Targeted resequencing of coding DNAsequences for SNPdiscovery in nonmodel species
Abstract 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 partic...
Published in: | Molecular Ecology Resources |
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Online Access: | http://dx.doi.org/10.1111/1755-0998.12924 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12924 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12924 |
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crwiley:10.1111/1755-0998.12924 2024-09-15T18:41:46+00:00 Targeted resequencing of coding DNAsequences for SNPdiscovery in nonmodel species Förster, Daniel W. Bull, James K. Lenz, Dorina Autenrieth, Marijke Paijmans, Johanna L. A. Kraus, Robert H. S. Nowak, Carsten Bayerl, Helmut Kuehn, Ralph Saveljev, Alexander P. Sindičić, Magda Hofreiter, Michael Schmidt, Krzysztof Fickel, Jörns Leibniz-Gemeinschaft Deutscher Akademischer Austauschdienst Narodowe Centrum Nauki 2018 http://dx.doi.org/10.1111/1755-0998.12924 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12924 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12924 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology Resources volume 18, issue 6, page 1356-1373 ISSN 1755-098X 1755-0998 journal-article 2018 crwiley https://doi.org/10.1111/1755-0998.12924 2024-07-18T04:27:23Z Abstract 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 SNP s 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 SNP s can be valuable for genetic monitoring of wildlife species. Article in Journal/Newspaper Lynx Lynx lynx lynx Wiley Online Library Molecular Ecology Resources 18 6 1356 1373 |
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Wiley Online Library |
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crwiley |
language |
English |
description |
Abstract 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 SNP s 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 SNP s can be valuable for genetic monitoring of wildlife species. |
author2 |
Leibniz-Gemeinschaft Deutscher Akademischer Austauschdienst Narodowe Centrum Nauki |
format |
Article in Journal/Newspaper |
author |
Förster, Daniel W. Bull, James K. Lenz, Dorina Autenrieth, Marijke Paijmans, Johanna L. A. Kraus, Robert H. S. Nowak, Carsten Bayerl, Helmut Kuehn, Ralph Saveljev, Alexander P. Sindičić, Magda Hofreiter, Michael Schmidt, Krzysztof Fickel, Jörns |
spellingShingle |
Förster, Daniel W. Bull, James K. Lenz, Dorina Autenrieth, Marijke Paijmans, Johanna L. A. Kraus, Robert H. S. Nowak, Carsten Bayerl, Helmut Kuehn, Ralph Saveljev, Alexander P. Sindičić, Magda Hofreiter, Michael Schmidt, Krzysztof Fickel, Jörns Targeted resequencing of coding DNAsequences for SNPdiscovery in nonmodel species |
author_facet |
Förster, Daniel W. Bull, James K. Lenz, Dorina Autenrieth, Marijke Paijmans, Johanna L. A. Kraus, Robert H. S. Nowak, Carsten Bayerl, Helmut Kuehn, Ralph Saveljev, Alexander P. Sindičić, Magda Hofreiter, Michael Schmidt, Krzysztof Fickel, Jörns |
author_sort |
Förster, Daniel W. |
title |
Targeted resequencing of coding DNAsequences for SNPdiscovery in nonmodel species |
title_short |
Targeted resequencing of coding DNAsequences for SNPdiscovery in nonmodel species |
title_full |
Targeted resequencing of coding DNAsequences for SNPdiscovery in nonmodel species |
title_fullStr |
Targeted resequencing of coding DNAsequences for SNPdiscovery in nonmodel species |
title_full_unstemmed |
Targeted resequencing of coding DNAsequences for SNPdiscovery in nonmodel species |
title_sort |
targeted resequencing of coding dnasequences for snpdiscovery in nonmodel species |
publisher |
Wiley |
publishDate |
2018 |
url |
http://dx.doi.org/10.1111/1755-0998.12924 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12924 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12924 |
genre |
Lynx Lynx lynx lynx |
genre_facet |
Lynx Lynx lynx lynx |
op_source |
Molecular Ecology Resources volume 18, issue 6, page 1356-1373 ISSN 1755-098X 1755-0998 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
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_ |
1810486153905700864 |