: 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.

A chromosome-level reference genome and pangenome for barn swallow population genomics / S. Secomandi, G.R. Gallo, M. Sozzoni, A. Iannucci, E. Galati, L. Abueg, J. Balacco, M. Caprioli, W. Chow, C. Ciofi, J. Collins, O. Fedrigo, L. Ferretti, A. Fungtammasan, B. Haase, K. Howe, W. Kwak, G. Lombardo, P. Masterson, G. Messina, A.P. Møller, J. Mountcastle, T.A. Mousseau, J. Ferrer Obiol, A. Olivieri, A. Rhie, D. Rubolini, M. Saclier, R. Stanyon, D. Stucki, F. Thibaud-Nissen, J. Torrance, A. Torroni, K. Weber, R. Ambrosini, A. Bonisoli-Alquati, E.D. Jarvis, L. Gianfranceschi, G. Formenti. - In: CELL REPORTS. - ISSN 2211-1247. - 42:1(2023 Jan 18), pp. 111992.1-111992.30. [10.1016/j.celrep.2023.111992]

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

S. Secomandi
Primo
;
G.R. Gallo
Secondo
;
E. Galati;M. Caprioli;G. Messina;J. Ferrer Obiol;A. Olivieri;D. Rubolini;M. Saclier;R. Ambrosini;A. Bonisoli-Alquati;L. Gianfranceschi
Penultimo
;
G. Formenti
Ultimo
2023

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.
CP: Molecular biology; barn swallow; comparative genomics; genetic marker catalog; genome assembly; linkage disequilibrium; pangenome graph; pangenomics; population genomics; reference genome; synanthropy
Settore BIO/18 - Genetica
Settore BIO/07 - Ecologia
Settore BIO/11 - Biologia Molecolare
18-gen-2023
Article (author)
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/953196
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