PoplarV1, Main, Exploration, bibRecord, 002B48

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

Identifieur interne : 002B48 ( Main/Exploration ); précédent : 002B47; suivant : 002B49

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

Auteurs : Eli Rodgers-Melnick [États-Unis] ; Shrinivasrao P. Mane ; Palitha Dharmawardhana ; Gancho T. Slavov ; Oswald R. Crasta ; Steven H. Strauss ; Amy M. Brunner ; Stephen P. Difazio

Source :

Genome research [ 1549-5469 ] ; 2012.

RBID : pubmed:21974993

Descripteurs français

English descriptors

KwdEn :
- Evolution, Molecular (MeSH), Gene Duplication (physiology), Gene Expression Regulation, Plant (physiology), Genome, Plant (physiology), Models, Genetic (MeSH), Plant Diseases (genetics), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (physiology), Signal Transduction (physiology), Transcription Factors (genetics), Transcription Factors (metabolism).
MESH :
- chemical , genetics : Plant Proteins, Transcription Factors.
- genetics : Plant Diseases.
- chemical , metabolism : Plant Proteins, Transcription Factors.
- physiology : Gene Duplication, Gene Expression Regulation, Plant, Genome, Plant, Populus, Signal Transduction.
- Evolution, Molecular, Models, Genetic.

Abstract

Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional categories are over-represented in each class of duplicates. In particular, disease resistance genes and receptor-like kinases commonly occur in tandem but are significantly under-retained following whole genome duplication, while whole genome duplicate pairs are enriched for members of signal transduction cascades and transcription factors. The shape of the distribution of expression divergence for duplicated pairs suggests that nearly half of the whole genome duplicates have diverged in expression by a random degeneration process. The remaining pairs have more conserved gene expression than expected by chance, consistent with a role for selection under the constraints of gene balance. We hypothesize that duplicate gene preservation in Populus is driven by a combination of subfunctionalization of duplicate pairs and purifying selection favoring retention of genes encoding proteins with large numbers of interactions.

DOI: 10.1101/gr.125146.111
PubMed: 21974993
PubMed Central: PMC3246211

Affiliations:

États-Unis

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Le document en format XML

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<term>Genome, Plant (physiology)</term>
<term>Models, Genetic (MeSH)</term>
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<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
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<term>Génome végétal (physiologie)</term>
<term>Maladies des plantes (génétique)</term>
<term>Modèles génétiques (MeSH)</term>
<term>Populus (physiologie)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (physiologie)</term>
<term>Transduction du signal (physiologie)</term>
<term>Évolution moléculaire (MeSH)</term>
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<term>Transcription Factors</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Diseases</term>
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<term>Protéines végétales</term>
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<term>Protéines végétales</term>
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<term>Régulation de l'expression des gènes végétaux</term>
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<term>Signal Transduction</term>
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<term>Models, Genetic</term>
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<front><div type="abstract" xml:lang="en">Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional categories are over-represented in each class of duplicates. In particular, disease resistance genes and receptor-like kinases commonly occur in tandem but are significantly under-retained following whole genome duplication, while whole genome duplicate pairs are enriched for members of signal transduction cascades and transcription factors. The shape of the distribution of expression divergence for duplicated pairs suggests that nearly half of the whole genome duplicates have diverged in expression by a random degeneration process. The remaining pairs have more conserved gene expression than expected by chance, consistent with a role for selection under the constraints of gene balance. We hypothesize that duplicate gene preservation in Populus is driven by a combination of subfunctionalization of duplicate pairs and purifying selection favoring retention of genes encoding proteins with large numbers of interactions.</div>
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<Abstract><AbstractText>Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional categories are over-represented in each class of duplicates. In particular, disease resistance genes and receptor-like kinases commonly occur in tandem but are significantly under-retained following whole genome duplication, while whole genome duplicate pairs are enriched for members of signal transduction cascades and transcription factors. The shape of the distribution of expression divergence for duplicated pairs suggests that nearly half of the whole genome duplicates have diverged in expression by a random degeneration process. The remaining pairs have more conserved gene expression than expected by chance, consistent with a role for selection under the constraints of gene balance. We hypothesize that duplicate gene preservation in Populus is driven by a combination of subfunctionalization of duplicate pairs and purifying selection favoring retention of genes encoding proteins with large numbers of interactions.</AbstractText>
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Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.

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