Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.

Tandem and segmental duplications significantly contribute to gene family expansion and genome evolution. Genome-wide identification of tandem and segmental genes has been analyzed before in several plant genomes. However, comparative studies in functional bias, expression divergence and their roles...

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Autores principales:	Shu-Ye Jiang, José M González, Srinivasan Ramachandran
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b088d5308ff24dddb67240eb41ae0f71
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spelling	oai:doaj.org-article:b088d5308ff24dddb67240eb41ae0f712021-11-18T07:45:29ZComparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.1932-620310.1371/journal.pone.0063551https://doaj.org/article/b088d5308ff24dddb67240eb41ae0f712013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23696832/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Tandem and segmental duplications significantly contribute to gene family expansion and genome evolution. Genome-wide identification of tandem and segmental genes has been analyzed before in several plant genomes. However, comparative studies in functional bias, expression divergence and their roles in species domestication are still lacking. We have carried out a genome-wide identification and comparative analysis of tandem and segmental genes in the rice genome. A total of 3,646 and 3,633 pairs of tandem and segmental genes, respectively, were identified in the genome. They made up around 30% of total annotated rice genes (excluding transposon-coding genes). Both tandem and segmental duplicates showed different physical locations and exhibited a biased subset of functions. These two types of duplicated genes were also under different functional constrains as shown by nonsynonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analysis. They are also differently regulated depending on the tissues and abiotic and biotic stresses based on transcriptomics data. The expression divergence might be related to promoter differentiation and DNA methylation status after tandem or segmental duplications. Both tandem and segmental duplications differ in their contribution to genetic novelty but evidence suggests that they play their role in species domestication and genome evolution.Shu-Ye JiangJosé M GonzálezSrinivasan RamachandranPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e63551 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Shu-Ye Jiang José M González Srinivasan Ramachandran Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
description	Tandem and segmental duplications significantly contribute to gene family expansion and genome evolution. Genome-wide identification of tandem and segmental genes has been analyzed before in several plant genomes. However, comparative studies in functional bias, expression divergence and their roles in species domestication are still lacking. We have carried out a genome-wide identification and comparative analysis of tandem and segmental genes in the rice genome. A total of 3,646 and 3,633 pairs of tandem and segmental genes, respectively, were identified in the genome. They made up around 30% of total annotated rice genes (excluding transposon-coding genes). Both tandem and segmental duplicates showed different physical locations and exhibited a biased subset of functions. These two types of duplicated genes were also under different functional constrains as shown by nonsynonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analysis. They are also differently regulated depending on the tissues and abiotic and biotic stresses based on transcriptomics data. The expression divergence might be related to promoter differentiation and DNA methylation status after tandem or segmental duplications. Both tandem and segmental duplications differ in their contribution to genetic novelty but evidence suggests that they play their role in species domestication and genome evolution.
format	article
author	Shu-Ye Jiang José M González Srinivasan Ramachandran
author_facet	Shu-Ye Jiang José M González Srinivasan Ramachandran
author_sort	Shu-Ye Jiang
title	Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
title_short	Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
title_full	Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
title_fullStr	Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
title_full_unstemmed	Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
title_sort	comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/b088d5308ff24dddb67240eb41ae0f71
work_keys_str_mv	AT shuyejiang comparativegenomicandtranscriptomicanalysisoftandemlyandsegmentallyduplicatedgenesinrice AT josemgonzalez comparativegenomicandtranscriptomicanalysisoftandemlyandsegmentallyduplicatedgenesinrice AT srinivasanramachandran comparativegenomicandtranscriptomicanalysisoftandemlyandsegmentallyduplicatedgenesinrice
_version_	1718422995350847488

Comparative genomic and transcriptomic analysis of tandemly and segmentally duplicated genes in rice.

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