The dynamics of functional classes of plant genes in rediploidized ancient polyploids
Buen, Abad Najar
AffiliationDepartment 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
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CitationChen et al. BMC Bioinformatics 2013, 14(Suppl 15):S19 http://www.biomedcentral.com/1471-2105/14/S15/S19
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)
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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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