A Survey of Whole-Genome Variation in Domestic Cats

Genetic diversity is a very important factor for health in animals yet artificial selection is known to increase the burden of deleterious variants. Both cats and dogs have been under strong artificial selection for a variety of traits, but cats in particular for aesthetic pleasing traits, such as, coat color, pattern or length. Given great efforts are being made to identify disease alleles and circumvent their dissemination within breeds of both species, extensive WGS data is needed to empower these studies. The 99 Lives Cat Genome Sequencing initiative was launched to sequence the genomes of domestic and wild felines to serve this purpose of providing a more comprehensive source of feline variation. We examined 65 unrelated domestic cat genomes of various breeds. Genome alignment was done with BWA to cat reference v.6.2, Platypus was used for variant calling and SnpEff for annotation, all performed by Maverix Biomics, Inc. We identified 38,907,808 variants, in which 27,915,282 are SNPs and 10,992,526 are small (< 6 bp) insertions or deletions. The loss of function (LoF) SNPs identified was 111, and the average between cats was 46. Cats had similar numbers of variants identified overall. A more systematic survey of LoF SNPs is being carried out to remove false positives and identify true variants that are tolerable or disease causing. By examining larger surveys of putatively deleterious variants among domestic cat breeds we hope to confirm their tolerance and aid disease investigations of causative alleles. On behalf of 99 Lives Cat Sequencing Consortium.