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 / Secomandi S.; Gallo G.R.; Sozzoni M.; Iannucci A.; Galati E.; Abueg L.; Balacco J.; Caprioli M.; Chow W.; Ciofi C.; Collins J.; Fedrigo O.; Ferretti L.; Fungtammasan A.; Haase B.; Howe K.; Kwak W.; Lombardo G.; Masterson P.; Messina G.; Moller A.P.; Mountcastle J.; Mousseau T.A.; Ferrer Obiol J.; Olivieri A.; Rhie A.; Rubolini D.; Saclier M.; Stanyon R.; Stucki D.; Thibaud-Nissen F.; Torrance J.; Torroni A.; Weber K.; Ambrosini R.; Bonisoli-Alquati A.; Jarvis E.D.; Gianfranceschi L.; Formenti G.. - In: CELL REPORTS. - ISSN 2211-1247. - ELETTRONICO. - 42:(2023), pp. 111992.0-111992.0. [10.1016/j.celrep.2023.111992]

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

Sozzoni M.;Iannucci A.;Ciofi C.;Stanyon R.;
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.
2023
42
0
0
Goal 15: Life on land
Secomandi S.; Gallo G.R.; Sozzoni M.; Iannucci A.; Galati E.; Abueg L.; Balacco J.; Caprioli M.; Chow W.; Ciofi C.; Collins J.; Fedrigo O.; Ferretti L.; Fungtammasan A.; Haase B.; Howe K.; Kwak W.; Lombardo G.; Masterson P.; Messina G.; Moller A.P.; Mountcastle J.; Mousseau T.A.; Ferrer Obiol J.; Olivieri A.; Rhie A.; Rubolini D.; Saclier M.; Stanyon R.; Stucki D.; Thibaud-Nissen F.; Torrance J.; Torroni A.; Weber K.; Ambrosini R.; Bonisoli-Alquati A.; Jarvis E.D.; Gianfranceschi L.; Formenti G.
File in questo prodotto:
File Dimensione Formato  
Secomandi et al 2023.pdf

accesso aperto

Tipologia: Pdf editoriale (Version of record)
Licenza: Open Access
Dimensione 8.02 MB
Formato Adobe PDF
8.02 MB Adobe PDF

I documenti in FLORE sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificatore per citare o creare un link a questa risorsa: https://hdl.handle.net/2158/1298528
Citazioni
  • ???jsp.display-item.citation.pmc??? ND
  • Scopus 6
  • ???jsp.display-item.citation.isi??? 6
social impact