Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species
Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly va...
Published in: | Molecular Ecology Resources |
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Online Access: | https://publishup.uni-potsdam.de/frontdoor/index/index/docId/51258 https://doi.org/10.1111/1755-0998.12924 |
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ftubpotsdam:oai:kobv.de-opus4-uni-potsdam:51258 2023-11-05T03:45:27+01:00 Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species Förster, Daniel W. Bull, James K. Lenz, Dorina Autenrieth, Marijke Paijmans, Johanna L. A. (Dr.) Kraus, Robert H. S. Nowak, Carsten Bayerl, Helmut Kühn, Ralph Saveljev, Alexander P. Sindicic, Magda Hofreiter, Michael Schmidt, Krzysztof Fickel, Jörns 2018-07-06 https://publishup.uni-potsdam.de/frontdoor/index/index/docId/51258 https://doi.org/10.1111/1755-0998.12924 eng eng https://publishup.uni-potsdam.de/frontdoor/index/index/docId/51258 https://doi.org/10.1111/1755-0998.12924 info:eu-repo/semantics/closedAccess ddc:570 Institut für Biochemie und Biologie article doc-type:article 2018 ftubpotsdam https://doi.org/10.1111/1755-0998.12924 2023-10-08T22:35:01Z Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species. Article in Journal/Newspaper Lynx Lynx lynx lynx University of Potsdam: publish.UP Molecular Ecology Resources 18 6 1356 1373 |
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Open Polar |
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University of Potsdam: publish.UP |
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ftubpotsdam |
language |
English |
topic |
ddc:570 Institut für Biochemie und Biologie |
spellingShingle |
ddc:570 Institut für Biochemie und Biologie Förster, Daniel W. Bull, James K. Lenz, Dorina Autenrieth, Marijke Paijmans, Johanna L. A. (Dr.) Kraus, Robert H. S. Nowak, Carsten Bayerl, Helmut Kühn, Ralph Saveljev, Alexander P. Sindicic, Magda Hofreiter, Michael Schmidt, Krzysztof Fickel, Jörns Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species |
topic_facet |
ddc:570 Institut für Biochemie und Biologie |
description |
Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species. |
format |
Article in Journal/Newspaper |
author |
Förster, Daniel W. Bull, James K. Lenz, Dorina Autenrieth, Marijke Paijmans, Johanna L. A. (Dr.) Kraus, Robert H. S. Nowak, Carsten Bayerl, Helmut Kühn, Ralph Saveljev, Alexander P. Sindicic, Magda Hofreiter, Michael Schmidt, Krzysztof Fickel, Jörns |
author_facet |
Förster, Daniel W. Bull, James K. Lenz, Dorina Autenrieth, Marijke Paijmans, Johanna L. A. (Dr.) Kraus, Robert H. S. Nowak, Carsten Bayerl, Helmut Kühn, Ralph Saveljev, Alexander P. Sindicic, Magda Hofreiter, Michael Schmidt, Krzysztof Fickel, Jörns |
author_sort |
Förster, Daniel W. |
title |
Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species |
title_short |
Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species |
title_full |
Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species |
title_fullStr |
Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species |
title_full_unstemmed |
Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species |
title_sort |
targeted resequencing of coding dna sequences for snp discovery in nonmodel species |
publishDate |
2018 |
url |
https://publishup.uni-potsdam.de/frontdoor/index/index/docId/51258 https://doi.org/10.1111/1755-0998.12924 |
genre |
Lynx Lynx lynx lynx |
genre_facet |
Lynx Lynx lynx lynx |
op_relation |
https://publishup.uni-potsdam.de/frontdoor/index/index/docId/51258 https://doi.org/10.1111/1755-0998.12924 |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1111/1755-0998.12924 |
container_title |
Molecular Ecology Resources |
container_volume |
18 |
container_issue |
6 |
container_start_page |
1356 |
op_container_end_page |
1373 |
_version_ |
1781707968727744512 |