Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing
Citation:
le Roex, N., Noyes, H., Brass, A., Bradley, D.G., Kemp, S.J., Kay, S., van Helden, P.D., Hoal, E.G., Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing, PLoS ONE, 7, 11, 2012, art. no. e48792Download Item:
Abstract:
The African buffalo,
Synceruscaffer
, is one of the most abundant and ecologically important species of megafauna in the
savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and
infectious diseases, such as bovine tuberculosis and corridor disease. Large-scale SNP discovery in this species would greatly
facilitate further research into the area of host genetics and disease susceptibility, as well as provide a wealth of sequence
information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9
animals, on an ABI SOLiD4 sequencer. The resulting short reads were mapped to the UMD3.1
Bostaurus
genome assembly
using both BWA and Bowtie software packages. A mean depth of 2.7
6
coverage over the mapped regions was obtained.
Btau4 gene annotation was added to all SNPs identified within gene regions. Bowtie and BWA identified a maximum of
2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was
validated by fluorescent genotyping in 87 individuals. 27 SNPs failed to amplify, and of the remaining 146 SNPs, 43?54% of
the Bowtie SNPs and 57?58% of the BWA SNPs were confirmed as polymorphic. dN/dS ratios found no evidence of positive
selection, and although there were genes that appeared to be under negative selection, these were more likely to be slowly
evolving house-keeping genes
Author's Homepage:
http://people.tcd.ie/dbradleyDescription:
PUBLISHED
Author: BRADLEY, DANIEL GERARD MARY
Type of material:
Journal ArticleCollections
Series/Report no:
PLoS ONE;7;
11;
Availability:
Full text availableKeywords:
savannah ecosystemMetadata
Show full item recordLicences: