Sequencing and annotated analysis of the Holstein cow genome

S. Kõks; R. Lilleoja; E. Reimann; A. Salumets; P. Reemann; Ü. Jaakma

doi:10.1007/s00335-013-9464-0

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Sequencing and annotated analysis of the Holstein cow genome

Journal article

Peer reviewed

Sequencing and annotated analysis of the Holstein cow genome

S. Kõks, R. Lilleoja, E. Reimann, A. Salumets, P. Reemann and Ü. Jaakma

Mammalian Genome, Vol.24(7-8), pp.309-321

2013

DOI: https://doi.org/10.1007/s00335-013-9464-0

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Abstract

The aim of our study was to create a high-quality Holstein cow genome reference sequence and describe the different types of variations in this genome compared to the reference Hereford breed. We generated one fragment and three mate-paired libraries from genomic DNA. Raw files were mapped and paired to the reference cow (Bos taurus) genome assemblies bosTau6/UMD_3.1. BioScope (v1.3) software was used for mapping and variant analysis. Initial sequencing resulted in 2,842,744,008 of 50-bp reads. Average mapping efficiency was 78.4 % and altogether 2,168,425,497 reads and 98,022,357,422 bp were successfully mapped, resulting in 36.7X coverage. Tertiary analysis found 5,923,230 SNPs in the bovine genome, of which 3,833,249 were heterozygous and 2,089,981 were homozygous variants. Annotation revealed that 4,241,000 of all discovered SNPs were annotated in the dbSNP database and 1,682,230 SNPs were considered as novel. Large indel variations accounted for 48,537,190 bp of the entire genome and there were 138,504 of them. The largest deletion was 18,594 bp and the largest insertion was 13,498 bp. Another group of variants, small indels (n = 458,061), accounted for the total variation of 1,839,872 nucleotides in the genome. Only 92,115 small indels were listed in the dbSNP and therefore 365,946 small indels were novel. Finally, we identified 1,876 inversions in the bovine genome. In conclusion, this is another description of the Holstein cow genome and, similar to previous studies, we found a large amount of novel variations. Better knowledge of these variations could explain significant phenotypic differences (e.g., health, production, reproduction) between different breeds.

Details

Title: Sequencing and annotated analysis of the Holstein cow genome
Authors/Creators: S. Kõks (Author/Creator) - University of Tartu
R. Lilleoja (Author/Creator) - Estonian University of Life Sciences
E. Reimann (Author/Creator) - University of Tartu
A. Salumets (Author/Creator) - Competence Centre on Health Technologies (Estonia)
P. Reemann (Author/Creator) - University of Tartu
Ü. Jaakma (Author/Creator) - Estonian University of Life Sciences
Publication Details: Mammalian Genome, Vol.24(7-8), pp.309-321
Publisher: Springer New York
Identifiers: 991005540402407891
Copyright: © 2013 Springer Science+Business Media New York
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration
Citation topics: 1 Clinical & Life Sciences; 1.189 Genome Studies; 1.189.310 Population Genetics
Web Of Science research areas: Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Genetics & Heredity
ESI research areas: Molecular Biology & Genetics