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do Nascimento Moreira C, Cardoso AL, Valeri MP, Ventura K, Ferguson-Smith MA, Yonenaga-Yassuda Y, Svartman M, Martins C. Characterization of repetitive DNA on the genome of the marsh rat Holochilus nanus (Cricetidae: Sigmodontinae). Mol Genet Genomics 2023:10.1007/s00438-023-02038-w. [PMID: 37233800 DOI: 10.1007/s00438-023-02038-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
Repetitive DNA are sequences repeated hundreds or thousands of times and an abundant part of eukaryotic genomes. SatDNA represents the majority of the repetitive sequences, followed by transposable elements. The species Holochilus nanus (HNA) belongs to the rodent tribe Oryzomyini, the most taxonomically diverse of Sigmodontinae subfamily. Cytogenetic studies on Oryzomyini reflect such diversity by revealing an exceptional range of karyotype variability. However, little is known about the repetitive DNA content and its involvement in chromosomal diversification of these species. In the search for a more detailed understanding about the composition of repetitive DNA on the genome of HNA and other species of Oryzomyini, we employed a combination of bioinformatic, cytogenetic and molecular techniques to characterize the repetitive DNA content of these species. RepeatExplorer analysis showed that almost half of repetitive content of HNA genome are composed by Long Terminal Repeats and a less significant portion are composed by Short Interspersed Nuclear Elements and Long Interspersed Nuclear Elements. RepeatMasker showed that more than 30% of HNA genome are composed by repetitive sequences, with two main waves of repetitive element insertion. It was also possible to identify a satellite DNA sequence present in the centromeric region of Oryzomyini species, and a repetitive sequence enriched on the long arm of HNA X chromosome. Also, comparative analysis between HNA genome with and without B chromosome did not evidence any repeat element enriched on the supernumerary, suggesting that B chromosome of HNA is composed by a fraction of repeats from all the genome.
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Affiliation(s)
- Camila do Nascimento Moreira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil.
| | - Adauto Lima Cardoso
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Mirela Pelizaro Valeri
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Karen Ventura
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Yatiyo Yonenaga-Yassuda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Cesar Martins
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
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Oliveira da Silva W, Rosa CC, Ferguson-Smith MA, O'Brien PCM, Saldanha J, Rossi RV, Pieczarka JC, Nagamachi CY. The emergence of a new sex-system (XX/XY 1Y 2) suggests a species complex in the "monotypic" rodent Oecomys auyantepui (Rodentia, Sigmodontinae). Sci Rep 2022; 12:8690. [PMID: 35610291 PMCID: PMC9130129 DOI: 10.1038/s41598-022-12706-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/11/2022] [Indexed: 11/15/2022] Open
Abstract
X-autosome translocation (XY1Y2) has been reported in distinct groups of vertebrates suggesting that the rise of a multiple sex system within a species may act as a reproductive barrier and lead to speciation. The viability of this system has been linked with repetitive sequences located between sex and autosomal portions of the translocation. Herein, we investigate Oecomys auyantepui, using chromosome banding and Fluorescence In Situ Hybridization with telomeric and Hylaeamys megacephalus whole-chromosome probes, and phylogenetic reconstruction using mtDNA and nuDNA sequences. We describe an amended karyotype for O. auyantepui (2n = 64♀65♂/FNa = 84) and report for the first time a multiple sex system (XX/XY1Y2) in Oryzomyini rodents. Molecular data recovered O. auyantepui as a monophyletic taxon with high support and cytogenetic data indicate that O. auyantepui may exist in two lineages recognized by distinct sex systems. The Neo-X exhibits repetitive sequences located between sex and autosomal portions, which would act as a boundary between these two segments. The G-banding comparisons of the Neo-X chromosomes of other Sigmodontinae taxa revealed a similar banding pattern, suggesting that the autosomal segment in the Neo-X can be shared among the Sigmodontinae lineages with a XY1Y2 sex system.
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Affiliation(s)
- Willam Oliveira da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Celina Coelho Rosa
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Juliane Saldanha
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Rogério Vieira Rossi
- Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
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Di-Nizo CB, Banci KRDS, Sato-Kuwabara Y, Silva MJDJ. Advances in cytogenetics of Brazilian rodents: cytotaxonomy, chromosome evolution and new karyotypic data. COMPARATIVE CYTOGENETICS 2017; 11:833-892. [PMID: 29362668 PMCID: PMC5769678 DOI: 10.3897/compcytogen.v11i4.19925] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/23/2017] [Indexed: 05/31/2023]
Abstract
Rodents constitute one of the most diversified mammalian orders. Due to the morphological similarity in many of the groups, their taxonomy is controversial. Karyotype information proved to be an important tool for distinguishing some species because some of them are species-specific. Additionally, rodents can be an excellent model for chromosome evolution studies since many rearrangements have been described in this group.This work brings a review of cytogenetic data of Brazilian rodents, with information about diploid and fundamental numbers, polymorphisms, and geographical distribution. We point out that, even with the recent efforts on cytogenetic studies in this group, many species lack karyotypic data. Moreover, we describe for the first time the karyotype of Carterodon sulcidens (Lund, 1838) (Family Echimyidae), a new fundamental number for an undescribed species of Neacomys Thomas, 1900 (Family Cricetidae, Subfamily Sigmodontinae), and illustrate the karyotype of a Brazilian specimen of Mus musculus Linnaeus, 1758 (Family Muridae). This review compiles the cytogenetic data on Brazilian rodents reported in the last three decades, after the last revision published in 1984, including synonyms, chromosomal variations, and geographic distribution. Additionally, it also reinforces that Brazilian biodiversity is still poorly known, considering the new data reported here.
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Affiliation(s)
- Camilla Bruno Di-Nizo
- Laboratório de Ecologia e Evolução, Instituto Butantan, Avenida Vital Brazil, 1500, CEP 05503-900, São Paulo, SP, Brazil
| | | | - Yukie Sato-Kuwabara
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, CEP 05508-900, São Paulo, SP, Brazil
| | - Maria José de J. Silva
- Laboratório de Ecologia e Evolução, Instituto Butantan, Avenida Vital Brazil, 1500, CEP 05503-900, São Paulo, SP, Brazil
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Suárez-Villota EY, Carmignotto AP, Brandão MV, Percequillo AR, Silva MJDJ. Systematics of the genus Oecomys (Sigmodontinae: Oryzomyini): molecular phylogenetic, cytogenetic and morphological approaches reveal cryptic species. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx095] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Elkin Y Suárez-Villota
- Laboratório de Ecologia e Evolução, Instituto Butantan, Av. Vital Brazil, São Paulo, Brazil
- Instituto de Ciencias Marinas y Limnológicas, Universidad Austral de Chile, Edificio Emilio Pugín, campus Isla Teja, Valdivia, Chile
| | - Ana Paula Carmignotto
- Laboratório de Diversidade Animal, Departamento de Biologia, Universidade Federal de São Carlos, campus Sorocaba, Rodovia João Leme dos Santos, Sorocaba, São Paulo, Brazil
| | - Marcus Vinícius Brandão
- Laboratório de Diversidade Animal, Departamento de Biologia, Universidade Federal de São Carlos, campus Sorocaba, Rodovia João Leme dos Santos, Sorocaba, São Paulo, Brazil
| | - Alexandre Reis Percequillo
- Departamento de Ciências Biolόgicas, Escola Superior de Agricultura ‘Luiz de Queiroz’, Universidade de São Paulo, Av. Pádua Dias, Piracicaba, São Paulo, Brazil
| | - Maria José de J Silva
- Laboratório de Ecologia e Evolução, Instituto Butantan, Av. Vital Brazil, São Paulo, Brazil
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