Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia
BACKGROUND: The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequ...
| Autores principales: | , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2016
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/82801 |
| _version_ | 1855537927926317056 |
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| author | Onyango, M.G. Aitken, N.C. Jack, C. Chuah, A. Oguya, J. Djikeng, Appolinaire Kemp, Stephen J. Bellis, G.A. Nicholas, A. Walker, P.J. Duchemin, J.B. |
| author_browse | Aitken, N.C. Bellis, G.A. Chuah, A. Djikeng, Appolinaire Duchemin, J.B. Jack, C. Kemp, Stephen J. Nicholas, A. Oguya, J. Onyango, M.G. Walker, P.J. |
| author_facet | Onyango, M.G. Aitken, N.C. Jack, C. Chuah, A. Oguya, J. Djikeng, Appolinaire Kemp, Stephen J. Bellis, G.A. Nicholas, A. Walker, P.J. Duchemin, J.B. |
| author_sort | Onyango, M.G. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | BACKGROUND: The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges. RESULTS: This study employed the GBS method to isolate SNP markers de novo from whole genome amplified Culicoides brevitarsis genomic DNA. The individuals were collected from regions representing two different Australian patterns of BTV strain distribution: the Northern Territory (NT) and the east coast. We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. Two loci showed a very strong signal for selection and were unique to the NT population. Bayesian analysis with STRUCTURE indicated a possible two-population cluster. CONCLUSIONS: The results suggest that genotyping vectors with high density markers in combination with biological and environmental data is useful. However, more extensive sampling over a wider spatial and temporal range is needed. The presence of sub-structure in populations and loci under natural selection indicates the need for further investigation of the role of vectors in shaping the two Australian systems of BTV transmission. The described workflow is transferable to genotyping of small, non-model organisms, including arthropod vectors of pathogens of economic and medical importance. |
| format | Journal Article |
| id | CGSpace82801 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2016 |
| publishDateRange | 2016 |
| publishDateSort | 2016 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace828012025-12-08T09:54:28Z Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia Onyango, M.G. Aitken, N.C. Jack, C. Chuah, A. Oguya, J. Djikeng, Appolinaire Kemp, Stephen J. Bellis, G.A. Nicholas, A. Walker, P.J. Duchemin, J.B. animal diseases animal genetics epidemiology livestock BACKGROUND: The advent of genotyping by Next Generation Sequencing has enabled rapid discovery of thousands of single nucleotide polymorphism (SNP) markers and high throughput genotyping of large populations at an affordable cost. Genotyping by sequencing (GBS), a reduced representation library sequencing method, allows highly multiplexed sequencing of genomic subsets. This method has limitations for small organisms with low amounts of genomic DNA, such as the bluetongue virus (BTV) vectors, Culicoides midges. RESULTS: This study employed the GBS method to isolate SNP markers de novo from whole genome amplified Culicoides brevitarsis genomic DNA. The individuals were collected from regions representing two different Australian patterns of BTV strain distribution: the Northern Territory (NT) and the east coast. We isolated 8145 SNPs using GBS. Phylogenetic analysis conducted using the filtered 3263 SNPs revealed the presence of a distinct C. brevitarsis sub-population in the NT and this was confirmed by analysis of mitochondrial DNA. Two loci showed a very strong signal for selection and were unique to the NT population. Bayesian analysis with STRUCTURE indicated a possible two-population cluster. CONCLUSIONS: The results suggest that genotyping vectors with high density markers in combination with biological and environmental data is useful. However, more extensive sampling over a wider spatial and temporal range is needed. The presence of sub-structure in populations and loci under natural selection indicates the need for further investigation of the role of vectors in shaping the two Australian systems of BTV transmission. The described workflow is transferable to genotyping of small, non-model organisms, including arthropod vectors of pathogens of economic and medical importance. 2016-12 2017-07-18T08:22:03Z 2017-07-18T08:22:03Z Journal Article https://hdl.handle.net/10568/82801 en Open Access Springer Onyango, M.G., Aitken, N.C., Jack, C., Chuah, A., Oguya, J., Djikeng, A., Kemp, S., Bellis, G.A., Nicholas, A., Walker, P.J. and Duchemin, J.B. 2016. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia. BMC Genomics 17(1):769. |
| spellingShingle | animal diseases animal genetics epidemiology livestock Onyango, M.G. Aitken, N.C. Jack, C. Chuah, A. Oguya, J. Djikeng, Appolinaire Kemp, Stephen J. Bellis, G.A. Nicholas, A. Walker, P.J. Duchemin, J.B. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia |
| title | Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia |
| title_full | Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia |
| title_fullStr | Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia |
| title_full_unstemmed | Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia |
| title_short | Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia |
| title_sort | genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of culicoides brevitarsis in the northern territory australia |
| topic | animal diseases animal genetics epidemiology livestock |
| url | https://hdl.handle.net/10568/82801 |
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