An autosomal genetic linkage map of the domestic cat, Felis silvestris catus

Menotti‐Raymond, Marilyn; David, Victor A.; Schäffer, Alejandro A.; Tomlin, James F.; Eizirik, Eduardo; Phillip, Cornel J.; Wells, David W.; Pontius, Joan; Hannah, Steven S.; O’Brien, Stephen J.

doi:10.1016/j.ygeno.2008.11.004

Cited by 41 publications

(32 citation statements)

References 39 publications

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“…Divergence in regions harboring homologous recombination genes (RAD51B, ZFYVE26, BRCA2) may contribute to the high recombination rate reported for domestic cats relative to other mammals (59). Previous studies have suggested that domestication may select for an increase in recombination as a mechanism to generate diversity (60).…”

Section: Resultsmentioning

confidence: 99%

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Montague

Gandolfi

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.Felis catus | domestication | genome T he domestic cat (Felis silvestris catus) is a popular pet species, with as many as 600 million individuals worldwide (1). Cats and other members of Carnivora last shared a common ancestor with humans ∼92 million years ago (2, 3). The cat family Felidae includes ∼38 species that are widely distributed across the world, inhabiting diverse ecological niches that have resulted in divergent morphological and behavioral adaptations (4). The earliest archaeological evidence for human coexistence with cats dates to ∼9.5 kya in Cyprus and ∼5 kya in central China (5, 6), during periods when human populations adopted more agricultural lifestyles. Given their sustained beneficial role surrounding vermin control since the human transition to agriculture, any selective forces acting on cats may have been minimal subsequent to their domestication. Unlike many other domesticated mammals bred for food, herding, hunting, or security, most of the 30-40 cat breeds originated recently, within the past 150 y, largely due to selection for aesthetic rather than functional traits.Previous studies have assessed breed differentiation (6, 7), phylogenetic origins of the domestic cat (8), and the extent of recent introgression between domestic cats and wildcats (9, 10). However, little is known regarding the impact of the domestication process within the genomes of modern cats and how this compares with genetic changes accompanying selection identified...

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Section: Resultsmentioning

confidence: 99%

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Montague

Gandolfi

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

285

269

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“…Fca-6.2 is anchored to chromosome coordinates with two physical framework maps, a radiation hybrid map [3] and a short tandem repeat (STR) linkage map [4]. Further, 1943 distinct sites identified in a recently built linkage map using a single nucleotide polymorphism (SNP) genotyping array including ≈60,000 SNPs from an Illumina custom cat genotyping array are also mapped to the assembly.…”

Section: Data Descriptionmentioning

confidence: 99%

Annotated features of domestic cat – Felis catus genome

Tamazian¹,

Simonov²,

Dobrynin³

et al. 2014

GigaSci

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BackgroundDomestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors.FindingsHere we report a preliminary annotation of the whole genome sequence of Cinnamon, a domestic cat living in Columbia (MO, USA), bisulfite sequencing of Boris, a male cat from St. Petersburg (Russia), and light 30× sequencing of Sylvester, a European wildcat progenitor of cat domestication. The annotation includes 21,865 protein-coding genes identified by a comparative approach, 217 loci of endogenous retrovirus-like elements, repetitive elements which comprise about 55.7% of the whole genome, 99,494 new SNVs, 8,355 new indels, 743,326 evolutionary constrained elements, and 3,182 microRNA homologues. The methylation sites study shows that 10.5% of cat genome cytosines are methylated. An assisted assembly of a European wildcat, Felis silvestris silvestris, was performed; variants between F. silvestris and F. catus genomes were derived and compared to F. catus.ConclusionsThe presented genome annotation extends beyond earlier ones by closing gaps of sequence that were unavoidable with previous low-coverage shotgun genome sequencing. The assembly and its annotation offer an important resource for connecting the rich veterinary and natural history of cats to genome discovery.

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“…Additionally, some of the older maps may underestimate the size if they do not cover the entirety of the X chromosome. Similarly, the recombination length of the domestic cat autosomal map is longer than that observed in most reported mammalian maps (Menotti-Raymond et al 2008).…”

Section: Resultsmentioning

confidence: 68%

A Domestic cat X Chromosome Linkage Map and the Sex-LinkedorangeLocus: Mapping oforange, Multiple Origins and Epistasis Overnonagouti

et al. 2009

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A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange (O) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.93 whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be .30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be ,0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.93-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level.

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An autosomal genetic linkage map of the domestic cat, Felis silvestris catus

Cited by 41 publications

References 39 publications

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

Annotated features of domestic cat – Felis catus genome

A Domestic cat X Chromosome Linkage Map and the Sex-LinkedorangeLocus: Mapping oforange, Multiple Origins and Epistasis Overnonagouti

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