Chromosome painting in Tragulidae facilitates the reconstruction of Ruminantia ancestral karyotype

Abstract

Although Tragulidae, as the basal family in Ruminantia phylogenetic tree, is the key taxon for understanding the early chromosome evolution of extant ruminants, comparative molecular cytogenetic data on the tragulids are scarce. Here, we present the first genome-wide comparative map of the Java mouse deer (Tragulus javanicus, Tragulidae) revealed by chromosome painting with human and dromedary probes. Together with the published comparative maps of major representative cetartiodactyl species established with the same set of probes, our results allowed us to reconstruct a 2n = 48 Ruminantia ancestral karyotype, which is similar to the cetartiodactyl ancestral karyotype. The karyotype evolution of T. javanicus has involved multiple rearrangements, most of which appear to be apomorphic and have not found in karyotype evolution of pecoran species (i.e., Ruminantia excluding Tragulidae). The rate of chromosome evolution of the mouse deer was rather low-0.4 R/Ma, while the estimated tempo of chromosome changes on the lineages leading from Cetartiodactyla ancestor to Ruminantia and from Ruminantia to Pecora were roughly the same (about 1.2 R/Ma).

Comparative Molecular Cytogenetics in Cetartiodactyla

“…According to their results the karyotype evolution of T. javanicus has involved multiple rearrangements, most of which appear to be apomorphic and have not been found in pecoran species. Kulemzina et al [2011] conclude that the rate of chromosome evolution of the mouse deer was rather low, while the estimated rate of chromosome changes to the lineages leading from Cetartiodactyla ancestor to Ruminantia and from Ruminantia to Pecora were roughly the same.…”

“…[Kulemzina et al, 2011]. It is noteworthy that the inversions played a big role in the formation of RAK and PAK as 16 inversions distinguished the PAK from CAK.…”

“…The same set of dromedary probes were hybridized onto chromosomes of Capreolus pygargus [Dementyeva et al, 2010] and Tragulus javanicus [Kulemzina et al, 2011]. These comparative maps of major representative cetartiodactyl species, established with the same set of probes, allowed the reconstruction of the Ruminantia ancestral karyotype (RAK).…”

“…Cytogenetic analysis of T. napu and T. javanicus [Kim et al, 2004] showed that these 2 species have identical diploid numbers (2n = 32) and similar autosomal complements but with notable difference in the size and morphology of the parms of X and Y chromosomes. Kulemzina et al [2011] published the comparative map of T. javanicus , established by cross-species chromosome painting with human and dromedary probes. According to their results the karyotype evolution of T. javanicus has involved multiple rearrangements, most of which appear to be apomorphic and have not been found in pecoran species.…”

High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

“…We expect that some of these fragmented matches are the result of chromosomal rearrangements between domestic cattle and the harbour porpoise, two species that diverged approximately 60 Myrs ago within the Cetartiodactyla (Gatesy et al., ); we also expect that some other gaps are missing pieces in our assembly. Previous examinations of chromosomal rearrangements at this level (Avila et al., ; Kulemzina et al., , ; Pauciullo et al., ) have shown similar levels of synteny (i.e., some entirely matching chromosomes, others matching two to three pieces in the other taxa) between camel, pig and domestic cattle (Balmus et al., ). Based on these comparisons, we infer that our assembly represents a nearly complete genome of P. phocoena and that our largest scaffolds are nearly complete chromosomes.…”