Black rat (Rattus rattus) genomic variability characterized by chromosome painting

Abstract

Black rats are of outstanding interest in parasitology and infective disease analysis. We used chromosome paints from both the mouse ( Mus musculus) and the Norway rat ( Rattus norvegicus) to characterize the genome of two Black rat subspecies from Italy. Both subspecies have two large metacentrics (n. 1, 4) not present in the Norway rat (2n = 42). Rattus rattus rattus has a diploid number of 2n = 38, while Rattus rattus frugivorous has two small metacentric "supernumerary" or B chromosomes for a diploid number of 2n = 38 + 2B. The 21 mouse paints gave 38 signals on the R. r. rattus karyotype and 39 signals in the R. r. frugivorous karyotype. The two metacentrics, not present in R. norvegicus, were hybridized by mouse 16/1/17 and mouse 4/10/15. These chromosomes are homologous to: RRA1 = RNO 5/7, and RRA4 = RNO 9/11 and not "4/7" and "11/12" as previously reported. Furthermore, the synteny of Chr 13 of the R. r. frugivorous with R. norvegicus Chr 16 and mouse Chrs 8/14 is not complete, because there is a small pericentromeric insertion of RNO Chr 18 (mouse Chr 18). If we consider only the two metacentrics, RRA1 and RRA4, the principal differences between R. norvegicus and R. rattus, then we can propose the derived synteny of 124 genes in the black rat. A comparison of the Z index between rats and mice shows an acceleration of genomic evolution among genus, species, and subspecies. The chromosomal differences between R. r. rattus x R. r. frugivorous suggest that they may be classified as different species because hybrids would produce 50% unbalanced gametes.

Are ribosomal DNA clusters rearrangement hotspots? A case study in the genus Mus (Rodentia, Muridae)

“…In rodents, both positions are commonly observed (58% pericentromeric/31% distal vs 11% interstitial) [25,27,49-56]. Few mammal species (8/126) exhibit clusters in an interstitial position and in several cases, these result from chromosomal rearrangements [50,57].…”

“…Animals were either obtained from the Conversatoire Génétique de la Souris Sauvage (Institut des Sciences de l'Evolution, Montpellier, France) or collected in the wild. Four additional species ( Mus booduga, M. terricolor, Apodemus sylvaticus, Rattus rattus ) for which rDNA cluster data were available, were included in the analyses [25-27]. …”

“…Apodemus sylvaticus and Rattus rattus were used as outgroups in all analyses. The chromosomal homology between these species and the house mouse was previously determined by Matsubara et al [27] and Cavagna et al [25] respectively. However, as Matsubara et al [27] did not discriminate a distal and proximal segment corresponding to mouse chromosome 1 in A. sylvaticus , the presence or absence of clusters on these segments was coded as "?…”

AFLP genome scan in the black rat (Rattus rattus) from Madagascar: detecting genetic markers undergoing plague‐mediated selection

“…Indeed, the two species diverged about 2.9 Myr ago (Robins et al. 2008), the proportion of variable sites between their mitochondrial genomes is 9.62% (estimated between R. rattus , Genbank Accession number: EU273707, and R. norvegicus Wistar strain, Genbank Accession number: NC_001665.2) and chromosome painting revealed complete homology and synteny between R. rattus and R. norvegicus in 16 of 18 chromosomes (Cavagna et al. 2002).…”

Contrasted Patterns of Selection on MHC-Linked Microsatellites in Natural Populations of the Malagasy Plague Reservoir

“…Indeed, the two species only diverged 2.9My ago [58], and the gene syntheny was shown to be extremely high between both species [59]. Consequently, it appears safe to assume that locations of the studied microsatellites are the same in R. rattus as in R. norvegicus .…”