Jiangping Duan, Mengmeng Yang, Haohui Li, Xixiang |
author_facet | Wang, Jinglei Qiu, Yang Cheng, Feng Chen, Xiaohua Zhang, Xiaohui Wang, Haiping Song, Jiangping Duan, Mengmeng Yang, Haohui Li, Xixiang |
author_sort | Wang, Jinglei |
collection | PubMed |
description | BACKGROUND: Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach. RESULTS: We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways. CONCLUSIONS: Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4377-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5738175 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57381752017-12-21 Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) Wang, Jinglei Qiu, Yang Cheng, Feng Chen, Xiaohua Zhang, Xiaohui Wang, Haiping Song, Jiangping Duan, Mengmeng Yang, Haohui Li, Xixiang BMC Genomics Research Article BACKGROUND: Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach. RESULTS: We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways. CONCLUSIONS: Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4377-z) contains supplementary material, which is available to authorized users. BioMed Central 2017-12-19 /pmc/articles/PMC5738175/ /pubmed/29258434 http://dx.doi.org/10.1186/s12864-017-4377-z Text en © The Author(s). 2017 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 Wang, Jinglei Qiu, Yang Cheng, Feng Chen, Xiaohua Zhang, Xiaohui Wang, Haiping Song, Jiangping Duan, Mengmeng Yang, Haohui Li, Xixiang Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
title | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
title_full | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
title_fullStr | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
title_full_unstemmed | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
title_short | Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.) |
title_sort | genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (raphanus sativus l.) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738175/ https://www.ncbi.nlm.nih.gov/pubmed/29258434 http://dx.doi.org/10.1186/s12864-017-4377-z |
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