Holochilus sciureus (HSC) (2n = 56+1B, and FN = 56) belongs to the rodent tribe Oryzomyini, the most taxonomically diverse tribe of the Sigmodontinae subfamily. Cytogenetic studies on the Oryzomyini reflect such diversity revealing an exceptional range of karyotype variability. Comparative cytogenetics by Zoo-FISH on 15 Oryzomyini species using the entire chromosome set of HSC revealed a highly genome reshuffling involving autosomal, sex, and B chromosomes. Hybridization of Bs, X, and Y chromosome probes of HSC on 12 Oryzomyini species revealed that Bs and sex chromosomes share a common heterochromatic region. Also, the diversity of Oryzomyini Bs in number, size, morphology, and genetic content may be explained by the independent origin of these chromosomes in different subgroups of species. Within mammals, Bs are most frequent in rodents, which account for 70% of the mammalian species that bear them. The use of chromosome-specific DNA libraries constructed by microdissection or chromosome flow sorting has allowed detailed analysis of the origin and molecular structure of Bs. Application of next-generation sequencing in the analysis of Bs revealed that they comprise fragments of standard chromosomes and organellar genomes. Therefore, we propose to analyze for the first time the whole genome sequence of HSC females with and without B chromosome, and the chromosomes B1, B2, X, and Y of HSC, isolated by flow sorting, in order to investigate the sequence homology shared between Bs and the sex chromosomes of HSC. In addition, the sequenced genome of HSC will be used to search for repetitive DNA clusters aiming at understanding the role of these elements in the karyotype variability of Oryzomyini species.
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