Biology Faculty Articles
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.
Additional Comments
Russian Ministry of Science grant #: 11.G34.31.0068; ERC Starting grant #: 260372; MCINN grant #: BFU2011-28549
NSUWorks Citation
Tamazian, Gaik; Serguei Simonov; Pavel Dobrynin; Alexey Makunin; Anton Logachev; Aleksey Komissarov; Andrey Shevchenko; Vladimir Brukhin; Nikolay Cherkasov; Anton Svitin; Klaus-Peter Koepfli; Joan Pontius; Carlos A. Driscoll; Kevin Blackistone; Cristina Barr; David Goldman; Agostinho Antunes; Javier Quilez; Belen Lorente-Galdos; Can Alkan; Tomas Marques-Bonet; Marilyn Menotti-Raymond; Victor A. David; Kristina Narfstrom; and Stephen J. O'Brien. 2014. "Annotated Features of Domestic Cat – Felis catus Genome." GigaScience 3, (13): 1-3. https://nsuworks.nova.edu/cnso_bio_facarticles/739
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
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.