Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.
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.
The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108;
Michael J
http://orcid.org/0000-0003-0253-4404
MJ
Montague
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843;
Gang
G
Li
Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201;
Barbara
B
Gandolfi
Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616;
Razib
R
Khan
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom;
Bronwen L
BL
Aken
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom;
Steven M J
SM
Searle
The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108;
Patrick
P
Minx
The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108;
LaDeana W
LW
Hillier
The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108;
Daniel C
DC
Koboldt
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843;
Brian W
BW
Davis
National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20886;
Carlos A
CA
Driscoll
National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20886;
Christina S
CS
Barr
National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD 20886;
Kevin
K
Blackistone
Catalan Institution for Research and Advanced Studies, Institute of Evolutionary Biology, Pompeu Fabra University, 08003 Barcelona, Spain;
Javier
J
Quilez
Catalan Institution for Research and Advanced Studies, Institute of Evolutionary Biology, Pompeu Fabra University, 08003 Barcelona, Spain;
Belen
B
Lorente-Galdos
Catalan Institution for Research and Advanced Studies, Institute of Evolutionary Biology, Pompeu Fabra University, 08003 Barcelona, Spain; Centro de Analisis Genomico 08028, Barcelona, Spain;
Tomas
T
Marques-Bonet
Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey;
Can
C
Alkan
Department of Biology, Indiana University, Bloomington, IN 47405;
Gregg W C
GW
Thomas
Department of Biology, Indiana University, Bloomington, IN 47405;
Matthew W
MW
Hahn
Laboratory of Genomic Diversity, Center for Cancer Research, Frederick, MD 21702;
Marilyn
M
Menotti-Raymond
Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg 199178, Russia; and Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL 33314.
Stephen J
SJ
O'Brien
The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108;
Richard K
RK
Wilson
Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201; wwarren@genome.wustl.edu wmurphy@cvm.tamu.edu lyonsla@missouri.edu.
Leslie A
LA
Lyons
Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843; wwarren@genome.wustl.edu wmurphy@cvm.tamu.edu lyonsla@missouri.edu.
William J
WJ
Murphy
The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108; wwarren@genome.wustl.edu wmurphy@cvm.tamu.edu lyonsla@missouri.edu.
Wesley C
WC
Warren
D000222:Adaptation, Physiological / Q000235:genetics; D000595:Amino Acid Sequence; D000818:Animals; D000829:Animals, Domestic / Q000235:genetics*; D000835:Animals, Wild / Q000235:genetics*; D060435:Carnivory; D002415:Cats / Q000145:classification / Q000235:genetics*; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D004285:Dogs; D005260:Female; D017353:Gene Deletion; D020440:Gene Duplication; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D008297:Male; D026901:Membrane Transport Proteins / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
D026901:Membrane Transport Proteins
Felis catus; domestication; genome