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

• Main Authors: Chen, Eric, Buen, Abad Najar, Zheng, Chunfang, Brandts, Alex, Lyons, Eric, Tang, Haibao, Carretero-Paulet, Lorenzo, Albert, Victor, Sankoff, David
• Other Authors: Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Canada, K1N 6N5
• Language: en
• Published: BioMed Central 2013
• Online Access: Chen et al. BMC Bioinformatics 2013, 14(Suppl 15):S19 http://www.biomedcentral.com/1471-2105/14/S15/S19; http://hdl.handle.net/10150/610254; http://arizona.openrepository.com/arizona/handle/10150/610254

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.