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

      Chen, Eric; Buen, Abad Najar; Zheng, Chunfang; Brandts, Alex; Lyons, Eric; Tang, Haibao; Carretero-Paulet, Lorenzo; Albert, Victor; Sankoff, David; Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, Canada, K1N 6N5; et al. (BioMed Central, 2013)
      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.