A high-resolution cat radiation hybrid and integrated FISH mapping resource for phylogenomic studies across Felidae

Abstract

We describe the construction of a high-resolution radiation hybrid (RH) map of the domestic cat genome, which includes 2662 markers, translating to an estimated average intermarker distance of 939 kilobases (kb). Targeted marker selection utilized the recent feline 1.9x genome assembly, concentrating on regions of low marker density on feline autosomes and the X chromosome, in addition to regions flanking interspecies chromosomal breakpoints. Average gap (breakpoint) size between cat-human ordered conserved segments is less than 900 kb. The map was used for a fine-scale comparison of conserved syntenic blocks with the human and canine genomes. Corroborative fluorescence in situ hybridization (FISH) data were generated using 129 domestic cat BAC clones as probes, providing independent confirmation of the long-range correctness of the map. Cross-species hybridization of BAC probes on divergent felids from the genera Profelis (serval) and Panthera (snow leopard) provides further evidence for karyotypic conservation within felids, and demonstrates the utility of such probes for future studies of chromosome evolution within the cat family and in related carnivores. The integrated map constitutes a comprehensive framework for identifying genes controlling feline phenotypes of interest, and to aid in assembly of a higher coverage feline genome sequence.

Figure 1

Integrated RH, FISH, and comparative maps for feline chromosome A3. CSOs for human chromosome 20 and 2 are shown to the right of each cat chromosome map (only the map scale is shown). Inferred centromere positions are shown by gray ovals. Comparative maps represent the output from AutoGRAPH-based analyses.

Figure 2

Lineage specific rearrangement totals for the domestic dog and domestic cat and rearrangement frequencies between the domestic cat, domestic dog, and human genomes. The lineage specific totals are #INTRA=the number of intrachromosomal and #INTER=the number of interchromosomal breakpoints. %INTRA=the percentage of rearrangements between two genomes that are the result of intrachromosomal breakpoints. %INTER=the percentage of rearrangements between two genomes that are the result of interchromosomal breakpoints.

Figure 3

FISH results for two feline BAC clone probes (green: 348A7; red: 348J11) hybridized to B4 orthologous on domestic cat (Fca), serval (Pse) and snow leopard (Pun) metaphase chromosomes. Note the same relative positioning of each probe in all three species. A summary of all FISH results relative to domestic cat chromosomes can be found in Supplementary Figure 2.