Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs
Hoffman J, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE . 2013;8(7): e68365. High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for gene...
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ftubbiepub:oai:pub.uni-bielefeld.de:2615293 2023-05-15T13:40:40+02:00 Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs Hoffman, Joseph Thorne, Michael A. S. McEwing, Rob Forcada, Jaume Ogden, Rob 2013 https://nbn-resolving.org/urn:nbn:de:0070-pub-26152930 https://pub.uni-bielefeld.de/record/2615293 https://pub.uni-bielefeld.de/download/2615293/2615300 eng eng Public Library of Science (PLoS) info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0068365 info:eu-repo/semantics/altIdentifier/issn/1932-6203 info:eu-repo/semantics/altIdentifier/wos/000322064300026 info:eu-repo/semantics/altIdentifier/pmid/23874599 https://nbn-resolving.org/urn:nbn:de:0070-pub-26152930 https://pub.uni-bielefeld.de/record/2615293 https://pub.uni-bielefeld.de/download/2615293/2615300 info:eu-repo/semantics/openAccess https://rightsstatements.org/vocab/InC/1.0/ ddc:570 http://purl.org/coar/resource_type/c_6501 info:eu-repo/semantics/article doc-type:article text 2013 ftubbiepub https://doi.org/10.1371/journal.pone.0068365 2022-02-08T22:33:14Z Hoffman J, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE . 2013;8(7): e68365. High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella PUB - Publications at Bielefeld University Antarctic Thorne ENVELOPE(-60.700,-60.700,-62.933,-62.933) PLoS ONE 8 7 e68365 |
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PUB - Publications at Bielefeld University |
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English |
topic |
ddc:570 |
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ddc:570 Hoffman, Joseph Thorne, Michael A. S. McEwing, Rob Forcada, Jaume Ogden, Rob Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
topic_facet |
ddc:570 |
description |
Hoffman J, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE . 2013;8(7): e68365. High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome. |
format |
Article in Journal/Newspaper |
author |
Hoffman, Joseph Thorne, Michael A. S. McEwing, Rob Forcada, Jaume Ogden, Rob |
author_facet |
Hoffman, Joseph Thorne, Michael A. S. McEwing, Rob Forcada, Jaume Ogden, Rob |
author_sort |
Hoffman, Joseph |
title |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_short |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_full |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_fullStr |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_full_unstemmed |
Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs |
title_sort |
cross-amplification and validation of snps conserved over 44 million years between seals and dogs |
publisher |
Public Library of Science (PLoS) |
publishDate |
2013 |
url |
https://nbn-resolving.org/urn:nbn:de:0070-pub-26152930 https://pub.uni-bielefeld.de/record/2615293 https://pub.uni-bielefeld.de/download/2615293/2615300 |
long_lat |
ENVELOPE(-60.700,-60.700,-62.933,-62.933) |
geographic |
Antarctic Thorne |
geographic_facet |
Antarctic Thorne |
genre |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella |
genre_facet |
Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0068365 info:eu-repo/semantics/altIdentifier/issn/1932-6203 info:eu-repo/semantics/altIdentifier/wos/000322064300026 info:eu-repo/semantics/altIdentifier/pmid/23874599 https://nbn-resolving.org/urn:nbn:de:0070-pub-26152930 https://pub.uni-bielefeld.de/record/2615293 https://pub.uni-bielefeld.de/download/2615293/2615300 |
op_rights |
info:eu-repo/semantics/openAccess https://rightsstatements.org/vocab/InC/1.0/ |
op_doi |
https://doi.org/10.1371/journal.pone.0068365 |
container_title |
PLoS ONE |
container_volume |
8 |
container_issue |
7 |
container_start_page |
e68365 |
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1766138313040723968 |