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Silva DMZDA, Ruiz-Ruano FJ, Utsunomia R, Martín-Peciña M, Castro JP, Freire PP, Carvalho RF, Hashimoto DT, Suh A, Oliveira C, Porto-Foresti F, Artoni RF, Foresti F, Camacho JPM. Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish. BMC Biol 2021; 19:52. [PMID: 33740955 PMCID: PMC7976721 DOI: 10.1186/s12915-021-00991-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/24/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Eukaryote genomes frequently harbor supernumerary B chromosomes in addition to the "standard" A chromosome set. B chromosomes are thought to arise as byproducts of genome rearrangements and have mostly been considered intraspecific oddities. However, their evolutionary transcendence beyond species level has remained untested. RESULTS Here we reveal that the large metacentric B chromosomes reported in several fish species of the genus Astyanax arose in a common ancestor at least 4 million years ago. We generated transcriptomes of A. scabripinnis and A. paranae 0B and 1B individuals and used these assemblies as a reference for mapping all gDNA and RNA libraries to quantify coverage differences between B-lacking and B-carrying genomes. We show that the B chromosomes of A. scabripinnis and A. paranae share 19 protein-coding genes, of which 14 and 11 were also present in the B chromosomes of A. bockmanni and A. fasciatus, respectively. Our search for B-specific single-nucleotide polymorphisms (SNPs) identified the presence of B-derived transcripts in B-carrying ovaries, 80% of which belonged to nobox, a gene involved in oogenesis regulation. Importantly, the B chromosome nobox paralog is expressed > 30× more than the A chromosome paralog. This indicates that the normal regulation of this gene is altered in B-carrying females, which could potentially facilitate B inheritance at higher rates than Mendelian law prediction. CONCLUSIONS Taken together, our results demonstrate the long-term survival of B chromosomes despite their lack of regular pairing and segregation during meiosis and that they can endure episodes of population divergence leading to species formation.
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Affiliation(s)
- Duílio Mazzoni Zerbinato de Andrade Silva
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
| | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, UNESP, Campus de Bauru, Bauru, SP, 17033-360, Brazil
| | | | - Jonathan Pena Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCAR, São Carlos, SP, 13565-905, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Paula Paccielli Freire
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, USP, São Paulo, SP, 05508-900, Brazil
| | - Robson Francisco Carvalho
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Diogo T Hashimoto
- Centro de Aquicultura, Universidade Estadual Paulista, UNESP, Campus Jaboticabal, Jaboticabal, SP, 14884-900, Brazil
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, UNESP, Campus de Bauru, Bauru, SP, 17033-360, Brazil
| | - Roberto Ferreira Artoni
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCAR, São Carlos, SP, 13565-905, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
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