Genome assembly of the Neotropical marsh rat Holochilus nanus (Cricetidae: Sigmodontinae) brings insights on B and sex chromosome evolution

The Neotropical region comprises approximately 27% of mammal diversity, and rodents of the tribe Oryzomyini represent a significant portion of that. This diversity is reflected in the karyotype variability of the tribe, with a huge number of chromosomal rearrangements involving autosomal, sex, and B chromosomes. Supernumerary B chromosomes were described for more than 10 species, four of them belonging to the genus Holochilus. Therefore, we sequenced the genome of two H. nanus specimens with different karyotypes: a female with (HNA-XXB) and a male without (HNA-XY) a B chromosome. We also sequenced previously flow-sorted chromosomes from this species: two B (HNA-B1, HNA-B2) and the Y chromosome (HNA-Y). Genome assemblies of HNA-XY and HNA-XXB were compared, enabling the identification of ancient genome duplications that could result from fragments of the B chromosome. In addition, more than fifty scaffolds containing sequence blocks shared between the libraries of HNA-B1, HNA-B2, and HNA-Y were found. The sequence blocks mapped in metaphases of H. nanus presented hybridization signals on the centromeric region of the chromosomes, highlighting that the centromeric composition of H. nanus is highly variable. In addition, qPCR and RT-qPCR analysis evidenced that these sequences are expressed, indicating a role in the genome structure. Briefly, supernumeraries of H. nanus appear to be a mosaic of the genome and may contain genes and sequences crucial for its maintenance, in addition to its repetitive DNA fraction.