Holochilus nanus Genome sequencing and assembly

Genomic analysis of the rodent Holochilus nanus (Cricetidae: Sigmodontinae: Oryzomyini) with emphasis on the interface between B and sex chromosomes.Holochilus nanus (HNA) (2n = 56 and FN = 56) belongs to the rodent tribe Oryzomyini, the most taxonomically diverse tribe of the Sigmodontinae subfamily. Comparative cytogenetic by ZooFISH on 15 Oryzomyini species using the entire chromosome set of HNA revealed a high genome reshuffling involving autosomal, sex, and B chromosomes. Within mammals, Bs are most frequent in rodents, which account for 70% of the mammalian species that bear them. Application of next generation sequencing in the analysis of B chromosomes 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 HNA specimens with and without B chromosome, and two B chromosomes plus the Y of HNA, isolated by flow sorting, in order to investigate the sequence homology shared between B and the sex chromosomes of HNA. In addition, the sequenced genome of HNA will be used to search for repetitive DNA sequences, aiming at understanding the role of these elements in the karyotype variability of Oryzomyini species.