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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Publications at this Location » Publication #328482
Title: Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing

Author
item DE SILVA, KALPANI - University Of Louisville
item Heaton, Michael - Mike
item KALBFLEISCH, THEODORE - University Of Louisville

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 2/12/2016
Publication Date: 4/8/2016
Citation: De Silva, K., Heaton, M.P., Kalbfleisch, T.S. 2016. Identification of conserved genomic regions and variation therein amongst Cetartiodactyla species using next generation sequencing. UT-KBRIN Bioinformatics Summit 2016, April 8-10, 2016, Lake Barkley State Resort Park, Cadiz, KY. Poster #16.

Interpretive Summary:

Technical Abstract: Background Next Generation Sequencing has created an opportunity to genetically characterize an individual both inexpensively and comprehensively. In earlier work produced in our collaboration [1], it was demonstrated that, for animals without a reference genome, their Next Generation Sequence data can be mapped to the reference genome of another animal from which it has recently evolutionarily diverged producing a wealth of data on regions which have been evolutionarily conserved, and variation therein which has been tolerated. Materials and methods Since then, 16 different animals spanning 10 different Cetartiodactyla species have been sequenced and mapped to the Bos taurus genome at an equivalent coverage of 10X. Here, we describe this resource which is publicly available and may be found at 10x WGS of Cetartiodactyla Species Mapped to Cattle [http://www.ars.usda.gov/Research/docs.htm?docid=25590]. Results Analysis of these mappings identifies genomic regions in the respective species that are highly conserved relative to cattle. Within these conserved regions, species specific alleles selected for by evolution can be identified as well as sites that vary within the respective species. Here we present a summary of non-bovine alleles that can be measured across these species relative to the Bovine reference genome, and identify those which appear to be common to the species, and those which are likely variant within the species. References 1. Kalbfleisch T, Heaton M: Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes. F1000Research 2014; 2:244.