The Penstemon kunthii draft genome: Integrating a genetic map with assembled sequence data

Schlenk, Noelle C

Publication

The Penstemon kunthii draft genome: Integrating a genetic map with assembled sequence data

Schlenk, Noelle C

Abstract

Trait evolution is often investigated with tools like quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS). These tools are made powerful by the integration of high-resolution genomes. Despite the recent uprise of accessible sequencing technology, many genomes remain largely unexplored and unsequenced, including most genomes in the emerging model system, Penstemon. Penstemon is the largest genus of North American flowering plants, has diversified in the last few million years, and during that diversification has undergone major shifts in flower form as multiple lineages adapted to hummingbird pollination from an ancestral condition of bee-adaptation. High-quality Penstemon genomes will be valuable in QTL and GWAS analyses used to determine the genetic architecture of floral trait differences between species of bee-adapted Penstemon (like P. amphorellae) and hummingbird-adapted Penstemon (like P. kunthii). In the interest of these investigations, I aim to broaden our knowledge and confidence in the existing P. kunthii genome assembly. In this study, I confirmed the accuracy of the Penstemon kunthii genome assembly by generating a genetic map from a population of 238 F2 hybrid offspring derived from a cross between P. kunthii and its sister species, P. amphorellae. I leveraged multiplex shotgun genotype (MSG) sequencing to generate short sequence reads, which were aligned to our reference genome (P. kunthii) and used these to construct a linkage map for each of the eight Penstemon chromosomes. Upon confirmation of proper ordering, I utilize this assembly to characterize other genomic properties such as the recombination landscape, intra-chromosomal GC content and repeat element density, all of which help point to the approximate location of the centromeres of each of the eight chromosomes. A confident assembly and future annotation of the P. kunthii genome will form the foundation for identifying genes discovered through QTL mapping and other genome-based methods.