A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel
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 (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the Europ...
Published in: | Molecular Ecology Resources |
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Language: | English |
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Online Access: | http://hdl.handle.net/11577/2579054 https://doi.org/10.1111/1755-0998.12117 |
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ftunivpadovairis:oai:www.research.unipd.it:11577/2579054 2024-04-21T08:01:41+00:00 A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel PUJOLAR CASTANER, JOSE' MARTIN ZANE, LORENZO M. W. Jacobsen J. Frydenberg T. D. Als P. F. Larsen G. E. Maes J. B. Jian L. Cheng M. M. Hansen PUJOLAR CASTANER, JOSE' MARTIN M. W., Jacobsen J., Frydenberg T. D., Al P. F., Larsen G. E., Mae Zane, Lorenzo J. B., Jian L., Cheng M. M., Hansen 2013 STAMPA http://hdl.handle.net/11577/2579054 https://doi.org/10.1111/1755-0998.12117 eng eng John Wiley & Sons Ltd. info:eu-repo/semantics/altIdentifier/pmid/23656721 info:eu-repo/semantics/altIdentifier/wos/WOS:000320396300015 volume:13 firstpage:706 lastpage:714 numberofpages:9 journal:MOLECULAR ECOLOGY RESOURCES http://hdl.handle.net/11577/2579054 doi:10.1111/1755-0998.12117 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84879420457 info:eu-repo/semantics/article 2013 ftunivpadovairis https://doi.org/10.1111/1755-0998.12117 2024-03-28T01:43:01Z 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 (SNPs) 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 SNPs 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 SNPs 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 Padua Research Archive (IRIS - Università degli Studi di Padova) Molecular Ecology Resources 13 4 706 714 |
institution |
Open Polar |
collection |
Padua Research Archive (IRIS - Università degli Studi di Padova) |
op_collection_id |
ftunivpadovairis |
language |
English |
description |
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 (SNPs) 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 SNPs 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 SNPs 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. |
author2 |
PUJOLAR CASTANER, JOSE' MARTIN M. W., Jacobsen J., Frydenberg T. D., Al P. F., Larsen G. E., Mae Zane, Lorenzo J. B., Jian L., Cheng M. M., Hansen |
format |
Article in Journal/Newspaper |
author |
PUJOLAR CASTANER, JOSE' MARTIN ZANE, LORENZO M. W. Jacobsen J. Frydenberg T. D. Als P. F. Larsen G. E. Maes J. B. Jian L. Cheng M. M. Hansen |
spellingShingle |
PUJOLAR CASTANER, JOSE' MARTIN ZANE, LORENZO M. W. Jacobsen J. Frydenberg T. D. Als P. F. Larsen G. E. Maes J. B. Jian L. Cheng M. M. Hansen A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel |
author_facet |
PUJOLAR CASTANER, JOSE' MARTIN ZANE, LORENZO M. W. Jacobsen J. Frydenberg T. D. Als P. F. Larsen G. E. Maes J. B. Jian L. Cheng M. M. Hansen |
author_sort |
PUJOLAR CASTANER, JOSE' MARTIN |
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 |
John Wiley & Sons Ltd. |
publishDate |
2013 |
url |
http://hdl.handle.net/11577/2579054 https://doi.org/10.1111/1755-0998.12117 |
genre |
European eel |
genre_facet |
European eel |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/23656721 info:eu-repo/semantics/altIdentifier/wos/WOS:000320396300015 volume:13 firstpage:706 lastpage:714 numberofpages:9 journal:MOLECULAR ECOLOGY RESOURCES http://hdl.handle.net/11577/2579054 doi:10.1111/1755-0998.12117 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-84879420457 |
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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1796941810394726400 |