Polyploidy (whole genome duplication) in plants is well documented, and most plant genomes exhibit evidence of repeated whole genome duplication in their evolutionary history. However, less is known about the way such recurring duplication events affect well established gene families which often have strong selective constraints on their copy number and functional localization. To address this question, we examined the omega-3 fatty acid desaturase gene family and its evolution within the Rosid clade. This gene family is involved in the production of polyunsaturated fatty acids, a type of fatty acid that has been linked to cold temperature adaptation in plants. In addition to the existing gene function data available for Arabidopsis thaliana, we performed de-novo localization and stress response analysis in cotton and used the published genome sequences of arabidopsis, papaya, cotton, cacao, and grape to elucidate the evolutionary trajectory of the genomic regions containing these genes. Using a combination of phylogenetic, synteny, and functional analyses, we identified signals of copy number reduction post-polyploidy in the genomes of arabidopsis and paleo-polyploid cotton and likely sub-functionalization into organs under selection in cultivated neo-polyploid cotton. Moreover, we show that similar (and likely anciently established) stress response functions are performed by different members of the gene family in arabidopsis and cotton due to gene copy loss following polyploidy duplication in the arabidopsis lineage.

• published: 05 Nov 2014
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