title: Annotated features of domestic cat - Felis catus genome.
abstract: BACKGROUND
  Domestic 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.
  
  
  RESULTS
  Here 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Gaik
authors.initials: G
authors.lastname: Tamazian
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Serguei
authors.initials: S
authors.lastname: Simonov
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Pavel
authors.initials: P
authors.lastname: Dobrynin
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Alexey
authors.initials: A
authors.lastname: Makunin
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Anton
authors.initials: A
authors.lastname: Logachev
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Aleksey
authors.initials: A
authors.lastname: Komissarov
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Andrey
authors.initials: A
authors.lastname: Shevchenko
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Brukhin
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Cherkasov
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Anton
authors.initials: A
authors.lastname: Svitin
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Klaus-Peter
authors.initials: KP
authors.lastname: Koepfli
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia.
authors.forename: Joan
authors.initials: J
authors.lastname: Pontius
authors.affiliation: Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA.
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Driscoll
authors.affiliation: Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Blackistone
authors.affiliation: Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA.
authors.forename: Cristina
authors.initials: C
authors.lastname: Barr
authors.affiliation: Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA.
authors.forename: David
authors.initials: D
authors.lastname: Goldman
authors.affiliation: CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, n. 289, 4050-123 Porto, Portugal.
authors.forename: Agostinho
authors.initials: A
authors.lastname: Antunes
authors.affiliation: Department of Animal and Food Science, Veterinary Molecular Genetics Service, Universitat Autónoma de Barcelona, 08003 Barcelona, Catalonia, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Quilez
authors.affiliation: IBE, Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, PRBB (The Barcelona Biomedical Research Park), 08003 Barcelona, Catalonia, Spain.
authors.forename: Belen
authors.initials: B
authors.lastname: Lorente-Galdos
authors.affiliation: Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey.
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
authors.affiliation: IBE, Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, PRBB (The Barcelona Biomedical Research Park), 08003 Barcelona, Catalonia, Spain.
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
authors.affiliation: Laboratory of Genomic Diversity, Frederick National Laboratory for Cancer Research, 21702 Frederick, MD, USA.
authors.forename: Marylin
authors.initials: M
authors.lastname: Menotti-Raymond
authors.affiliation: Laboratory of Genomic Diversity, Frederick National Laboratory for Cancer Research, 21702 Frederick, MD, USA.
authors.forename: Victor A
authors.initials: VA
authors.lastname: David
authors.affiliation: Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, 08028 Columbia, MO, USA.
authors.forename: Kristina
authors.initials: K
authors.lastname: Narfström
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia ; Oceanographic Center, Nova Southeastern University, 33004 Ft Lauderdale, FL, USA.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
keywords: Annotation; Assembly; Domestic cat; European wildcat; Felis catus; Felis silvestris silvestris; Genome sequence