Light whole genome sequence for SNP discovery across domestic cat breeds

Mullikin, James C.; Hansen, Nancy F.; Shen, Lei; Ebling, Heather; Donahue, William F.; Tao, Wei; Saranga, David J.; Brand, Adrianne; Rubenfield, Marc; Young, Alice; Cruz, Pedro; Driscoll, Carlos A.; David, Victor A.; Al-Murrani, Samer; Locniskar, Mary; Abrahamsen, Mitchell S.; O’Brien, Stephen J.; Smith, Douglas R.; Brockman, Jeffrey A.

doi:10.1186/1471-2164-11-406

Cited by 52 publications

(56 citation statements)

References 18 publications

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“…The assembly (FelCat5) comprises 2.35 gigabases (Gb) assigned to all 18 autosomes and the X chromosome relying on physical and linkage maps (11) with a further 11 megabases (Mb) in unplaced scaffolds. The assembly is represented by an N50 contig length of 20.6 kb and a scaffold N50 of 4.7 Mb, both of which show substantial improvement over previous light-coverage genome survey sequences that included only 60% of the genome (12,13). The Felis catus genome is predicted to contain 19,493 protein-coding genes and 1,855 noncoding RNAs, similar to dog (14).…”

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.

263

257

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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.

263

257

View full text Add to dashboard Cite

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“…We also analyzed a more conservative subset of the SNP matrix (40,225 SNPs) that excluded all SNP markers whose flanking probe sequence failed to produce a single unique BLAST hit with 100% nucleotide identity to the felCat5 (v6.2) genome reference sequence. This precaution was taken because SNPs on the array were identified from previous low coverage (1.9×) assemblies of the domestic cat genome, i.e., versions felCat3/4 Mullikin et al 2010). …”

Section: Mitochondrial Genome Sequencing and Assemblymentioning

confidence: 99%

“…The 63K array was designed using the domestic genome sequence as a reference with 62,897 SNPs ascertained from six domestic cats and an African wild cat (Felis lybica) (Mullikin et al 2010), distributed across all 18 autosomes and the X Chromosome. The vast majority of the SNPs on the array were ascertained in a pool of domestic cat breeds from low-coverage whole-genome sequencing (Mullikin et al 2010). Illumina array genotypes for all individuals were filtered to include only SNP call rates >95%.…”

Section: Snp Genotyping and Analysismentioning

confidence: 99%

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

et al. 2015

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Inter-species hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here, we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X-and Y-linked variants to sample ∼150 kb of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid time tree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination cold spots, which were highly enriched for signatures of selection-driven postdivergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the tree of life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.

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“…The European wildcat is an example of such a 'genome-enabled' taxon (Kohn et al, 2006), benefitting from the cross-species applicability of domestic cat data. Specifically, the recent sequencing of the domestic cat genome (Pontius et al, 2007;Mullikin et al, 2010;Montague et al, 2014;Tamazian et al, 2014), which has included SNP discovery in the African wildcat subspecies (Felis silvestris cafra), provides useful reference data for the discovery of new nuclear markers for assessing the introgression of domestic cat genes in the wild counterparts. Nussberger et al (2013) recently described a set of 48 nuclear SNPs for identifying European wildcats, domestic cats and their admixed progeny.…”

Section: Introductionmentioning

confidence: 99%

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

et al. 2015

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Endemic gene pools have been severely endangered by human-mediated hybridization, which is posing new challenges in the conservation of several vertebrate species. The endangered European wildcat is an example of this problem, as several natural populations are suffering introgression of genes from the domestic cat. The implementation of molecular methods for detecting hybridization is crucial for supporting appropriate conservation programs on the wildcat. In this study, genetic variation at 158 single-nucleotide polymorphisms (SNPs) was analyzed in 139 domestic cats, 130 putative European wildcats and 5 captive-bred hybrids (N = 274). These SNPs were variable both in wild (H E = 0.107) and domestic cats (H E = 0.340). Although we did not find any SNP that was private in any population, 22 SNPs were monomorphic in wildcats and pairwise F CT values revealed marked differences between domestic and wildcats, with the most divergent 35 loci providing an average F CT 40.74. The power of all the loci to accurately identify admixture events and discriminate the different hybrid categories was evaluated. Results from simulated and real genotypes show that the 158 SNPs provide successful estimates of admixture, with 100% hybrid individuals (two to three generations in the past) being correctly identified in STRUCTURE and over 92% using the NEWHYBRIDS' algorithm. None of the unclassified cats were wrongly allocated to another hybrid class. Thirty-five SNPs, showing the highest F CT values, provided the most parsimonious panel for robust inferences of parental and first generations of admixed ancestries. This approach may be used to further reconstruct the evolution of wildcat populations and, hopefully, to develop sound conservation guidelines for its legal protection in Europe.

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Light whole genome sequence for SNP discovery across domestic cat breeds

Cited by 52 publications

References 18 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

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

Toward a genome-wide approach for detecting hybrids: informative SNPs to detect introgression between domestic cats and European wildcats (Felis silvestris)

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