1
|
Secomandi S, Gallo GR, 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, Møller AP, Mountcastle J, Mousseau TA, 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 ED, Gianfranceschi L, Formenti G. A chromosome-level reference genome and pangenome for barn swallow population genomics. Cell Rep 2023; 42:111992. [PMID: 36662619 PMCID: PMC10044405 DOI: 10.1016/j.celrep.2023.111992] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/20/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
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.
Collapse
Affiliation(s)
- 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
| | | | - 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
| | | | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
| | | | - 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
| | | | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | - 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
| | | | - Anders P Møller
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France
| | | | - 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
| | | | - Roscoe Stanyon
- Department of Biology, University of Florence, Sesto Fiorentino (FI), Italy
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | | | - 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
| | | | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
2
|
Kauzálová T, Tomášek O, Mulder E, Verhulst S, Albrecht T. Telomere length is highly repeatable and shorter in individuals with more elaborate sexual ornamentation in a short-lived passerine. Mol Ecol 2022; 31:6172-6183. [PMID: 35150467 DOI: 10.1111/mec.16397] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 01/18/2022] [Accepted: 02/01/2022] [Indexed: 01/31/2023]
Abstract
Quantifying an individual's state as a fitness proxy has proven challenging, but accumulating evidence suggests that telomere length and attrition may indicate individual somatic state and success at self-maintenance, respectively. Sexual ornamentation is also thought to signal phenotypic quality, but links between telomeres and sexual ornamentation have been little explored. To address this issue, we examined whether telomere length and dynamics are predicted by the expression of a sexually selected ornament, the length of the outermost tail feathers (streamers), using longitudinal data from a population of European barn swallows (Hirundo rustica). In 139 adult individuals, each measured twice, we further assessed associations of telomere length with age, sex, breeding status and survival. Telomere length showed high individual repeatability (R = .97) across years while shortening with age in both sexes. Telomere length and dynamics were not significantly associated with survival to the next year, remaining lifespan or reproduction status (comparing breeding and nonbreeding yearlings). Tail streamer length, a sexually selected trait in barn swallows, was negatively associated with telomere length, independent of sex. Thus, telomere length may reflect the costs of carrying an elaborated sexual ornament, although ornament size did not significantly predict telomere shortening. In conclusion, telomere length in adult barn swallows is a highly consistent trait that shows a negative relationship with sexual ornamentation, suggesting a trade-off between sexual ornamentation and telomere length.
Collapse
Affiliation(s)
- Tereza Kauzálová
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Oldřich Tomášek
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ellis Mulder
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
| | - Tomáš Albrecht
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Brno, Czech Republic.,Department of Zoology, Faculty of Science, Charles University in Prague, Praha, Czech Republic
| |
Collapse
|