Open Access Highly Accessed Data Note

Annotated features of domestic cat – Felis catus genome

Gaik Tamazian1, Serguei Simonov1, Pavel Dobrynin1, Alexey Makunin1, Anton Logachev1, Aleksey Komissarov1, Andrey Shevchenko1, Vladimir Brukhin1, Nikolay Cherkasov1, Anton Svitin1, Klaus-Peter Koepfli1, Joan Pontius1, Carlos A Driscoll2, Kevin Blackistone2, Cristina Barr2, David Goldman2, Agostinho Antunes3, Javier Quilez4, Belen Lorente-Galdos5, Can Alkan6, Tomas Marques-Bonet5, Marylin Menotti-Raymond7, Victor A David7, Kristina Narfström8 and Stephen J O’Brien19*

Author Affiliations

1 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 199004, St. Petersburg, Russia

2 Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, 20852 Rockville, MD, USA

3 CIIMAR — Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, n. 289, 4050–123 Porto, Portugal

4 Department of Animal and Food Science, Veterinary Molecular Genetics Service, Universitat Autónoma de Barcelona, 08003 Barcelona, Catalonia, Spain

5 IBE, Institute of Evolutionary Biology, Universitat Pompeu Fabra-CSIC, PRBB (The Barcelona Biomedical Research Park), 08003 Barcelona, Catalonia, Spain

6 Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey

7 Laboratory of Genomic Diversity, Frederick National Laboratory for Cancer Research, 21702 Frederick, MD, USA

8 Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, 08028 Columbia, MO, USA

9 Oceanographic Center, Nova Southeastern University, 33004 Ft Lauderdale, FL, USA

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GigaScience 2014, 3:13  doi:10.1186/2047-217X-3-13

Published: 5 August 2014

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.

Findings

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.

Keywords:
Felis catus; Domestic cat; Felis silvestris silvestris; European wildcat; Genome sequence; Annotation; Assembly