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...
Main Authors: | , , , , , , , , , , , |
---|---|
Format: | Article in Journal/Newspaper |
Language: | unknown |
Published: |
2013
|
Subjects: | |
Online Access: | http://hdl.handle.net/10255/dryad.43780 https://doi.org/10.5061/dryad.39sc7 |
id |
ftdryad:oai:v1.datadryad.org:10255/dryad.43780 |
---|---|
record_format |
openpolar |
spelling |
ftdryad:oai:v1.datadryad.org:10255/dryad.43780 2023-05-15T17:07:40+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 Adriatic (Mediterranean Sea) Azov Sea Caspian Sea River Lena River Ob 2013-01-07T17:41:47Z http://hdl.handle.net/10255/dryad.43780 https://doi.org/10.5061/dryad.39sc7 unknown doi:10.5061/dryad.39sc7/2 doi:10.1111/mec.12234 PMID:23473098 doi:10.5061/dryad.39sc7 Ogden R, Gharbi K, Mugue N, Martinsohn J, Senn H, Davey J, Pourkazemi M, McEwing R, Eland C, Vidotto M, Sergeev A, Congiu L (2013) Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Molecular Ecology 22(11): 3112–3123. http://hdl.handle.net/10255/dryad.43780 Acipenser caviar traceability wildlife forensics fisheries DNA Article 2013 ftdryad https://doi.org/10.5061/dryad.39sc7 https://doi.org/10.5061/dryad.39sc7/2 https://doi.org/10.1111/mec.12234 2020-01-01T14:58:37Z 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. Article in Journal/Newspaper lena river Dryad Digital Repository (Duke University) |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
Acipenser caviar traceability wildlife forensics fisheries DNA |
spellingShingle |
Acipenser caviar traceability wildlife forensics fisheries DNA Ogden, Rob Gharbi, Karim Mugue, Nikolai Martinsohn, Jann Senn, Helen Davey, John Pourkazemi, Mohammad McEwing, Ross Eland, Cathlene Vidotto, Michele Sergeev, Alexander Congiu, Leonardo Data from: Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing |
topic_facet |
Acipenser caviar traceability wildlife forensics fisheries DNA |
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. |
format |
Article in Journal/Newspaper |
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 |
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 |
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 |
publishDate |
2013 |
url |
http://hdl.handle.net/10255/dryad.43780 https://doi.org/10.5061/dryad.39sc7 |
op_coverage |
Adriatic (Mediterranean Sea) Azov Sea Caspian Sea River Lena River Ob |
genre |
lena river |
genre_facet |
lena river |
op_relation |
doi:10.5061/dryad.39sc7/2 doi:10.1111/mec.12234 PMID:23473098 doi:10.5061/dryad.39sc7 Ogden R, Gharbi K, Mugue N, Martinsohn J, Senn H, Davey J, Pourkazemi M, McEwing R, Eland C, Vidotto M, Sergeev A, Congiu L (2013) Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing. Molecular Ecology 22(11): 3112–3123. http://hdl.handle.net/10255/dryad.43780 |
op_doi |
https://doi.org/10.5061/dryad.39sc7 https://doi.org/10.5061/dryad.39sc7/2 https://doi.org/10.1111/mec.12234 |
_version_ |
1766063149403865088 |