Poster

         Population Genetics/Genomics

Resistance gene evolution in the Hawaiian Metrosideros radiation

Presenting Author
Hossein Madhani
Description
Hybrid necrosis (HN) is a common type of hybrid incompatibility in plants that results from negative epistasis between alleles at resistance genes (R genes), leading to hyperactivation of the plant immune system (autoimmunity) in hybrids. Recent studies demonstrate the importance of selection on R genes in the evolution of HN and their role as barriers to gene flow during speciation. However, such studies are largely restricted to model species. Adaptive radiations that capture different stages of speciation are among the best candidates to test the role of selection on R genes in the evolution of gene flow barriers during speciation. Hawaiian Metrosideros is an ongoing adaptive radiation in trees that captures a wide range of isolating barriers between populations, including HN in multiple F1 hybrid genotypes. To explore the possible role of R gene incompatibilities in HN in Metrosideros, we identified putative R genes in the five reference genomes available for Hawaiian Metrosideros using the NLR-Annotator pipeline and HMM search implemented in HMMER. We verified the presence of canonical domains of R proteins in the identified R proteins using PfamScan. We searched for known motifs and domains of plant R genes using MEME-suite and CD-Search, respectively. Firstly, we identified a set of more than 200 pseudogenes in the reference genomes, suggesting a dynamic and complex evolutionary history of R genes in the Hawaiian Metrosideros radiation. We also identified 180 putatively functional R genes and used variant-calling and population genetic analyses to investigate evidence of selection in these R genes across the radiation. Specifically, we calculated π and pairwise FST and Dxy values using SNP data from 131 individuals in 12 populations. While overall π, pairwise FST and Dxy values for all R genes between populations were similar to the genome-wide values, a subset of R genes on chromosomes 3, 7, and 10 showed high nucleotide diversity and were highly differentiated between most taxa examined in pairwise comparisons. These results suggest that a subset of R genes are under selection across the radiation and are possibly involved in necrosis observed in F1 hybrids. To measure introgression between taxa and further investigate the possible role of R genes in reproductive isolation between taxa that produce necrotic F1 hybrids, we calculated D statistics in sliding windows. The D statistics revealed genomic regions that are less introgressed between taxa that produce necrotic hybrids; however, these regions were not limited to the genomic regions containing the identified R genes. Overall, our results suggest a role for R genes in the HN observed in the Hawaiian Metrosideros radiation and point to a subset of candidate R genes underlying reproductive isolation in these trees. This work sets the stage for the precise identification of the locus (loci) putatively causing HN, and exploring the genetic and physiological mechanisms of HN in Hawaiian Metrosideros using RNA sequencing and metabolite profiling. By illuminating the role of immune system incompatibilities in the evolution of reproductive isolation in adaptive radiations, this study advances our understanding of the mechanisms underlying speciation in plants.