Light whole genome sequence for SNP discovery across domestic cat breeds
Open accessAbstract
BACKGROUND: The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus--FeLV, feline coronavirus--FECV, feline immunodeficiency virus--FIV) that are homologues to human scourges (cancer, SARS, and AIDS respectively). However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery. DESCRIPTION: To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the publicly available 2X cat whole genome sequence. All sequence reads were assembled together to form a 3X whole genome assembly allowing the discovery of over three million SNPs. To reduce potential false positive SNPs due to the low coverage assembly, a low upper-limit was placed on sequence coverage and a high lower-limit on the quality of the discrepant bases at a potential variant site. In all domestic cats of different breeds: female Abyssinian, female American shorthair, male Cornish Rex, female European Burmese, female Persian, female Siamese, a male Ragdoll and a female African wildcat were sequenced lightly. We report a total of 964 k common SNPs suitable for a domestic cat SNP genotyping array and an additional 900 k SNPs detected between African wildcat and domestic cats breeds. An empirical sampling of 94 discovered SNPs were tested in the sequenced cats resulting in a SNP validation rate of 99%. CONCLUSIONS: These data provide a large collection of mapped feline SNPs across the cat genome that will allow for the development of SNP genotyping platforms for mapping feline diseases.
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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 [13]
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- Authors
- Mullikin, J. C., Hansen, N. F., Shen, L., Ebling, H., Donahue, W. F., Tao, W., Saranga, D. J., Brand, A., Rubenfield, M. J., Young, A. C., Cruz, P., Sequencing, N. C., Driscoll, C., David, V., Al-Murrani, S. W. K., Locniskar, M. F., Abrahamsen, M. S., O'Brien, S. J., Smith, D. R., & Brockman, J. A.
- Affiliations
- National Institutes of Health (US)
- National Cancer Institute (US)
- Hill's Pet Nutrition (United States) (US)
- Corresponding author
- Mullikin, James C
- ORCID
- Venue
- BMC Genomics
- Published
- 2010
- Volume
- 11
- Issue
- 1
- Pages
- 406
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC2996934
- OpenAlex
- W1969537396
- Cited by
- 56
- References
- 20
- Citations by year
- 2024: 2 · 2023: 1 · 2022: 2 · 2021: 2 · 2020: 3 · 2019: 2 · 2018: 1 · 2017: 1 · 2016: 5 · 2015: 8 · 2014: 5 · 2013: 9 · 2012: 10
- FWCI
- 4.31
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- NSUWorks (Nova Southeastern University) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- cats, single nucleotide polymorphisms, SNP discovery, cat breeds, SNP genotyping array, feline leukemia virus, feline coronavirus, feline immunodeficiency virus, SNP validation
- MeSH terms
- Animals, Cats, Chromosome Mapping, Female, Male, Reproducibility of Results, Polymerase Chain Reaction, Mutagenesis, Insertional, Genome, Sequence Analysis, DNA, DNA Primers, Polymorphism, Single Nucleotide, Genomics, Databases, Genetic
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