PoplarV1, Main, Exploration, bibRecord, 002524

Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants.

Identifieur interne : 002524 ( Main/Exploration ); précédent : 002523; suivant : 002525

Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants.

Auteurs : Wen-Kai Jiang [République populaire de Chine] ; Yun-Long Liu ; En-Hua Xia ; Li-Zhi Gao

Source :

Plant physiology [ 1532-2548 ] ; 2013.

RBID : pubmed:23396833

Descripteurs français

English descriptors

Abstract

The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs.

DOI: 10.1104/pp.112.200147
PubMed: 23396833
PubMed Central: PMC3613460

Affiliations:

République populaire de Chine

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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Evolution, Molecular (MeSH)</term>
<term>Flowers (genetics)</term>
<term>Gene Duplication (genetics)</term>
<term>Genes, Duplicate (genetics)</term>
<term>Genes, Plant (genetics)</term>
<term>Logistic Models (MeSH)</term>
<term>Magnoliopsida (genetics)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Principal Component Analysis (MeSH)</term>
<term>Segmental Duplications, Genomic (genetics)</term>
<term>Selection, Genetic (MeSH)</term>
<term>Synteny (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse en composantes principales (MeSH)</term>
<term>Annotation de séquence moléculaire (MeSH)</term>
<term>Duplication de gène (génétique)</term>
<term>Duplications génomiques segmentaires (génétique)</term>
<term>Fleurs (génétique)</term>
<term>Gènes de plante (génétique)</term>
<term>Gènes dupliqués (génétique)</term>
<term>Magnoliopsida (génétique)</term>
<term>Modèles logistiques (MeSH)</term>
<term>Synténie (génétique)</term>
<term>Sélection génétique (MeSH)</term>
<term>Évolution moléculaire (MeSH)</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Flowers</term>
<term>Gene Duplication</term>
<term>Genes, Duplicate</term>
<term>Genes, Plant</term>
<term>Magnoliopsida</term>
<term>Segmental Duplications, Genomic</term>
<term>Synteny</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Duplication de gène</term>
<term>Duplications génomiques segmentaires</term>
<term>Fleurs</term>
<term>Gènes de plante</term>
<term>Gènes dupliqués</term>
<term>Magnoliopsida</term>
<term>Synténie</term>
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<keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term>
<term>Logistic Models</term>
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<term>Selection, Genetic</term>
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<term>Annotation de séquence moléculaire</term>
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<front><div type="abstract" xml:lang="en">The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs.</div>
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<Abstract><AbstractText>The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs.</AbstractText>
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Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants.

Prevalent role of gene features in determining evolutionary fates of whole-genome duplication duplicated genes in flowering plants.

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