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


ABSTRACT: 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.

SUBMITTER: Secomandi S 

PROVIDER: S-EPMC10044405 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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

Secomandi Simona S   Gallo Guido R GR   Sozzoni Marcella M   Iannucci Alessio A   Galati Elena E   Abueg Linelle L   Balacco Jennifer J   Caprioli Manuela M   Chow William W   Ciofi Claudio C   Collins Joanna J   Fedrigo Olivier O   Ferretti Luca L   Fungtammasan Arkarachai A   Haase Bettina B   Howe Kerstin K   Kwak Woori W   Lombardo Gianluca G   Masterson Patrick P   Messina Graziella G   Møller Anders P AP   Mountcastle Jacquelyn J   Mousseau Timothy A TA   Ferrer Obiol Joan J   Olivieri Anna A   Rhie Arang A   Rubolini Diego D   Saclier Marielle M   Stanyon Roscoe R   Stucki David D   Thibaud-Nissen Françoise F   Torrance James J   Torroni Antonio A   Weber Kristina K   Ambrosini Roberto R   Bonisoli-Alquati Andrea A   Jarvis Erich D ED   Gianfranceschi Luca L   Formenti Giulio G  

Cell reports 20230119 1


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 conserve  ...[more]

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