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dc.contributor.authorChen, Eric
dc.contributor.authorBuen, Abad Najar
dc.contributor.authorZheng, Chunfang
dc.contributor.authorBrandts, Alex
dc.contributor.authorLyons, Eric
dc.contributor.authorTang, Haibao
dc.contributor.authorCarretero-Paulet, Lorenzo
dc.contributor.authorAlbert, Victor
dc.contributor.authorSankoff, David
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.
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
refterms.dateFOA2018-09-11T10:58:00Z
html.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.


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