Cell Reports (Jan 2023)
A chromosome-level reference genome and pangenome for barn swallow population genomics
- 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,
- Giulio Formenti
Affiliations
- Simona Secomandi
- Department of Biosciences, University of Milan, Milan, Italy; Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- Guido R. Gallo
- Department of Biosciences, University of Milan, Milan, Italy
- Marcella Sozzoni
- Department of Biosciences, University of Milan, Milan, Italy
- Alessio Iannucci
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
- Elena Galati
- Department of Biosciences, University of Milan, Milan, Italy
- Linelle Abueg
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Jennifer Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Manuela Caprioli
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
- William Chow
- Wellcome Sanger Institute, Cambridge, UK
- Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
- Joanna Collins
- Wellcome Sanger Institute, Cambridge, UK
- Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Luca Ferretti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Arkarachai Fungtammasan
- DNAnexus, Inc., Mountain View, CA, USA
- Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Kerstin Howe
- Wellcome Sanger Institute, Cambridge, UK
- Woori Kwak
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon 14662, Korea
- Gianluca Lombardo
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- Graziella Messina
- Department of Biosciences, University of Milan, Milan, Italy
- Anders P. Møller
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France
- Jacquelyn Mountcastle
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- Timothy A. Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
- Joan Ferrer Obiol
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
- Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Diego Rubolini
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
- Marielle Saclier
- Department of Biosciences, University of Milan, Milan, Italy
- Roscoe Stanyon
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
- David Stucki
- Pacific Biosciences, Menlo Park, CA, USA
- Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
- James Torrance
- Wellcome Sanger Institute, Cambridge, UK
- Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Kristina Weber
- Pacific Biosciences, Menlo Park, CA, USA
- Roberto Ambrosini
- Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
- Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA, USA
- Erich D. Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA; The Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Luca Gianfranceschi
- Department of Biosciences, University of Milan, Milan, Italy; Corresponding author
- Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA; Corresponding author
- Journal volume & issue
-
Vol. 42,
no. 1
p. 111992
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.
