PD and AA searched for Numts. PD assembled F. All authors read and approved the final manuscript. Petersburg Academy of Veterinary Medicine for preparing samples of Boris the cat. This work was supported, in part, by Russian Ministry of Science Mega-grant no. National Center for Biotechnology Information , U. Journal List Gigascience v. Published online Aug 5. Petersburg, Russia Find articles by Gaik Tamazian. Petersburg, Russia Find articles by Serguei Simonov. Petersburg, Russia Find articles by Pavel Dobrynin. Petersburg, Russia Find articles by Alexey Makunin.
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Corresponding author. Gaik Tamazian: moc. Received Dec 1; Accepted Jul This article has been cited by other articles in PMC. Abstract Background Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly genetic diseases analogous to human disorders. 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. Conclusions The presented genome annotation extends beyond earlier ones by closing gaps of sequence that were unavoidable with previous low-coverage shotgun genome sequencing.
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How do I Write the Annotation? What is an Annotated Bibliography? Pantheon, The cat family has two well-characterized numt loci: 1 Lopez- numt in domestic cats, which comprises a 7. One large kb scaffold scaffold ID , showed 12 Lopez- numt s and likely represents the chromosome D2 numt tandem repeat.
S2 shows the chromosome distribution of numt s. Phylogenetic analyses of homologous numt s suggest multiple numt historic insertions over time in the cat genome Fig. In addition, novel numt sequences that included mitochondrial genes not present in Lopez- numt e. Based on differences in mutational rates and differences in the genetic code between the mitochondrial and nuclear genomes, it would seem that the transpositions of numt sequence across the cat genome and in other species are likely vestigial and with no function.
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The chromosomal disposition of feline numt and the multiple phylogenetic lineages reflect a more recent record of dynamic mitochondrial DNA transposition to disparate chromosomal positions in the ancestors of modern cats, providing yet another informative character for genomic inferences. Domestic cats carry endogenous retroviral genomic sequences descended from ancestral infections and integrations into the germline.
Full-length RD virus is inducible with halogenated pyrimidines.
Because RD is relatively innocuous but replicates well in human tissues, RDbased vector constructs have been used extensively in human gene therapy applications Relander et al. Endogenous feline leukemia viruses enFeLVs are a second group with nine to 16 copies per cat genome, many of them truncated and insertionally polymorphic, with sequences related to exogenous feline leukemia virus exFeLV Roca et al.
By themselves, enFeLVs do not cause disease, but they recombine with exogenous viruses to create new virus subtypes that can augment the pathogenicity of exogenous FeLV Roy-Burman A phylogenetic analysis of endogenous FeLV LTR sequences from the cat genome sequence defined two distinct lineages, suggesting that at least two different germline FeLV infections occurred in the history of cats Fig. Numerous RDrelated traces were also evident, consistent with the presence of both functional and truncated endogenous RD sequences Supplemental Fig.
The other less abundant FERV sequences were related to human ERV lineages and to other mammalian retroviruses including mouse mammary tumor viruses. The contig sequence reads were examined to discover sites of nucleotide variation in cats or, more precisely, sites of heterozygous SNPs in Cinnamon.
The long stretches of alternating homozygous and heterozygous segments are likely a consequence of the domestication process, close inbreeding during Abyssinian breed development, and disease pedigree establishment. Homozygous segments also occur in dogs, possibly for the same reasons Lindblad-Toh et al. The FLA region sequence Fig.
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To explore the breed-specific patterns of common segment homozygosity, as well as to estimate the size of linkage disequilibrium stretches in cat breeds, a group of SNPs were genotyped in multiple individuals from each of 24 certified cat breeds. For each region, eight SNPs fell within 15 kb of each other, while an additional 27 SNPs were added at kb intervals to fill out the kb. Conditional on homozygosity within the first kb window, the extent of homozygosity was recorded, and the fraction of loci that remained homozygous at different distances was plotted Supplemental Fig.
The fraction of homozygous loci decays as a function of physical distance roughly threefold faster in cats than in dogs Lindblad-Toh et al. A rough estimate based on genotyping two to three individuals per breed would suggest approximately three to five haplotypes per breed within kb and kb windows, very similar to that seen for dog breeds. The extent of homozygosity together with haplotype diversity can be used to infer the number of equally spaced SNPs required for genomewide association mapping within a specific breed.
The feline genome sequence, here annotated, has immediate value in many aspects of biology, particularly in the discovery of the genetic basis of hereditary and infectious diseases Table 5 ; Supplemental Table S1.
Other areas to benefit include comparative genomics for which mammalian CSBs, representing both long genes and short conserved elements, provide the means of reconstructing chromosome exchanges that punctuate mammal evolution. Forensic evidence from cats, already established in legal precedent Menotti-Raymond et al. Cat models of emerging infectious agents can now be approached in the context of host genetic variation in immune response, such as the cat FLA complex studied here.
In spite of the benefits derived from the comparative genomics-based genome annotation presented here, there are some notable weaknesses due to a light coverage. These limitations notwithstanding, our analysis of the cat genome sequence in a comparative context has allowed an examination of genome structure and features, genome evolution, and useful applications for comparative genomics and cat biology. The cat genome annotation has increased the depth of evolutionary perspective required for comparative inference.
We anticipate that genome annotation of additional species will reveal the cryptic process of species differentiation, development and adaptation. S1 ; however, the availability of the marker cat RH map, the BAC and fosmid libraries, breed populations, linkage map, and gene discovery analyses has aptly complemented the cat genome annotation exercise.
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Saranga, Marc Rubenfield, Matthew J. View all Initial sequence and comparative analysis of the cat genome Joan U. Pontius 1 , 17 , James C.