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Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean
BACKGROUND: Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases in plant. A number of reports have demonstrated that plant LRR-RLKs play important roles in growth, development, differentiation, and stress responses. However, no comprehensive...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776374/ https://www.ncbi.nlm.nih.gov/pubmed/26935840 http://dx.doi.org/10.1186/s12870-016-0744-1 |
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author | Zhou, Fulai Guo, Yong Qiu, Li-Juan |
author_facet | Zhou, Fulai Guo, Yong Qiu, Li-Juan |
author_sort | Zhou, Fulai |
collection | PubMed |
description | BACKGROUND: Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases in plant. A number of reports have demonstrated that plant LRR-RLKs play important roles in growth, development, differentiation, and stress responses. However, no comprehensive analysis of this gene family has been carried out in legume species. RESULTS: Based on the principles of sequence similarity and domain conservation, a total of 467 LRR-RLK genes were identified in soybean genome. The GmLRR-RLKs are non-randomly distributed across all 20 chromosomes of soybean and about 73.3 % of them are located in segmental duplicated regions. The analysis of synonymous substitutions for putative paralogous gene pairs indicated that most of these gene pairs resulted from segmental duplications in soybean genome. Furthermore, the exon/intron organization, motif composition and arrangements were considerably conserved among members of the same groups or subgroups in the constructed phylogenetic tree. The close phylogenetic relationship between soybean LRR-RLK genes with identified Arabidopsis genes in the same group also provided insight into their putative functions. Expression profiling analysis of GmLRR-RLKs suggested that they appeared to be differentially expressed among different tissues and some of duplicated genes exhibited divergent expression patterns. In addition, artificial selected GmLRR-RLKs were also identified by comparing the SNPs between wild and cultivated soybeans and 17 genes were detected in regions previously reported to contain domestication-related QTLs. CONCLUSIONS: Comprehensive and evolutionary analysis of soybean LRR-RLK gene family was performed at whole genome level. The data provides valuable tools in future efforts to identify functional divergence of this gene family and gene diversity among different genotypes in legume species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0744-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4776374 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-47763742016-03-04 Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean Zhou, Fulai Guo, Yong Qiu, Li-Juan BMC Plant Biol Research Article BACKGROUND: Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases in plant. A number of reports have demonstrated that plant LRR-RLKs play important roles in growth, development, differentiation, and stress responses. However, no comprehensive analysis of this gene family has been carried out in legume species. RESULTS: Based on the principles of sequence similarity and domain conservation, a total of 467 LRR-RLK genes were identified in soybean genome. The GmLRR-RLKs are non-randomly distributed across all 20 chromosomes of soybean and about 73.3 % of them are located in segmental duplicated regions. The analysis of synonymous substitutions for putative paralogous gene pairs indicated that most of these gene pairs resulted from segmental duplications in soybean genome. Furthermore, the exon/intron organization, motif composition and arrangements were considerably conserved among members of the same groups or subgroups in the constructed phylogenetic tree. The close phylogenetic relationship between soybean LRR-RLK genes with identified Arabidopsis genes in the same group also provided insight into their putative functions. Expression profiling analysis of GmLRR-RLKs suggested that they appeared to be differentially expressed among different tissues and some of duplicated genes exhibited divergent expression patterns. In addition, artificial selected GmLRR-RLKs were also identified by comparing the SNPs between wild and cultivated soybeans and 17 genes were detected in regions previously reported to contain domestication-related QTLs. CONCLUSIONS: Comprehensive and evolutionary analysis of soybean LRR-RLK gene family was performed at whole genome level. The data provides valuable tools in future efforts to identify functional divergence of this gene family and gene diversity among different genotypes in legume species. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0744-1) contains supplementary material, which is available to authorized users. BioMed Central 2016-03-02 /pmc/articles/PMC4776374/ /pubmed/26935840 http://dx.doi.org/10.1186/s12870-016-0744-1 Text en © Zhou et al. 2016 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 Zhou, Fulai Guo, Yong Qiu, Li-Juan Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean |
title | Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean |
title_full | Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean |
title_fullStr | Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean |
title_full_unstemmed | Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean |
title_short | Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean |
title_sort | genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776374/ https://www.ncbi.nlm.nih.gov/pubmed/26935840 http://dx.doi.org/10.1186/s12870-016-0744-1 |
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