The dynamics of functional classes of plant genes in rediploidized ancient polyploids

Persistent Link:
http://hdl.handle.net/10150/610254
Title:
The dynamics of functional classes of plant genes in rediploidized ancient polyploids
Author:
Chen, Eric; Buen, Abad Najar; Zheng, Chunfang; Brandts, Alex; Lyons, Eric; Tang, Haibao; Carretero-Paulet, Lorenzo; Albert, Victor; Sankoff, David
Affiliation:
Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Canada, K1N 6N5; Facultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Distrito Federal, México; Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada, K1N 6N5; School of Plant Sciences, iPlant Collaborative Bio5 Institute, University of Arizona, 1657 E Helen St, Tucson, AZ 85745, USA; J Craig Venter Institute, 9704 Medical Center Dr, 20850 Rockville, MD, USA; Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260, USA
Issue Date:
2013
Publisher:
BioMed Central
Citation:
Chen et al. BMC Bioinformatics 2013, 14(Suppl 15):S19 http://www.biomedcentral.com/1471-2105/14/S15/S19
Journal:
BMC Bioinformatics
Rights:
© 2013 Chen et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids fixed as whole genome duplicates, including patterns of retention of duplicate, triplicate, etc. genes.RESULTS:We measure the simultaneous dynamics of duplicate orthologous gene loss in rosids, in asterids, and in monocots, as influenced by biological functional class. This pan-angiosperm view confirms common tendencies and consistency through time for both ancient and more recent whole genome polyploidization events.CONCLUSIONS:The gene loss analysis represents an assessment of post-polyploidization evolution, at the level of individual gene families within and across sister genomes. Functional analysis confirms universal trends previously reported for more recent plant polyploidy events: genes involved with regulation and responses were retained in multiple copies, while genes involved with metabolic and catalytic processes tended to lose copies, across all three groups of plants.
EISSN:
1471-2105
DOI:
10.1186/1471-2105-14-S15-S19
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2105/14/S15/S19

Full metadata record

DC FieldValue Language
dc.contributor.authorChen, Ericen
dc.contributor.authorBuen, Abad Najaren
dc.contributor.authorZheng, Chunfangen
dc.contributor.authorBrandts, Alexen
dc.contributor.authorLyons, Ericen
dc.contributor.authorTang, Haibaoen
dc.contributor.authorCarretero-Paulet, Lorenzoen
dc.contributor.authorAlbert, Victoren
dc.contributor.authorSankoff, Daviden
dc.date.accessioned2016-05-20T09:02:18Z-
dc.date.available2016-05-20T09:02:18Z-
dc.date.issued2013en
dc.identifier.citationChen et al. BMC Bioinformatics 2013, 14(Suppl 15):S19 http://www.biomedcentral.com/1471-2105/14/S15/S19en
dc.identifier.doi10.1186/1471-2105-14-S15-S19en
dc.identifier.urihttp://hdl.handle.net/10150/610254-
dc.description.abstractBACKGROUND:To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids fixed as whole genome duplicates, including patterns of retention of duplicate, triplicate, etc. genes.RESULTS:We measure the simultaneous dynamics of duplicate orthologous gene loss in rosids, in asterids, and in monocots, as influenced by biological functional class. This pan-angiosperm view confirms common tendencies and consistency through time for both ancient and more recent whole genome polyploidization events.CONCLUSIONS:The gene loss analysis represents an assessment of post-polyploidization evolution, at the level of individual gene families within and across sister genomes. Functional analysis confirms universal trends previously reported for more recent plant polyploidy events: genes involved with regulation and responses were retained in multiple copies, while genes involved with metabolic and catalytic processes tended to lose copies, across all three groups of plants.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2105/14/S15/S19en
dc.rights© 2013 Chen et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleThe dynamics of functional classes of plant genes in rediploidized ancient polyploidsen
dc.typeArticleen
dc.identifier.eissn1471-2105en
dc.contributor.departmentDepartment of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Canada, K1N 6N5en
dc.contributor.departmentFacultad de Ciencias, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Distrito Federal, Méxicoen
dc.contributor.departmentDepartment of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Canada, K1N 6N5en
dc.contributor.departmentSchool of Plant Sciences, iPlant Collaborative Bio5 Institute, University of Arizona, 1657 E Helen St, Tucson, AZ 85745, USAen
dc.contributor.departmentJ Craig Venter Institute, 9704 Medical Center Dr, 20850 Rockville, MD, USAen
dc.contributor.departmentDepartment of Biological Sciences, University at Buffalo, Buffalo, New York 14260, USAen
dc.identifier.journalBMC Bioinformaticsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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