Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput SequencingCitation formats

  • External authors:
  • Nikki le Roex
  • Harry Noyes
  • Daniel G. Bradley
  • Steven J. Kemp
  • Suzanne Kay
  • Paul D. van Helden
  • Eileen G. Hoal

Standard

Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing. / le Roex, Nikki; Noyes, Harry; Brass, Andrew; Bradley, Daniel G.; Kemp, Steven J.; Kay, Suzanne; van Helden, Paul D.; Hoal, Eileen G.

In: PLoS ONE, Vol. 7, No. 11, e48792, 07.11.2012.

Research output: Contribution to journalArticlepeer-review

Harvard

le Roex, N, Noyes, H, Brass, A, Bradley, DG, Kemp, SJ, Kay, S, van Helden, PD & Hoal, EG 2012, 'Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing', PLoS ONE, vol. 7, no. 11, e48792. https://doi.org/10.1371/journal.pone.0048792

APA

le Roex, N., Noyes, H., Brass, A., Bradley, D. G., Kemp, S. J., Kay, S., van Helden, P. D., & Hoal, E. G. (2012). Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing. PLoS ONE, 7(11), [e48792]. https://doi.org/10.1371/journal.pone.0048792

Vancouver

Author

le Roex, Nikki ; Noyes, Harry ; Brass, Andrew ; Bradley, Daniel G. ; Kemp, Steven J. ; Kay, Suzanne ; van Helden, Paul D. ; Hoal, Eileen G. / Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing. In: PLoS ONE. 2012 ; Vol. 7, No. 11.

Bibtex

@article{4d26de9e743443048c0d88784aaf234a,
title = "Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing",
abstract = "The African buffalo, Syncerus caffer, 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 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× 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. {\textcopyright} 2012 le Roex et al.",
author = "{le Roex}, Nikki and Harry Noyes and Andrew Brass and Bradley, {Daniel G.} and Kemp, {Steven J.} and Suzanne Kay and {van Helden}, {Paul D.} and Hoal, {Eileen G.}",
note = "GR066764MA, Wellcome Trust, United Kingdom",
year = "2012",
month = nov,
day = "7",
doi = "10.1371/journal.pone.0048792",
language = "English",
volume = "7",
journal = "PL o S One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "11",

}

RIS

TY - JOUR

T1 - Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing

AU - le Roex, Nikki

AU - Noyes, Harry

AU - Brass, Andrew

AU - Bradley, Daniel G.

AU - Kemp, Steven J.

AU - Kay, Suzanne

AU - van Helden, Paul D.

AU - Hoal, Eileen G.

N1 - GR066764MA, Wellcome Trust, United Kingdom

PY - 2012/11/7

Y1 - 2012/11/7

N2 - The African buffalo, Syncerus caffer, 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 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× 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. © 2012 le Roex et al.

AB - The African buffalo, Syncerus caffer, 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 Bos taurus genome assembly using both BWA and Bowtie software packages. A mean depth of 2.7× 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. © 2012 le Roex et al.

U2 - 10.1371/journal.pone.0048792

DO - 10.1371/journal.pone.0048792

M3 - Article

C2 - 23144973

VL - 7

JO - PL o S One

JF - PL o S One

SN - 1932-6203

IS - 11

M1 - e48792

ER -