Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homoeologs in Polyploid Cotton (Gossypium)

Polyploidy is an important force in the evolution of flowering plants. Genomic merger and doubling induce an extensive array of genomic effects, including immediate and long-term alterations in the expression of duplicate genes ('homoeologs') 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 homoeolog 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 2,177 successful expression assays permitted us 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 homoeologs are transcriptionally biased in at least one stage of cotton development, that genome merger per se has a large effect on relative expression of homoeologs, 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 on expression evolution of duplicate genomes and add to our understanding of the importance of polyploidy in plants.

Key Words: Gossypium, cotton, expression evolution, homoeolog, mass-spectrometry

Online ISSN: 1943-2361  Print ISSN: 0016-6731
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