Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes

Abstract

The emergence of genome-integrated molecular cytogenetic resources allows for comprehensive comparative analysis of gross karyotype architecture across related species. The identification of evolutionarily conserved chromosome segment (ECCS) boundaries provides deeper insight into the process of chromosome evolution associated with speciation. We evaluated the genome-wide distribution and relative orientation of ECCSs in three wild canid species with diverse karyotypes (red fox, Chinese raccoon dog, and gray fox). Chromosome-specific panels of dog genome-integrated bacterial artificial chromosome (BAC) clones spaced at ∼10-Mb intervals were used in fluorescence in situ hybridization analysis to construct integrated physical genome maps of these three species. Conserved evolutionary breakpoint regions (EBRs) shared between their karyotypes were refined across these and eight additional wild canid species using targeted BAC panels spaced at ∼1-Mb intervals. Our findings suggest that the EBRs associated with speciation in the Canidae are compatible with recent phylogenetic groupings and provide evidence that these breakpoints are also recurrently associated with spontaneous canine cancers. We identified several regions of domestic dog sequence that share homology with canid B chromosomes, including additional cancer-associated genes, suggesting that these supernumerary elements may represent more than inert passengers within the cell. We propose that the complex karyotype rearrangements associated with speciation of the Canidae reflect unstable chromosome regions described by the fragile breakage model.

Identification of polymorphisms and transcriptional activity of the proto-oncogene KIT located on both autosomal and B chromosomes of the Chinese raccoon dog

“…Several copies of KIT paralogs have previously been found on B chromosomes in the Chinese raccoon dog, whereas there is a single copy on chromosome 6 (Becker et al, 2011). Sequence alignment between the Chinese raccoon dog, arctic fox, silver fox, and dog suggested it was possible to distinguish paralogs on the B chromosome from those on the A chromosome.…”

“…The B chromosomes range in size and are characterized as Bi, Bii, and Biii types (Becker et al, 2011). The proto-oncogene KIT is present on all B chromosomes of the Chinese raccoon dog, in addition to chromosome 6 (Graphodatsky et al, 2005;Yudkin et al, 2007;Becker et al, 2011).…”

“…The B chromosomes range in size and are characterized as Bi, Bii, and Biii types (Becker et al, 2011). The proto-oncogene KIT is present on all B chromosomes of the Chinese raccoon dog, in addition to chromosome 6 (Graphodatsky et al, 2005;Yudkin et al, 2007;Becker et al, 2011). The proto-oncogene KIT is also localized on all B chromosomes of red fox and the structure and sequence of the B-specific KIT were found to be highly conserved (Graphodatsky et al, 2005;Yudkin et al, 2007).…”

Three-Dimensional Positioning of B Chromosomes in Fibroblast Nuclei of the Red Fox and the Chinese Raccoon Dog

“…The painting probes generated by microdissection of one B chromosome were specific to all Bs, suggesting their high homology [Trifonov et al, 2002]. The recent observation that specific canine probes hybridize in different patterns to the 3 B chromosome types of the Chinese racoon dog [Becker et al, 2011] offers new possibilities for distinction between the B types. However, identification of characteristic FISH patterns on interphase nuclei seems to be more difficult than on metaphase chromosomes.…”

“…Localization of a gene locus (the proto-oncogene C-KIT ) in Bs of the red fox and the Chinese and Japanese raccoon dogs has changed this view [Graphodatsky et al, 2005]. Then, other additional autosomal regions homologous to canine autosomes were identified in canid Bs [Yudkin et al, 2007;Becker et al, 2011]. However, until now there is no unequivocal evidence that these gene copies are transcribed.…”