De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos)
Development of molecular markers that are well-suited for use in studies on wildlife dispersal can greatly enhance conservation efforts of species affected by climate change and human-induced landscape alterations. Single nucleotide polymorphisms (SNPs) are a promising marker for such studies; howev...
| Autor principal: | |
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| Formato: | H2 |
| Lenguaje: | Inglés |
| Publicado: |
SLU/Dept. of Wildlife, Fish and Environmental Studies
2011
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| Materias: |
| _version_ | 1855570510616723456 |
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| author | Norman, Anita J |
| author_browse | Norman, Anita J |
| author_facet | Norman, Anita J |
| author_sort | Norman, Anita J |
| collection | Epsilon Archive for Student Projects |
| description | Development of molecular markers that are well-suited for use in studies on wildlife dispersal can greatly enhance conservation efforts of species affected by climate change and human-induced landscape alterations. Single nucleotide polymorphisms (SNPs) are a promising marker for such studies; however, development of SNPs in non-model species with limited or no sequence data can be challenging. This study addresses these challenges in a unique way. Reduced representation libraries (RRL) of ten individual brown bears representing the geographic range in Sweden were high-throughput sequenced on one lane of the Illumina HiSeq2000, yielding reads 100 bases in length. These reads were filtered and processed following two methods: assembly using ABySS and alignment using Stacks. Putative SNPs were then called. The alignment-only method using Stacks was not only simpler and more efficient, it also utilized 4X more reads and yielded 30X more SNPs than the assembly method. The putative SNPs showed a clear haplotype pattern that distinguished the two known lineages of brown bear in Sweden. The outcome of this study is a good start for further work in the development of a SNP-based dispersal model with the brown bear as the model species. |
| format | H2 |
| id | RepoSLU2994 |
| institution | Swedish University of Agricultural Sciences |
| language | Inglés |
| publishDate | 2011 |
| publishDateSort | 2011 |
| publisher | SLU/Dept. of Wildlife, Fish and Environmental Studies |
| publisherStr | SLU/Dept. of Wildlife, Fish and Environmental Studies |
| record_format | eprints |
| spelling | RepoSLU29942024-07-11T11:56:26Z De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos) Sekvensering och SNP svep hos brunbjörn Norman, Anita J SNPs brown bear Ursus arctos reduced representation high-throughput sequencing Development of molecular markers that are well-suited for use in studies on wildlife dispersal can greatly enhance conservation efforts of species affected by climate change and human-induced landscape alterations. Single nucleotide polymorphisms (SNPs) are a promising marker for such studies; however, development of SNPs in non-model species with limited or no sequence data can be challenging. This study addresses these challenges in a unique way. Reduced representation libraries (RRL) of ten individual brown bears representing the geographic range in Sweden were high-throughput sequenced on one lane of the Illumina HiSeq2000, yielding reads 100 bases in length. These reads were filtered and processed following two methods: assembly using ABySS and alignment using Stacks. Putative SNPs were then called. The alignment-only method using Stacks was not only simpler and more efficient, it also utilized 4X more reads and yielded 30X more SNPs than the assembly method. The putative SNPs showed a clear haplotype pattern that distinguished the two known lineages of brown bear in Sweden. The outcome of this study is a good start for further work in the development of a SNP-based dispersal model with the brown bear as the model species. SLU/Dept. of Wildlife, Fish and Environmental Studies 2011 H2 eng https://stud.epsilon.slu.se/2994/ |
| spellingShingle | SNPs brown bear Ursus arctos reduced representation high-throughput sequencing Norman, Anita J De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos) |
| title | De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos) |
| title_full | De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos) |
| title_fullStr | De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos) |
| title_full_unstemmed | De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos) |
| title_short | De novo sequencing and SNP discovery in the Scandinavian brown bear (Ursus arctos) |
| title_sort | de novo sequencing and snp discovery in the scandinavian brown bear (ursus arctos) |
| topic | SNPs brown bear Ursus arctos reduced representation high-throughput sequencing |