Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing
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 d...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Public Library of Science
2012
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/129387 |
| _version_ | 1855539850618339328 |
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| author | le Roex, Nikki Noyes, Harry Brass, Andrew Bradley, Daniel G. Kemp, Stephen J. Kay, Suzanne Helden, Paul D. van Hoal, Eileen G. |
| author_browse | Bradley, Daniel G. Brass, Andrew Helden, Paul D. van Hoal, Eileen G. Kay, Suzanne Kemp, Stephen J. Noyes, Harry le Roex, Nikki |
| author_facet | le Roex, Nikki Noyes, Harry Brass, Andrew Bradley, Daniel G. Kemp, Stephen J. Kay, Suzanne Helden, Paul D. van Hoal, Eileen G. |
| author_sort | le Roex, Nikki |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace129387 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2012 |
| publishDateRange | 2012 |
| publishDateSort | 2012 |
| publisher | Public Library of Science |
| publisherStr | Public Library of Science |
| record_format | dspace |
| spelling | CGSpace1293872025-01-24T14:20:45Z Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing le Roex, Nikki Noyes, Harry Brass, Andrew Bradley, Daniel G. Kemp, Stephen J. Kay, Suzanne Helden, Paul D. van Hoal, Eileen G. syncerus caffer snp 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. 2012-11-07 2023-03-10T14:34:14Z 2023-03-10T14:34:14Z Journal Article https://hdl.handle.net/10568/129387 en Open Access Public Library of Science le Roex, Nikki; Noyes, Harry; Brass, Andrew; Bradley, Daniel G.; Kemp, Stephen J.; Kay, Suzanne; Helden, Paul D. van; Hoal, Eileen G. 2012. Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing. PLoS ONE 7: e48792 |
| spellingShingle | syncerus caffer snp le Roex, Nikki Noyes, Harry Brass, Andrew Bradley, Daniel G. Kemp, Stephen J. Kay, Suzanne Helden, Paul D. van Hoal, Eileen G. Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing |
| title | Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing |
| title_full | Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing |
| title_fullStr | Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing |
| title_full_unstemmed | Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing |
| title_short | Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing |
| title_sort | novel snp discovery in african buffalo syncerus caffer using high throughput sequencing |
| topic | syncerus caffer snp |
| url | https://hdl.handle.net/10568/129387 |
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