Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model 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...
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ftzenodo:oai:zenodo.org:4953012 2024-09-15T18:41:46+00:00 Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model 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, Joerns Paijmans, Johanna L. A. Kraus, Robert H. S. 2018-06-06 https://doi.org/10.5061/dryad.3f4jr01 unknown Zenodo https://doi.org/10.1111/1755-0998.12924 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.3f4jr01 oai:zenodo.org:4953012 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode genetic monitoring CDS Eurasian lynx Lynx lynx single-nucleotide polymorphism hybridization capture info:eu-repo/semantics/other 2018 ftzenodo https://doi.org/10.5061/dryad.3f4jr0110.1111/1755-0998.12924 2024-07-26T23:43:16Z 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 non-model 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 non-model 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 bi-allelic 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. CDS-baits and SNP data This ZIP folder contains bait sequences (FASTA), the 96 SNP-panel, SNP genotypes (Illumina and Fluidigm), and an R script. Details can be found in the READ ME file. DRYAD.zip Other/Unknown Material Lynx Lynx lynx lynx Zenodo |
institution |
Open Polar |
collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
genetic monitoring CDS Eurasian lynx Lynx lynx single-nucleotide polymorphism hybridization capture |
spellingShingle |
genetic monitoring CDS Eurasian lynx Lynx lynx single-nucleotide polymorphism hybridization capture 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, Joerns Paijmans, Johanna L. A. Kraus, Robert H. S. Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species |
topic_facet |
genetic monitoring CDS Eurasian lynx Lynx lynx single-nucleotide polymorphism hybridization capture |
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 non-model 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 non-model 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 bi-allelic 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. CDS-baits and SNP data This ZIP folder contains bait sequences (FASTA), the 96 SNP-panel, SNP genotypes (Illumina and Fluidigm), and an R script. Details can be found in the READ ME file. DRYAD.zip |
format |
Other/Unknown Material |
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, Joerns Paijmans, Johanna L. A. Kraus, Robert H. S. |
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, Joerns Paijmans, Johanna L. A. Kraus, Robert H. S. |
author_sort |
Förster, Daniel W. |
title |
Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species |
title_short |
Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species |
title_full |
Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species |
title_fullStr |
Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species |
title_full_unstemmed |
Data from: Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species |
title_sort |
data from: targeted re-sequencing of coding dna sequences for snp discovery in non-model species |
publisher |
Zenodo |
publishDate |
2018 |
url |
https://doi.org/10.5061/dryad.3f4jr01 |
genre |
Lynx Lynx lynx lynx |
genre_facet |
Lynx Lynx lynx lynx |
op_relation |
https://doi.org/10.1111/1755-0998.12924 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.3f4jr01 oai:zenodo.org:4953012 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.3f4jr0110.1111/1755-0998.12924 |
_version_ |
1810486146265776128 |