A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales

Persistent Link:
http://hdl.handle.net/10150/614772
Title:
A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales
Author:
McKain, Michael R.; Tang, Haibao; McNeal, Joel R.; Ayyampalayam, Saravanaraj; Davis, Jerrold I.; dePamphilis, Claude W.; Givnish, Thomas J.; Pires, J. Chris; Stevenson, Dennis Wm.; Leebens-Mack, Jim H.
Affiliation:
Univ Arizona, iPlant Collaborat, Sch Plant Sci
Issue Date:
2016-03-17
Publisher:
OXFORD UNIV PRESS
Citation:
A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales 2016:evw060 Genome Biology and Evolution
Journal:
Genome Biology and Evolution
Rights:
© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/).
Collection Information:
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.
Abstract:
Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (rho), sigma (sigma), and tau (tau), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification.
ISSN:
1759-6653
DOI:
10.1093/gbe/evw060
Keywords:
whole-genome duplication; grasses; monocots; GC content
Version:
Final published version
Additional Links:
http://gbe.oxfordjournals.org/lookup/doi/10.1093/gbe/evw060

Full metadata record

DC FieldValue Language
dc.contributor.authorMcKain, Michael R.en
dc.contributor.authorTang, Haibaoen
dc.contributor.authorMcNeal, Joel R.en
dc.contributor.authorAyyampalayam, Saravanarajen
dc.contributor.authorDavis, Jerrold I.en
dc.contributor.authordePamphilis, Claude W.en
dc.contributor.authorGivnish, Thomas J.en
dc.contributor.authorPires, J. Chrisen
dc.contributor.authorStevenson, Dennis Wm.en
dc.contributor.authorLeebens-Mack, Jim H.en
dc.date.accessioned2016-06-25T01:25:25Z-
dc.date.available2016-06-25T01:25:25Z-
dc.date.issued2016-03-17-
dc.identifier.citationA phylogenomic assessment of ancient polyploidy and genome evolution across the Poales 2016:evw060 Genome Biology and Evolutionen
dc.identifier.issn1759-6653-
dc.identifier.doi10.1093/gbe/evw060-
dc.identifier.urihttp://hdl.handle.net/10150/614772-
dc.description.abstractComparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (rho), sigma (sigma), and tau (tau), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification.en
dc.language.isoenen
dc.publisherOXFORD UNIV PRESSen
dc.relation.urlhttp://gbe.oxfordjournals.org/lookup/doi/10.1093/gbe/evw060en
dc.rights© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/).en
dc.subjectwhole-genome duplicationen
dc.subjectgrassesen
dc.subjectmonocotsen
dc.subjectGC contenten
dc.titleA phylogenomic assessment of ancient polyploidy and genome evolution across the Poalesen
dc.typeArticleen
dc.contributor.departmentUniv Arizona, iPlant Collaborat, Sch Plant Scien
dc.identifier.journalGenome Biology and Evolutionen
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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