Journal
GENETICS
Volume 182, Issue 2, Pages 503-517Publisher
OXFORD UNIV PRESS INC
DOI: 10.1534/genetics.109.102608
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Funding
- National Research Initiative of the United States Department of Agriculture Cooperative State Research
- Education and Extension Service [2005-35301-15700]
- Department of Biotechnology, India
- Plant Sciences Institute at Iowa State University
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Polyploidy is all important force in the evolution of flowering plants. Genomic merger and doubling induce all extensive array of genomic effects, including immediate and long-term alterations in the expression of duplicate genes (homeologs). Here we employed a novel high-resolution, genome-specific, mass-spectrometry technology, and a well-established phylogenetic framework to investigate relative expression levels of each homeolog for 63 gene pairs in 24 tissues in naturally occurring allopolyploid cotton (Gossypium L.), a synthetic allopolyploid of the same genomic composition, and models of the diploid progenitor species. Results from a total of 2177 successful expression assays permitted its to determine the extent of expression evolution accompanying genomic merger of divergent diploid parents, genome doubling, and genomic coevolution in a common nucleus subsequent to polyploid formation. We demonstrate that 40% of homeologs are transcriptionally biased in at least one stage of cotton development, that genome merger per se has a large effect on relative expression of homeologs, and that the majority of these alterations are caused by cis-regulatory divergence between the diploid progenitors. We describe the scope of transcriptional subfunctionalization and 15 cases of probable neofunctionalization among 8 tissues. To our knowledge, this study represents the first characterization of transcriptional neofunctionalization in an allopolyploid. These results provide a novel temporal perspective oil expression evolution of duplicate genomes and acid to our understanding of the importance of polyploidy in plants.
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