Genomic characterization of divergent haplotypes of large structural variants in the genus Helianthus

Recent analyses of the genomes of three wild sunflower species (Helianthus annuus, H. petiolaris, H. argophyllus) have uncovered 37 non-recombining, highly divergent haploblocks, all of which are megabases long. The lack of recombination between alternate haplotypes of these regions has been shown to result from segregating chromosomal structural variants (SVs) in many cases. These SVs are distributed along environmental clines. Genome-Wide Association Studies (GWAS) and Genome-Environment Association (GEA) analyses indicate that the SVs are strongly associated with certain climate and soil conditions, as well as a wide range of phenotypic traits and ecotypes. They are also significant from an evolutionary standpoint by providing a potential explanation for how these species are able to maintain a wide variety of locally adapted ecotypes and ecospecies despite considerable gene flow between distinct populations. However, while substantial high-level work has been done to identify the phenotypic traits, habitat associations, and phylogenetic origins of these SVs, there had been little characterization of the genes housed within the SVs before now. Through the subsequent analyses, I characterize the haplotype-specific genetic and transcriptomic divergence between gene variants using a mix of genomic and transcriptomic data sets previously generated by the Rieseberg Lab and collaborators. In so doing, I find that alternate haplotypes of these SVs demonstrate remarkable divergence in genes potentially related to local adaptation and the functions predicted in previous studies. I also investigate the evolutionary forces acting on each SV to show that both haplotype-specific positive and negative selection appear abundant. Finally, through population genetics I provide evidence that these SVs had introgressive origins.Science, Faculty ofGraduat