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Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases

LRR-kinases constitute the largest subfamily of receptor-like kinases in plants and regulate a wide variety of processes related to development and defense. Through a reiterative process of sequence analysis and re-annotation, we identified 309 LRR-kinase genes in the rice genome (Nipponbare). Among...

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Autores principales: Sun, Xinli, Wang, Guo-Liang
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3050792/
https://www.ncbi.nlm.nih.gov/pubmed/21408199
http://dx.doi.org/10.1371/journal.pone.0016079
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author Sun, Xinli
Wang, Guo-Liang
author_facet Sun, Xinli
Wang, Guo-Liang
author_sort Sun, Xinli
collection PubMed
description LRR-kinases constitute the largest subfamily of receptor-like kinases in plants and regulate a wide variety of processes related to development and defense. Through a reiterative process of sequence analysis and re-annotation, we identified 309 LRR-kinase genes in the rice genome (Nipponbare). Among them, 127 genes in the Rice Annotation Project Database and 85 in Refseq of NCBI were amended (in addition, 62 LRR-kinase genes were not annotated in Refseq). The complete set of LRR-kinases was characterized. These LRR-kinases were classified into five groups according to phylogenetic analysis, and the genes in groups 1, 2, 3 and 4 usually have fewer introns than those in group 5. The introns in the LRR domain, which are highly conserved in regards to their positions and configurations, split the first Leu or other amino residues at this position of the ‘xxLxLxx’ motif with phase 2 and usually separate one or more LRR repeats exactly. Tandemly repeated LRR motifs have evolved from exon duplication, mutation and exon shuffling. The extensive distribution and diversity of the LRR-kinase genes have been mainly generated by tandem duplication and mutation after whole genome duplication. Positive selection has made a limited contribution to the sequence diversity after duplication, but positively selected sites located in the LRR domain are thought to involve in the protein-protein interaction.
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spelling pubmed-30507922011-03-15 Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases Sun, Xinli Wang, Guo-Liang PLoS One Research Article LRR-kinases constitute the largest subfamily of receptor-like kinases in plants and regulate a wide variety of processes related to development and defense. Through a reiterative process of sequence analysis and re-annotation, we identified 309 LRR-kinase genes in the rice genome (Nipponbare). Among them, 127 genes in the Rice Annotation Project Database and 85 in Refseq of NCBI were amended (in addition, 62 LRR-kinase genes were not annotated in Refseq). The complete set of LRR-kinases was characterized. These LRR-kinases were classified into five groups according to phylogenetic analysis, and the genes in groups 1, 2, 3 and 4 usually have fewer introns than those in group 5. The introns in the LRR domain, which are highly conserved in regards to their positions and configurations, split the first Leu or other amino residues at this position of the ‘xxLxLxx’ motif with phase 2 and usually separate one or more LRR repeats exactly. Tandemly repeated LRR motifs have evolved from exon duplication, mutation and exon shuffling. The extensive distribution and diversity of the LRR-kinase genes have been mainly generated by tandem duplication and mutation after whole genome duplication. Positive selection has made a limited contribution to the sequence diversity after duplication, but positively selected sites located in the LRR domain are thought to involve in the protein-protein interaction. Public Library of Science 2011-03-08 /pmc/articles/PMC3050792/ /pubmed/21408199 http://dx.doi.org/10.1371/journal.pone.0016079 Text en Sun, Wang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Sun, Xinli
Wang, Guo-Liang
Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases
title Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases
title_full Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases
title_fullStr Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases
title_full_unstemmed Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases
title_short Genome-Wide Identification, Characterization and Phylogenetic Analysis of the Rice LRR-Kinases
title_sort genome-wide identification, characterization and phylogenetic analysis of the rice lrr-kinases
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3050792/
https://www.ncbi.nlm.nih.gov/pubmed/21408199
http://dx.doi.org/10.1371/journal.pone.0016079
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