Characterization of repetitive DNA on the genome of the marsh rat Holochilus nanus (Cricetidae: Sigmodontinae)

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dc.contributor.authordo Nascimento Moreira, Camila [UNESP]
dc.contributor.authorCardoso, Adauto Lima [UNESP]
dc.contributor.authorValeri, Mirela Pelizaro
dc.contributor.authorVentura, Karen
dc.contributor.authorFerguson-Smith, Malcolm Andrew
dc.contributor.authorYonenaga-Yassuda, Yatiyo
dc.contributor.authorSvartman, Marta
dc.contributor.authorMartins, Cesar [UNESP]
dc.contributor.institutionUniversidade Estadual Paulista (UNESP)
dc.contributor.institutionUniversidade Federal de Minas Gerais (UFMG)
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.contributor.institutionUniversity of Cambridge
dc.date.accessioned2023-07-29T16:14:39Z
dc.date.available2023-07-29T16:14:39Z
dc.date.issued2023-01-01
dc.description.abstractRepetitive 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.en
dc.description.affiliationDepartamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista, SP
dc.description.affiliationDepartamento de Genética Ecologia e Evolução Instituto de Ciências Biológicas Universidade Federal de Minas Gerais, MG
dc.description.affiliationDepartamento de Genética e Biologia Evolutiva Instituto de Biociências Universidade de São Paulo, SP
dc.description.affiliationCambridge Resource Centre for Comparative Genomics Department of Veterinary Medicine University of Cambridge
dc.description.affiliationUnespDepartamento de Biologia Estrutural e Funcional Instituto de Biociências Universidade Estadual Paulista, SP
dc.identifierhttp://dx.doi.org/10.1007/s00438-023-02038-w
dc.identifier.citationMolecular Genetics and Genomics.
dc.identifier.doi10.1007/s00438-023-02038-w
dc.identifier.issn1617-4623
dc.identifier.issn1617-4615
dc.identifier.scopus2-s2.0-85160218495
dc.identifier.urihttp://hdl.handle.net/11449/249984
dc.language.isoeng
dc.relation.ispartofMolecular Genetics and Genomics
dc.sourceScopus
dc.subjectB chromosomes
dc.subjectCentromere
dc.subjectLong terminal repeats
dc.subjectSatellite DNA
dc.subjectX chromosomes
dc.titleCharacterization of repetitive DNA on the genome of the marsh rat Holochilus nanus (Cricetidae: Sigmodontinae)en
dc.typeArtigo
unesp.author.orcid0000-0001-9490-5457[1]
unesp.author.orcid0000-0002-7287-5039[2]
unesp.author.orcid0000-0003-1286-2567[3]
unesp.author.orcid0000-0002-9106-1663[4]
unesp.author.orcid0000-0001-9372-1381[5]
unesp.author.orcid0000-0001-8879-0542[6]
unesp.author.orcid0000-0003-3239-1862[7]
unesp.author.orcid0000-0003-3534-974X[8]

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