Professor Barbara Mable, University of Glasgow
"Adding complexity to complexity: gene family evolution in polyploids"
Comparative genomics of non-model organisms has resurrected whole genome duplication from being viewed as a somewhat obscure process that happens in plants to a primary driver of eukaryotic diversification. The shadow of past ploidy increases has left a strong signature of duplicated genes organised into gene families, even in small genomes that have undergone effectively complete rediploidisation. Nevertheless, despite continually advancing technologies and bioinformatics pipelines, resolving the fate of duplicate genes remains a substantial challenge. For example, many important recognition processes are driven not only by allelic expansion through retention of duplicates but also by diversification and copy number variation. This creates technical difficulties with assembly to reference genomes and accurate interpretation of homology. Thus, relatively little is known about the impacts of recent polyploidisation and hybridisation on the evolution of gene families under selective forces that maintain diversity, such as balancing selection. We have been using a complex of species in the genus Arabidopsis (A. lyrata and A. arenosa) as a model to investigate the evolutionary dynamics of two large and complicated gene families known to be under strong balancing or diversifying selection: the S-related kinases involved with signalling processes regulating self-incompatibility and R-genes involved in host-pathogen interactions. I use this example to highlight specific issues to consider when interpreting gene family evolution, particularly in relation to polyploids but also more generally in diploids. I conclude with recommendations for how to overcome the challenges of resolving such complex loci in the future, using deep sequencing approaches.