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A chromosome-level reference genome and pangenome for barn swallow population genomics.
Secomandi, Simona; Gallo, Guido R; Sozzoni, Marcella; Iannucci, Alessio; Galati, Elena; Abueg, Linelle; Balacco, Jennifer; Caprioli, Manuela; Chow, William; Ciofi, Claudio; Collins, Joanna; Fedrigo, Olivier; Ferretti, Luca; Fungtammasan, Arkarachai; Haase, Bettina; Howe, Kerstin; Kwak, Woori; Lombardo, Gianluca; Masterson, Patrick; Messina, Graziella; Møller, Anders P; Mountcastle, Jacquelyn; Mousseau, Timothy A; Ferrer Obiol, Joan; Olivieri, Anna; Rhie, Arang; Rubolini, Diego; Saclier, Marielle; Stanyon, Roscoe; Stucki, David; Thibaud-Nissen, Françoise; Torrance, James; Torroni, Antonio; Weber, Kristina; Ambrosini, Roberto; Bonisoli-Alquati, Andrea; Jarvis, Erich D; Gianfranceschi, Luca; Formenti, Giulio.
Affiliation
  • Secomandi S; Department of Biosciences, University of Milan, Milan, Italy; Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
  • Gallo GR; Department of Biosciences, University of Milan, Milan, Italy.
  • Sozzoni M; Department of Biosciences, University of Milan, Milan, Italy.
  • Iannucci A; Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy.
  • Galati E; Department of Biosciences, University of Milan, Milan, Italy.
  • Abueg L; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
  • Balacco J; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
  • Caprioli M; Department of Environmental Sciences and Policy, University of Milan, Milan, Italy.
  • Chow W; Wellcome Sanger Institute, Cambridge, UK.
  • Ciofi C; Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy.
  • Collins J; Wellcome Sanger Institute, Cambridge, UK.
  • Fedrigo O; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
  • Ferretti L; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.
  • Fungtammasan A; DNAnexus, Inc., Mountain View, CA, USA.
  • Haase B; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
  • Howe K; Wellcome Sanger Institute, Cambridge, UK.
  • Kwak W; Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon 14662, Korea.
  • Lombardo G; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.
  • Masterson P; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Messina G; Department of Biosciences, University of Milan, Milan, Italy.
  • Møller AP; Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France.
  • Mountcastle J; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
  • Mousseau TA; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
  • Ferrer Obiol J; Department of Environmental Sciences and Policy, University of Milan, Milan, Italy.
  • Olivieri A; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.
  • Rhie A; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
  • Rubolini D; Department of Environmental Sciences and Policy, University of Milan, Milan, Italy.
  • Saclier M; Department of Biosciences, University of Milan, Milan, Italy.
  • Stanyon R; Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy.
  • Stucki D; Pacific Biosciences, Menlo Park, CA, USA.
  • Thibaud-Nissen F; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
  • Torrance J; Wellcome Sanger Institute, Cambridge, UK.
  • Torroni A; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.
  • Weber K; Pacific Biosciences, Menlo Park, CA, USA.
  • Ambrosini R; Department of Environmental Sciences and Policy, University of Milan, Milan, Italy.
  • Bonisoli-Alquati A; Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA, USA.
  • Jarvis ED; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA; The Howard Hughes Medical Institute, Chevy Chase, MD, USA.
  • Gianfranceschi L; Department of Biosciences, University of Milan, Milan, Italy. Electronic address: luca.gianfranceschi@unimi.it.
  • Formenti G; Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA. Electronic address: gformenti@rockefeller.edu.
Cell Rep ; 42(1): 111992, 2023 01 31.
Article in En | MEDLINE | ID: mdl-36662619
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.
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Full text: 1 Database: MEDLINE Main subject: Swallows Limits: Animals Language: En Year: 2023 Type: Article
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Full text: 1 Database: MEDLINE Main subject: Swallows Limits: Animals Language: En Year: 2023 Type: Article