Assement of Gene Conversion following polyploidy
Armel Salmon, Lex Flagel, Amala Balu, Bao Ying, Kara Grupp, Jonathan Wendel
Whole genome doubling (polyploidization), or segmental duplication of genomes (e.g tandem repeats) leads to redundant genomic information whose fate is of particular interest in genome evolution. Due to the release of functional and selective pressure, one of the duplicate can either evolve independently by neofunctionalization, pseudogenization, or loss (divergent evolution). An additional and poorly explored possibility is that the two duplicates may evolve in a more interactive, or dependent fashion, by undergoing gene conversion via non-reciprocal transfer of genic material by its homoeolog.
Various fates of duplicated genes in cotton
- Many low copy genes evolve independently (Cronn et al., 1999)
- Some duplicated genes exhibit strikingly different evolutionary rates (Small et al., 2000)
- At least some high-copy repets, such as ribosomal ITS sequences display bidirectional gene conversion, with 4 polyploid species exhibiting only D-like copies, while the 5th contains only A-like copies.
Genomic resources developed over the last decade in cotton have allowed us to detect homeolog-specific SNPs using ESTs sequences from G. arboreum (A genome), G. raimondii (D genome), and G. hirsutum (AD genome). Using this our homeoSNPs database, we are studying duplicate gene evolution in polyploid cotton to determine the frequency, scope, and timing of gene conversion events that have affected the polyploid genome of cotton.
This project entails bioinformatic inference of gene conversion events, followed by laboratory experiments to test the bioinformatic inferences. To validate putative gene conversion events, and to ensure that those events are not due to either sequencing errors or to PCR recombination, we amplify, clone and sequencee targeted regions (30 to date). To ensure that those recombinant ESTs were not due to post-transcriptional events such as co-splicing of exons from A- or D- mRNA copies, a subset of primers have been designed to amplify both exonic and intronic regions. In addition, we are following up on validated gene conversion events using the well-established phylogenetic framework for the 5 polyploid species. This work will permit us to address the question of whether gene conversion in polyploids is a phenomenon chararacterizing the earliest stages of polyploidy formation, or if instead it plays out over a more extended period during polyploid speciation.