Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing
Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Eur...
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Format: | Dataset |
Language: | English |
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Dryad
2013
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Online Access: | https://doi.org/10.5061/dryad.39sc7 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::b7cf4ebdba10c39b00c038fedfec74ff 2023-05-15T13:01:55+02:00 Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing Ogden, Rob Gharbi, Karim Mugue, Nikolai Martinsohn, Jann Senn, Helen Davey, John Pourkazemi, Mohammad McEwing, Ross Eland, Cathlene Vidotto, Michele Sergeev, Alexander Congiu, Leonardo Vidotto, M. Congiu, L. Senn, H. Davey, J. W. Martinsohn, J. Gharbi, K. Eland, C. 2013-01-01 https://doi.org/10.5061/dryad.39sc7 en eng Dryad http://dx.doi.org/10.5061/dryad.39sc7 https://dx.doi.org/10.5061/dryad.39sc7 lic_creative-commons 10.5061/dryad.39sc7 oai:easy.dans.knaw.nl:easy-dataset:82635 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:82635 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Acipenser naccarii DNA Acipenser fisheries wildlife forensics Acipenser gueldenstaedtii Acipenser baerii Traceability Acipenser persicus caviar Life sciences medicine and health care Adriatic (Mediterranean Sea) Azov Sea Caspian Sea River Lena River Ob archeo envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2013 fttriple https://doi.org/10.5061/dryad.39sc7 2023-01-22T19:12:53Z Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping-by-sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools. mec12-0761_DRYAD entry Dataset Acipenser baerii lena river Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
Acipenser naccarii DNA Acipenser fisheries wildlife forensics Acipenser gueldenstaedtii Acipenser baerii Traceability Acipenser persicus caviar Life sciences medicine and health care Adriatic (Mediterranean Sea) Azov Sea Caspian Sea River Lena River Ob archeo envir |
spellingShingle |
Acipenser naccarii DNA Acipenser fisheries wildlife forensics Acipenser gueldenstaedtii Acipenser baerii Traceability Acipenser persicus caviar Life sciences medicine and health care Adriatic (Mediterranean Sea) Azov Sea Caspian Sea River Lena River Ob archeo envir Ogden, Rob Gharbi, Karim Mugue, Nikolai Martinsohn, Jann Senn, Helen Davey, John Pourkazemi, Mohammad McEwing, Ross Eland, Cathlene Vidotto, Michele Sergeev, Alexander Congiu, Leonardo Vidotto, M. Congiu, L. Senn, H. Davey, J. W. Martinsohn, J. Gharbi, K. Eland, C. Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
topic_facet |
Acipenser naccarii DNA Acipenser fisheries wildlife forensics Acipenser gueldenstaedtii Acipenser baerii Traceability Acipenser persicus caviar Life sciences medicine and health care Adriatic (Mediterranean Sea) Azov Sea Caspian Sea River Lena River Ob archeo envir |
description |
Caviar-producing sturgeons belonging to the genus Acipenser are considered to be one of the most endangered species groups in the world. Continued overfishing in spite of increasing legislation, zero catch quotas and extensive aquaculture production have led to the collapse of wild stocks across Europe and Asia. The evolutionary relationships among Adriatic, Russian, Persian and Siberian sturgeons are complex because of past introgression events and remain poorly understood. Conservation management, traceability and enforcement suffer a lack of appropriate DNA markers for the genetic identification of sturgeon at the species, population and individual level. This study employed RAD sequencing to discover and characterize single nucleotide polymorphism (SNP) DNA markers for use in sturgeon conservation in these four tetraploid species over three biological levels, using a single sequencing lane. Four population meta-samples and eight individual samples from one family were barcoded separately before sequencing. Analysis of 14.4 Gb of paired-end RAD data focused on the identification of SNPs in the paired-end contig, with subsequent in silico and empirical validation of candidate markers. Thousands of putatively informative markers were identified including, for the first time, SNPs that show population-wide differentiation between Russian and Persian sturgeons, representing an important advance in our ability to manage these cryptic species. The results highlight the challenges of genotyping-by-sequencing in polyploid taxa, while establishing the potential genetic resources for developing a new range of caviar traceability and enforcement tools. mec12-0761_DRYAD entry |
format |
Dataset |
author |
Ogden, Rob Gharbi, Karim Mugue, Nikolai Martinsohn, Jann Senn, Helen Davey, John Pourkazemi, Mohammad McEwing, Ross Eland, Cathlene Vidotto, Michele Sergeev, Alexander Congiu, Leonardo Vidotto, M. Congiu, L. Senn, H. Davey, J. W. Martinsohn, J. Gharbi, K. Eland, C. |
author_facet |
Ogden, Rob Gharbi, Karim Mugue, Nikolai Martinsohn, Jann Senn, Helen Davey, John Pourkazemi, Mohammad McEwing, Ross Eland, Cathlene Vidotto, Michele Sergeev, Alexander Congiu, Leonardo Vidotto, M. Congiu, L. Senn, H. Davey, J. W. Martinsohn, J. Gharbi, K. Eland, C. |
author_sort |
Ogden, Rob |
title |
Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_short |
Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_full |
Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_fullStr |
Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_full_unstemmed |
Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
title_sort |
data from: sturgeon conservation genomics: snp discovery and validation using rad sequencing |
publisher |
Dryad |
publishDate |
2013 |
url |
https://doi.org/10.5061/dryad.39sc7 |
genre |
Acipenser baerii lena river |
genre_facet |
Acipenser baerii lena river |
op_source |
10.5061/dryad.39sc7 oai:easy.dans.knaw.nl:easy-dataset:82635 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:82635 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.39sc7 https://dx.doi.org/10.5061/dryad.39sc7 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.39sc7 |
_version_ |
1766290073587810304 |