View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

Phlox wildflowers are a formative model of plant ecological and evolutionary research. One species, P. drummondii, has become a model for studying patterns of evolutionary divergence and reinforcement during the speciation process. In this system, selection against hybridization with the closely related species P. cuspidata has driven the evolution of flower color divergence within P. drummondii to increased reproductive isolation. While extensive research has characterized the selective landscape surrounding flower color divergence and its role in speciation, progress towards understanding the mutational basis of this trait and a broader understanding of the genomic patterns surrounding the speciation process are limited by genomic resources in this system. Here we present the contiguous, complete assembly of the repeat-dense 6.5 Gbase Phlox drummondii genome. To generate this assembly, we used high coverage Oxford Nanopore sequencing, including a fraction of ultra-long reads for scaffolding. This genome is highly complete, as measured by BUSCO score (>98% complete), and reasonably contiguous, comparing favorably to other long-read assemblies of plants with much smaller genomes. The quality of this assembly gives us the opportunity to characterize the repetitive landscape of the genome, which we estimate to be composed of ~90% repetitive elements, mostly interspersed elements. Using low coverage, long-read population resequencing, we find evidence for widespread structural variation across the Phlox genome. We describe patterns of variation both within and between Phlox species, including evidence for structural polymorphisms in regions of interest underlying reproductive isolation between the species.

Structural variation in the 6.5 Gb genome of the flowering plant Phlox drummondii