Biology Faculty Articles

Authors

Gaik Tamazian, St. Petersburg State University - Russia
Serguei Simonov, St. Petersburg State University - Russia
Pavel Dobrynin, St. Petersburg State University - Russia
Alexey Makunin, St. Petersburg State University - Russia
Anton Logachev, St. Petersburg State University - Russia
Aleksey Komissarov, St. Petersburg State University - Russia
Andrey Shevchenko, St. Petersburg State University - Russia
Vladimir Brukhin, St. Petersburg State University - Russia
Nikolay Cherkasov, St. Petersburg State University - Russia
Anton Svitin, St. Petersburg State University - Russia
Klaus-Peter Koepfli, St. Petersburg State University - Russia
Joan Pontius, St. Petersburg State University - Russia
Carlos A. Driscoll, National Institute on Alcohol Abuse and Alcoholism
Kevin Blackistone, National Institute on Alcohol Abuse and Alcoholism
Cristina Barr, National Institute on Alcohol Abuse and Alcoholism
David Goldman, National Institute on Alcohol Abuse and Alcoholism
Agostinho Antunes, Universidade do Porto - Portugal
Javier Quilez, Universitat Autonoma de Barcelona - Spain
Belen Lorente-Galdos, Universitat Pompeu Fabra-CSIC - Barcelona, Spain
Can Alkan, Bilkent University - Ankara, Turkey
Tomas Marques-Bonet, Universitat Pompeu Fabra-CSIC - Barcelona, Spain
Marilyn Menotti-Raymond, National Cancer Institute at Frederick
Victor A. David, National Cancer Institute at Frederick
Kristina Narfstrom, University of Missouri - Columbia
Stephen J. O'Brien, St. Petersburg State University - Russia; Nova Southeastern UniversityFollow

Document Type

Article

Publication Date

8-5-2014

Publication Title

GigaScience

Keywords

Felis catus, Domestic cat, Felis silvestris silvestris, European wildcat, Genome sequence, Annotation, Assembly

ISSN

2047-217X

Volume

3

Issue/No.

13

First Page

1

Last Page

3

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.

Comments

© 2014 Tamazian et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Additional Comments

Russian Ministry of Science grant #: 11.G34.31.0068; ERC Starting grant #: 260372; MCINN grant #: BFU2011-28549

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015

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