1. A chromosome-level reference genome and pangenome for barn swallow population genomics
- Author
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Simona Secomandi, Guido R. Gallo, Marcella Sozzoni, Alessio Iannucci, Elena Galati, Linelle Abueg, Jennifer Balacco, Manuela Caprioli, William Chow, Claudio Ciofi, Joanna Collins, Olivier Fedrigo, Luca Ferretti, Arkarachai Fungtammasan, Bettina Haase, Kerstin Howe, Woori Kwak, Gianluca Lombardo, Patrick Masterson, Graziella Messina, Anders P. Møller, Jacquelyn Mountcastle, Timothy A. Mousseau, Joan Ferrer Obiol, Anna Olivieri, Arang Rhie, Diego Rubolini, Marielle Saclier, Roscoe Stanyon, David Stucki, Françoise Thibaud-Nissen, James Torrance, Antonio Torroni, Kristina Weber, Roberto Ambrosini, Andrea Bonisoli-Alquati, Erich D. Jarvis, Luca Gianfranceschi, and Giulio Formenti
- Subjects
CP: Molecular biology ,Biology (General) ,QH301-705.5 - Abstract
Summary: 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.
- Published
- 2023
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