A chromosome-level reference genome and pangenome for barn swallow population genomics

Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome. [Display omitted] •Generation of a high-quality annotated reference genome and pangenome for barn swallow•Generation of comprehensive barn swallow genetic variants catalog•Multispecies alignment and variants catalog detected list of candidate genes•Pangenome improves read mapping and variant calling Secomandi et al. present a chromosome-level genome and pangenome for the barn swallow. They generate a large catalog of worldwide genetic variants and identify genomic regions potentially under selection. They also compare the barn swallow genome with that of other bird species to detect conserved and accelerated genes.