A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel
Abstract Reduced representation genome sequencing such as restriction‐site‐associated DNA ( RAD ) sequencing is finding increased use to identify and genotype large numbers of single‐nucleotide polymorphisms ( SNP s) in model and nonmodel species. We generated a unique resource of novel SNP markers...
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crwiley:10.1111/1755-0998.12117 2024-06-02T08:06:15+00:00 A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel Pujolar, J. M. Jacobsen, M. W. Frydenberg, J. Als, T. D. Larsen, P. F. Maes, G. E. Zane, L. Jian, J. B. Cheng, L. Hansen, M. M. 2013 http://dx.doi.org/10.1111/1755-0998.12117 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12117 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12117 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.12117 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology Resources volume 13, issue 4, page 706-714 ISSN 1755-098X 1755-0998 journal-article 2013 crwiley https://doi.org/10.1111/1755-0998.12117 2024-05-03T11:23:11Z Abstract Reduced representation genome sequencing such as restriction‐site‐associated DNA ( RAD ) sequencing is finding increased use to identify and genotype large numbers of single‐nucleotide polymorphisms ( SNP s) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome‐wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome‐wide set of SNP markers was available until now. The generated SNP s were widely distributed across the eel genome, aligning to 4779 different contigs and 19 703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long‐term effective population size was estimated to range between 132 000 and 1 320 000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82 425 loci and 376 918 associated SNP s provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome. Article in Journal/Newspaper European eel Wiley Online Library Molecular Ecology Resources 13 4 706 714 |
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Open Polar |
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Wiley Online Library |
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crwiley |
language |
English |
description |
Abstract Reduced representation genome sequencing such as restriction‐site‐associated DNA ( RAD ) sequencing is finding increased use to identify and genotype large numbers of single‐nucleotide polymorphisms ( SNP s) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome‐wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome‐wide set of SNP markers was available until now. The generated SNP s were widely distributed across the eel genome, aligning to 4779 different contigs and 19 703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long‐term effective population size was estimated to range between 132 000 and 1 320 000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82 425 loci and 376 918 associated SNP s provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome. |
format |
Article in Journal/Newspaper |
author |
Pujolar, J. M. Jacobsen, M. W. Frydenberg, J. Als, T. D. Larsen, P. F. Maes, G. E. Zane, L. Jian, J. B. Cheng, L. Hansen, M. M. |
spellingShingle |
Pujolar, J. M. Jacobsen, M. W. Frydenberg, J. Als, T. D. Larsen, P. F. Maes, G. E. Zane, L. Jian, J. B. Cheng, L. Hansen, M. M. A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel |
author_facet |
Pujolar, J. M. Jacobsen, M. W. Frydenberg, J. Als, T. D. Larsen, P. F. Maes, G. E. Zane, L. Jian, J. B. Cheng, L. Hansen, M. M. |
author_sort |
Pujolar, J. M. |
title |
A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel |
title_short |
A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel |
title_full |
A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel |
title_fullStr |
A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel |
title_full_unstemmed |
A resource of genome‐wide single‐nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel |
title_sort |
resource of genome‐wide single‐nucleotide polymorphisms generated by rad tag sequencing in the critically endangered european eel |
publisher |
Wiley |
publishDate |
2013 |
url |
http://dx.doi.org/10.1111/1755-0998.12117 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2F1755-0998.12117 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.12117 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.12117 |
genre |
European eel |
genre_facet |
European eel |
op_source |
Molecular Ecology Resources volume 13, issue 4, page 706-714 ISSN 1755-098X 1755-0998 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/1755-0998.12117 |
container_title |
Molecular Ecology Resources |
container_volume |
13 |
container_issue |
4 |
container_start_page |
706 |
op_container_end_page |
714 |
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1800751184662757376 |