A Radiation Hybrid Map of the Cat Genome: Implications for Comparative Mapping

Abstract

Ordered gene maps of mammalian species are becoming increasingly valued in assigning gene variants to function in human and animal models, as well as recapitulating the natural history of genome organization. To extend this power to the domestic cat, a radiation hybrid (RH) map of the cat was constructed integrating 424 Type I-coding genes with 176 microsatellite markers, providing coverage over all 20 feline chromosomes. Alignment of parallel RH maps of human and cat reveal 100 conserved segments ordered (CSOs) between the species, nearly three times the number observed with reciprocal chromosome painting analyses. The observed number is equivalent to theoretical predictions of the number of conserved segments to be found between cat and human, implying that 300-400 Type I gene markers is sufficient to reveal nearly all conserved segments for species that exhibit the most frequently observed "slow" rate of genome reorganization. The cat-human RH map comparisons provide a new genomic tool for comparative gene mapping in the cat and related Felidae, and provide confirmation that the cat genome organization is remarkably conserved compared with human. These data demonstrate that ordered RH-based gene maps provide the most precise assessment of comparing genomes, short of contig construction or full-sequence determination.

Recurrent Sites for New Centromere Seeding

“…Great apes: common chimpanzee (Pan troglodytes, PTR), gorilla (Gorilla gorilla, GGO), Borneo (Pongo pygmaeus pygmaeus, PPY-B), and Sumatra (Pongo pygmaeus abelii PPY-S) orangutan; Old World Monkeys (OWM): rhesus monkey (Macaca mulatta, MMU, Cercopithecinae), sacred baboon (Papio hamadryas, PHA, Cercopithecinae), African green monkey (Cercopithecus aethiops, CAE, Cercopithecinae), silvered leaf-monkey (Presbytis cristata, PCR, Colobinae); New World Monkeys (NWM): wooly monkey (Lagothrix lagothricha, LLA, Atelinae), common marmoset (Callithrix jacchus, CJA, Callitrichinae), dusky titi (Callicebus moloch, CMO, Callicebinae), squirrel monkey (Saimiri boliviensis, SBO); prosimians: ring-tailed lemur (Lemur catta, LCA). The domestic cat (Felix Catus, FCA) was used as an outgroup because its karyotype is highly conserved and closely resembles the ancestral karyotype of mammals (Murphy et al 2000;Yang et al 2000). The sequence encompassed by each human BAC reported in Table 1 (BACs in regular style) was searched for conservation against mouse genome.…”

Inherited Motor Neuron Disease in Domestic Cats: A Model of Spinal Muscular Atrophy

“…7). To determine whether the homology of synteny in the SMN region was maintained between cats and humans, we used PCR primers designed from exon 3 and intron 3 to amplify DNA of a feline radiation hybrid panel (14,19). Feline SMN mapped as a single locus on feline chromosome A1 near the genes HEXB and PPAP2A and~15 cR from the feline microsatellite FCA084 (data not shown) (16).…”

“…The PCR step was carried out in 50-L reactions that contained 1.5 mM of MgCl 2 for 35 cycles at 95°C for 20 s, 57°C for 30 s, and 72°C for 1 60 s. The product was sequenced by automated dideoxy nucleotide chain termination chemistry in the University of Michigan DNA Sequencing Core Laboratory. The primers 5'-TTGGTCAGAAGACGGCT-GCGTT-3' and 5'-CCAGCATGATAGGAAGTGTGGTGG-3' designed from the feline SMN cDNA sequence were used in a pooled PCR-based method (13) to screen 3 ϫ 10 7 pfu of a cat testis cDNA bacteriophage library (14). After plaque purification, clones were rescued into the phagemid pBluescript (Stratagene, La Jolla, CA) and sequenced completely on both strands.…”

“…PCR products were separated on 12% polyacrylamide gels and stained with ethidium bromide. PCR-based radiation hybrid mapping of feline SMN was performed on a 93-hybrid 5000-rad feline wholegenome radiation hybrid panel as described (14,16).…”

The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals

“…Radiation hybrid mapping of additional feline Type 1 gene markers assigned loci to intervals on feline chromosomes C1, D2, or F1, predicted a priori based on previously identified CSOs (Murphy et al 2000), and further refine the F1-C1 syntenic boundary to the vicinity of 1q21 in the human genome ( Fig. 2; see Supplemental Material available online at www.genome.org).…”