Phylogenomics of the dog and fox family (Canidae, Carnivora) revealed by chromosome painting

Abstract

Canid species (dogs and foxes) have highly rearranged karyotypes and thus represent a challenge for conventional comparative cytogenetic studies. Among them, the domestic dog is one of the best-mapped species in mammals, constituting an ideal reference genome for comparative genomic study. Here we report the results of genome-wide comparative mapping of dog chromosome-specific probes onto chromosomes of the dhole, fennec fox, and gray fox, as well as the mapping of red fox chromosome-specific probes onto chromosomes of the corsac fox. We also present an integrated comparative chromosome map between the species studied here and all canids studied previously. The integrated map demonstrates an extensive conservation of whole chromosome arms across different canid species. In addition, we have generated a comprehensive genome phylogeny for the Canidae on the basis of the chromosome rearrangements revealed by comparative painting. This genome phylogeny has provided new insights into the karyotypic relationships among the canids. Our results, together with published data, allow the formulation of a likely Canidae ancestral karyotype (CAK, 2n = 82), and reveal that at least 6-24 chromosomal fission/fusion events are needed to convert the CAK karyotype to that of the modern canids.

Comparative Genomics of 3 Farm Canids in Relation to the Dog

“…Thus, a comparison of their genomes has been mainly carried out with the use of comparative chromosome painting. Results of these studies, conducted with the use of whole chromosome painting probes for the dog, red fox and Japanese raccoon dog, were recently summarized by Graphodatsky et al [2008]. The authors hypothesized that the Canidae ancestral karyotype (CAK) was most likely composed of 41 chromosome pairs, including sex chromosomes (2n = 82).…”

Comparative cytogenetic mapping of three genes involved in sex determination in four species of the family <i>Canidae</i>

“…The chromosome comparative painting, with regard to the dog, red fox and arctic fox genomes, was performed by Graphodatsky et al (2000Graphodatsky et al ( , 2008. Altogether, 42 highly conserved segments in these species were identified.…”

“…Karyotypes of these species differ significantly from each other and their evolution has been extensively studied (Switonski et al, 2003;Graphodatsky et al, 2008). Foxes and Chinese raccoon dogs are also kept in captivity on fur farms.…”

“…Comparative analysis of genome organization in the family Canidae was mainly carried out using the socalled comparative chromosome painting (Graphodatsky et al, 2008). In addition, comparative analyses were conducted by mapping of DNA microsatellite markers or genes in chromosomes of the red fox, arctic fox and Chinese raccoon dog, but the number of the FISH mapped loci is still very low (Switonski et al, 2009).…”

A Comparison of Coding Sequence and Cytogenetic Localization of the Myostatin Gene in the Dog, Red Fox, Arctic Fox and Chinese Raccoon Dog

“…On the other hand, comparative chromosome painting of different canids brought a complete picture of karyotype evolution in this family [Graphodatsky et al, 2008]. It was proven that centric fusion and fission events were the main rearrangements in this process.…”