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Pangenomics provides insights into the role of synanthropy in barn swallow evolution

View ORCID ProfileSimona Secomandi, View ORCID ProfileGuido Roberto Gallo, Marcella Sozzoni, Alessio Iannucci, Elena Galati, Linelle Abueg, Jennifer Balacco, Manuela Caprioli, William Chow, Claudio Ciofi, Joanna Collins, View ORCID ProfileOlivier Fedrigo, Luca Ferretti, Arkarachai Fungtammasan, Bettina Haase, Kerstin Howe, Woori Kwak, Gianluca Lombardo, Patrick Masterson, View ORCID ProfileGraziella Messina, Anders Pape 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, View ORCID ProfileLuca Gianfranceschi, View ORCID ProfileGiulio Formenti
doi: https://doi.org/10.1101/2022.03.28.486082
Simona Secomandi
1Department of Biosciences, University of Milan, Milan, Italy
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Guido Roberto Gallo
1Department of Biosciences, University of Milan, Milan, Italy
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Marcella Sozzoni
1Department of Biosciences, University of Milan, Milan, Italy
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Alessio Iannucci
2Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
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Elena Galati
1Department of Biosciences, University of Milan, Milan, Italy
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Linelle Abueg
3Vertebrate Genome Lab, The Rockefeller University, New York City, USA
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Jennifer Balacco
3Vertebrate Genome Lab, The Rockefeller University, New York City, USA
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Manuela Caprioli
4Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
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William Chow
5Wellcome Sanger Institute, Cambridge, UK
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Claudio Ciofi
2Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
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Joanna Collins
5Wellcome Sanger Institute, Cambridge, UK
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Olivier Fedrigo
3Vertebrate Genome Lab, The Rockefeller University, New York City, USA
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  • ORCID record for Olivier Fedrigo
Luca Ferretti
6Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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Arkarachai Fungtammasan
7DNAnexus Inc, USA
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Bettina Haase
3Vertebrate Genome Lab, The Rockefeller University, New York City, USA
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Kerstin Howe
5Wellcome Sanger Institute, Cambridge, UK
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Woori Kwak
8Hoonygen, Seoul, Republic of Korea; Hoonygen, Seoul, Korea
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Gianluca Lombardo
6Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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Patrick Masterson
9National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Graziella Messina
1Department of Biosciences, University of Milan, Milan, Italy
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Anders Pape Møller
10Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France
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Jacquelyn Mountcastle
3Vertebrate Genome Lab, The Rockefeller University, New York City, USA
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Timothy A. Mousseau
11Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
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Joan Ferrer-Obiol
4Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
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Anna Olivieri
6Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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Arang Rhie
12Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome, National Human Genome Research Institute, National Institutes of Health (Bethesda, Maryland, USA)
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Diego Rubolini
4Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
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Marielle Saclier
13Department of Developmental and Stem Cell Biology, Institut Pasteur/CNRS UMR3738, Cellular Plasticity and Disease Modelling, 25 Rue du Docteur Roux, 75015 Paris
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Roscoe Stanyon
2Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
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David Stucki
14Pacific Biosciences, Menlo Park, CA, USA
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Françoise Thibaud-Nissen
9National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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James Torrance
5Wellcome Sanger Institute, Cambridge, UK
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Antonio Torroni
6Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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Kristina Weber
14Pacific Biosciences, Menlo Park, CA, USA
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Roberto Ambrosini
4Department of Environmental Sciences and Policy, University of Milan, Milan, Italy
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Andrea Bonisoli-Alquati
15Department of Biological Sciences, California State Polytechnic University - Pomona, Pomona, CA, USA
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Erich D. Jarvis
16The Rockefeller University (New York, NY, USA), Vertebrate Genome Laboratory, and HHMI
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Luca Gianfranceschi
1Department of Biosciences, University of Milan, Milan, Italy
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  • For correspondence: luca.gianfranceschi@unimi.it gformenti@rockefeller.edu
Giulio Formenti
16The Rockefeller University (New York, NY, USA), Vertebrate Genome Laboratory, and HHMI
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  • For correspondence: luca.gianfranceschi@unimi.it gformenti@rockefeller.edu
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Abstract

Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica. We then generated a reference-free multialignment with other bird genomes to identify genes under selection. Conservation analyses pointed at genes enriched for transcriptional regulation and neurodevelopment. The most conserved gene is CAMK2N2, with a potential role in fear memory formation. In addition, using all publicly available data, we generated a comprehensive catalogue of genetic markers. Genome-wide linkage disequilibrium scans identified potential selection signatures at multiple loci. The top candidate region comprises several genes and includes BDNF, a gene involved in stress response, fear memory formation, and tameness. We propose that the strict association with humans in this species is linked with the evolution of pathways typically under selection in domesticated taxa.

Competing Interest Statement

David Stucki and Kristina Weber are full-time employees at Pacific Biosciences, a company commercialising single-molecule sequencing technologies.

Footnotes

  • (simona.secomandi{at}unimi.it)

  • (guido.gallo{at}unimi.it)

  • (marcella.sozzoni{at}studenti.unimi.it)

  • (alessio.iannucci{at}unifi.it)

  • (elena.galati{at}unimi.it)

  • (labueg{at}rockefeller.edu)

  • (jbalacco{at}rockefeller.edu)

  • (manuela.caprioli{at}unimi.it)

  • (wc2{at}sanger.ac.uk)

  • (claudio.ciofi{at}unifi.it)

  • (jcc{at}sanger.ac.uk)

  • (ofedrigo{at}rockefeller.edu)

  • (luca.ferretti{at}unipv.it)

  • (chai{at}dnanexus.com)

  • (bet.ha{at}gmx.de)

  • (kj2{at}sanger.ac.uk)

  • (woori{at}hoonygen.com)

  • (gianluca.lombardo01{at}universitadipavia.it)

  • (patrick.masterson{at}nih.gov)

  • (graziella.messina{at}unimi.it)

  • (anders.moller{at}universite-paris-saclay.fr)

  • (jmountcast{at}rockefeller.edu)

  • (mousseau{at}sc.edu)

  • (joan.ferrer{at}unimi.it)

  • (anna.olivieri{at}unipv.it)

  • (arang.rhie{at}nih.gov)

  • (diego.rubolini{at}unimi.it)

  • (marielle.saclier{at}pasteur.fr)

  • (roscoe.stanyon{at}unifi.it)

  • (dstucki{at}pacificbiosciences.com)

  • (thibaudf{at}ncbi.nlm.nih.gov)

  • (james.torrance{at}sanger.ac.uk)

  • (antonio.torroni{at}unipv.it)

  • (kweber{at}pacb.com)

  • (roberto.ambrosini{at}unimi.it)

  • (aalquati{at}cpp.edu)

  • (ejarvis{at}rockefeller.edu)

  • ↵* Co-first authors.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Pangenomics provides insights into the role of synanthropy in barn swallow evolution
Simona Secomandi, Guido Roberto 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 Pape 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
bioRxiv 2022.03.28.486082; doi: https://doi.org/10.1101/2022.03.28.486082
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Pangenomics provides insights into the role of synanthropy in barn swallow evolution
Simona Secomandi, Guido Roberto 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 Pape 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
bioRxiv 2022.03.28.486082; doi: https://doi.org/10.1101/2022.03.28.486082

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