Annotated features of domestic cat – Felis catus genome

Tamazian, Gaik; Simonov, Serguei; Dobrynin, Pavel; Makunin, Alexey; Logachev, Anton; Komissarov, Aleksey; Shevchenko, Andrey; Brukhin, Vladimir; Cherkasov, Nikolay; Svitin, Anton; Goldman, David B. (David Benjamin); Antunes, Agostinho; Quilez Oliete, Javier; Lorente-Galdós, Belén, 1981-; Alkan, Can; Marquès i Bonet, Tomàs, 1975-; Menotti-Raymond, Marylin; David, Victor A; Narfström, Kristina; O’Brien, Stephen J.

Annotated features of domestic cat – Felis catus genome

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dc.contributor.author Tamazian, Gaikca
dc.contributor.author Simonov, Sergueica
dc.contributor.author Dobrynin, Pavelca
dc.contributor.author Makunin, Alexeyca
dc.contributor.author Logachev, Antonca
dc.contributor.author Komissarov, Alekseyca
dc.contributor.author Shevchenko, Andreyca
dc.contributor.author Brukhin, Vladimirca
dc.contributor.author Cherkasov, Nikolayca
dc.contributor.author Svitin, Antonca
dc.contributor.author Goldman, David B. (David Benjamin)ca
dc.contributor.author Antunes, Agostinhoca
dc.contributor.author Quilez Oliete, Javierca
dc.contributor.author Lorente-Galdós, Belén, 1981-ca
dc.contributor.author Alkan, Canca
dc.contributor.author Marquès i Bonet, Tomàs, 1975-ca
dc.contributor.author Menotti-Raymond, Marylinca
dc.contributor.author David, Victor Aca
dc.contributor.author Narfström, Kristinaca
dc.contributor.author O’Brien, Stephen J.ca
dc.date.accessioned 2015-12-18T09:16:03Z
dc.date.available 2015-12-18T09:16:03Z
dc.date.issued 2014ca
dc.description.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./nFindings. 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./nConclusions. 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.
dc.description.sponsorship This work was supported, in part, by Russian Ministry of Science Mega-grant no.11.G34.31.0068; Stephen J. O’Brien, Principal Investigator and ERC Starting Grant (260372) and MICINN (Spain) BFU2011-28549 grants to Tomas Marques-Bonet.
dc.format.mimetype application/pdfca
dc.identifier.citation Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A et al. Annotated features of domestic cat – Felis catus genome. GigaScience. 2014;3:13. DOI: 10.1186/2047-217X-3-13ca
dc.identifier.doi http://dx.doi.org/10.1186/2047-217X-3-13
dc.identifier.issn 2047-217Xca
dc.identifier.uri http://hdl.handle.net/10230/25467
dc.language.iso engca
dc.publisher BioMed Centralca
dc.relation.ispartof GigaScience. 2014;3:13
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BFU2011-28549
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/260372
dc.rights © 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.ca
dc.rights.accessRights info:eu-repo/semantics/openAccessca
dc.rights.uri http://creativecommons.org/licenses/by/2.0
dc.subject.keyword Felis catus
dc.subject.keyword Domestic cat
dc.subject.keyword Felis silvestris silvestris
dc.subject.keyword European wildcat
dc.subject.keyword Genome sequence
dc.subject.keyword Annotation
dc.subject.keyword Assembly
dc.subject.other Gats
dc.subject.other Genomes
dc.title Annotated features of domestic cat – Felis catus genomeca
dc.type info:eu-repo/semantics/articleca
dc.type.version info:eu-repo/semantics/publishedVersionca

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