A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

Buckley, R.; Davis, Brian W.; Brashear, Wesley; Farias, Fabiana; Kuroki, Kei; Graves, Tina; Hillier, La Deana W.; Kremitzki, Milinn; Li, Gang; Middleton, Rondo; Minx, Patrick; Tomlinson, Chad; Lyons, Leslie A.; Murphy, William J.; Warren, Wesley C.

doi:10.1371/journal.pgen.1008926

Cited by 101 publications

(121 citation statements)

References 99 publications

(140 reference statements)

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“…Approximately 12% SNPs (n = 6,955) had a MAF between (0 and 0.05) across all populations and were excluded. Overall, 50709 autosomal SNPs that were accurately mapped to the latest cat genome assembly (felCat 9.0 [ 51 ]) were included in downstream analyses.…”

Section: Resultsmentioning

confidence: 99%

Patterns of allele frequency differences among domestic cat breeds assessed by a 63K SNP array

2021

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Cats are ubiquitous companion animals that have been keenly associated with humans for thousands of years and only recently have been intentionally bred for aesthetically appealing coat looks and body forms. The intense selection on single gene phenotypes and the various breeding histories of cat breeds have left different marks on the genomes. Using a previously published 63K Feline SNP array dataset of twenty-six cat breeds, this study utilized a genetic differentiation-based method (di) to empirically identify candidate regions under selection. Defined as three or more overlapping (500Kb) windows of high levels of population differentiation, we identified a total of 205 candidate regions under selection across cat breeds with an average of 6 candidate regions per breed and an average size of 1.5 Mb per candidate region. Using the combined size of candidate regions of each breed, we conservatively estimate that a minimum of ~ 0.1–0.7% of the autosomal genome is potentially under selection in cats. As positive controls and tests of our methodology, we explored the candidate regions of known breed-defining genes (e.g., FGF5 for longhaired breeds) and we were able to detect the genes within candidate regions, each in its corresponding breed. For breed specific exploration of candidate regions under selection, eleven representative candidate regions were found to encompass potential candidate genes for several phenotypes such as brachycephaly of Persian (DLX6, DLX5, DLX2), curled ears of American Curl (MCRIP2, PBX1), and body-form of Siamese and Oriental (ADGRD1), which encourages further molecular investigations. The current assessment of the candidate regions under selection is empiric and detailed analyses are needed to rigorously disentangle effects of demography and population structure from artificial selection.

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Section: Resultsmentioning

confidence: 99%

Patterns of allele frequency differences among domestic cat breeds assessed by a 63K SNP array

2021

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“…Burmese cats, however, display a similar phenotype and gene dosage effects to ALX1/4 mutations in humans (Farlie et al, 2016). The recent improvement of the cat reference sequence (Buckley et al, 2020; Gandolfi et al, 2018) will further the utility of feline models of NTDs.…”

Section: Use Of Underutilized Animal Models May Better Inform Human Ntdsmentioning

confidence: 99%

Comparison of inherited neural tube defects in companion animals and livestock

Zarzycki

Thomas

Mazrier

2020

Birth Defects Research

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Neural tube defects (NTDs) are congenital malformations resulting from the improper or incomplete closure of the neural tube during embryonic development. A number of similar malformations of the protective coverings surrounding the central nervous system are also often included under this umbrella term, which may not strictly fit this definition. A range of NTD phenotypes exist and have been reported in humans and a wide range of domestic and livestock species. In the veterinary literature, these include cases of anencephaly, encephalocele, dermoid sinus, spina bifida, and craniorachischisis. While environmental factors have a role, genetic predisposition may account for a significant part of the risk of NTDs in these animal cases. Studies of laboratory model species (fish, birds, amphibians, and rodents) have been instrumental in improving our understanding of the neurulation process. In mice, over 200 genes that may be involved in this process have been identified and variant phenotypes investigated. Like laboratory mouse models, domestic animals and livestock species display a wide range of NTD phenotypes. They remain, however, a largely underutilized population and could complement already established laboratory models. Here we review reports of NTDs in companion animals and livestock, and compare these to other animal species and human cases. We aim to highlight the potential of nonlaboratory animal models for mutation discovery as well as general insights into the mechanisms of neurulation and the development of NTDs.

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“…This process allows for a rapid filtering of millions of variants to hundreds or tens of variants that can then be prioritized rapidly based upon the currently understood function of a particular gene. Next-generation reference genomes built using long-range sequencing technology [ 6 , 7 ], along with ever-improving genome annotations, are also rapidly improving the feasibility of using whole-genome resequencing to identify variants of interest for a particular trait or condition.…”

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confidence: 99%