Initial sequence and comparative analysis of the cat genome
Open accessAbstract
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing approximately 65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.
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The FelCat5 assembly has an N50 contig length of 20.6 kb and a scaffold N50 of 4.7 Mb, both substantially improved over previous light-coverage genome survey sequences that included only 60% of the genome.
“The assembly is represented by an N50 contig length of 20.6 kb and a scaffold N50 of 4.7 Mb, both of which show substantial improvement over previous light-coverage genome survey sequences that included only 60% of the genome (12,13).”
From Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication (2014) · cites this paper as [12]
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Self-citation
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Sequencing technologies and genome sequencing
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- Authors
- Pontius, J. U., Mullikin, J. C., Smith, D. R., Agencourt Sequencing Team, Lindblad-Toh, K., Gnerre, S., Clamp, M., Chang, J., Stephens, R., Neelam, B., Volfovsky, N., Schäffer, A. A., Agarwala, R., Narfström, K., Murphy, W. J., Giger, U., Roca, A. L., Antunes, A., Menotti-Raymond, M., Yuhki, N., Pecon-Slattery, J., Johnson, W. E., Bourque, G., Tesler, G., Program, N. C. S., & O’Brien, S. J.
- Affiliations
- National Cancer Institute (US)
- National Human Genome Research Institute (US)
- Broad Institute (US)
- National Institutes of Health (US)
- University of Missouri (US)
- University of Pennsylvania (US)
- Universidade do Porto (PT)
- University of California San Diego (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2007-11
- Volume
- 17
- Issue
- 11
- Pages
- 1675-1689
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2045150
- OpenAlex
- W2098353360
- Cited by
- 368
- References
- 106
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 18 · 2023: 15 · 2022: 16 · 2021: 18 · 2020: 13 · 2019: 22 · 2018: 15 · 2017: 9 · 2016: 24 · 2015: 23 · 2014: 29 · 2013: 20 · 2012: 18
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- NSUWorks (Nova Southeastern University) (submittedVersion)
- Funders
- U.S. Department of Health and Human Services
- Winn Feline Foundation
- National Institutes of Health (n01co12400-79-0-22, N01-CO-12400)
- National Human Genome Research Institute
- National Cancer Institute (N01CO12400, N01-CO-012400)
- National Center for Research Resources (RR02512, P40RR002512)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- Abyssinian cat, genome assembly, comparative genomics, genome annotation, conserved sequence blocks, orthologs, repetitive elements, endogenous retroviruses, mitochondrial pseudogenes, microRNA, chromosomal inversions, translocation, single nucleotide polymorphisms, insertion/deletion polymorphism, microsatellite markers, mammalian genome evolution
- MeSH terms
- Animals, Cats, Dogs, Humans, Models, Genetic, Repetitive Sequences, Nucleic Acid, Genome, Microsatellite Repeats, Polymorphism, Single Nucleotide, Genomics, MicroRNAs, Mice, Rats
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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