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

Secomandi Simona and Gallo Guido R and Sozzoni Marcella and Iannucci Alessio and Galati Elena and Abueg Linelle and Balacco Jennifer and Caprioli Manuela and Chow William and Ciofi Claudio and Collins Joanna and Fedrigo Olivier and Ferretti L

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.

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January, 2023



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