Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome
Hoffman J. Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources . 2011;11(4):703-710. Next-generation sequencing provides a powerful new approach for developing functional genomic tools for nonmodel species, helping to narrow the gap betwee...
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ftubbiepub:oai:pub.uni-bielefeld.de:2307149 2023-05-15T13:43:26+02:00 Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome Hoffman, Joseph 2011 https://pub.uni-bielefeld.de/record/2307149 eng eng Wiley-Blackwell info:eu-repo/semantics/altIdentifier/doi/10.1111/j.1755-0998.2011.02999.x info:eu-repo/semantics/altIdentifier/issn/1755-098X info:eu-repo/semantics/altIdentifier/wos/000292478500012 info:eu-repo/semantics/altIdentifier/pmid/21466659 https://pub.uni-bielefeld.de/record/2307149 info:eu-repo/semantics/closedAccess single nucleotide polymorphism 454 sequencing expressed sequence tags marine mammal dog (Canis lupis familiaris) pinniped microsatellite http://purl.org/coar/resource_type/c_6501 info:eu-repo/semantics/article doc-type:article text 2011 ftubbiepub https://doi.org/10.1111/j.1755-0998.2011.02999.x 2022-02-08T22:30:17Z Hoffman J. Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources . 2011;11(4):703-710. Next-generation sequencing provides a powerful new approach for developing functional genomic tools for nonmodel species, helping to narrow the gap between studies of model organisms and those of natural populations. Consequently, massively parallel 454 sequencing was used to characterize a normalized cDNA library derived from skin biopsy samples of twelve Antarctic fur seal (Arctocephalus gazella) individuals. Over 412 Mb of sequence data were generated, comprising 1.4 million reads of average length 286 bp. De nova assembly using Newbler 2.3 yielded 156 contigs plus 22 869 isotigs, which in turn clustered into 18 576 isogroups. Almost half of the assembled transcript sequences showed significant similarity to the nr database, revealing a functionally diverse array of genes. Moreover, 97.9% of these mapped to the dog (Canis lupis familiaris) genome, with a strong positive relationship between the number of sequences locating to a given chromosome and the length of that chromosome in the dog indicating a broad genomic distribution. Average depth of coverage was also almost 20-fold, sufficient to detect several thousand putative microsatellite loci and single nucleotide polymor-phistns. This study constitutes an important step towards developing genomic resources with which to address consequential questions in pinniped ecology and evolution. It also supports an earlier but smaller study showing that skin tissue can be a rich source of expressed genes, with important implications for studying the genomics not only of marine mammals, but also more generally of species that cannot be destructively sampled. Article in Journal/Newspaper Antarc* Antarctic Antarctic Fur Seal Arctocephalus gazella PUB - Publications at Bielefeld University Antarctic The Antarctic Molecular Ecology Resources 11 4 703 710 |
institution |
Open Polar |
collection |
PUB - Publications at Bielefeld University |
op_collection_id |
ftubbiepub |
language |
English |
topic |
single nucleotide polymorphism 454 sequencing expressed sequence tags marine mammal dog (Canis lupis familiaris) pinniped microsatellite |
spellingShingle |
single nucleotide polymorphism 454 sequencing expressed sequence tags marine mammal dog (Canis lupis familiaris) pinniped microsatellite Hoffman, Joseph Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome |
topic_facet |
single nucleotide polymorphism 454 sequencing expressed sequence tags marine mammal dog (Canis lupis familiaris) pinniped microsatellite |
description |
Hoffman J. Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources . 2011;11(4):703-710. Next-generation sequencing provides a powerful new approach for developing functional genomic tools for nonmodel species, helping to narrow the gap between studies of model organisms and those of natural populations. Consequently, massively parallel 454 sequencing was used to characterize a normalized cDNA library derived from skin biopsy samples of twelve Antarctic fur seal (Arctocephalus gazella) individuals. Over 412 Mb of sequence data were generated, comprising 1.4 million reads of average length 286 bp. De nova assembly using Newbler 2.3 yielded 156 contigs plus 22 869 isotigs, which in turn clustered into 18 576 isogroups. Almost half of the assembled transcript sequences showed significant similarity to the nr database, revealing a functionally diverse array of genes. Moreover, 97.9% of these mapped to the dog (Canis lupis familiaris) genome, with a strong positive relationship between the number of sequences locating to a given chromosome and the length of that chromosome in the dog indicating a broad genomic distribution. Average depth of coverage was also almost 20-fold, sufficient to detect several thousand putative microsatellite loci and single nucleotide polymor-phistns. This study constitutes an important step towards developing genomic resources with which to address consequential questions in pinniped ecology and evolution. It also supports an earlier but smaller study showing that skin tissue can be a rich source of expressed genes, with important implications for studying the genomics not only of marine mammals, but also more generally of species that cannot be destructively sampled. |
format |
Article in Journal/Newspaper |
author |
Hoffman, Joseph |
author_facet |
Hoffman, Joseph |
author_sort |
Hoffman, Joseph |
title |
Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome |
title_short |
Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome |
title_full |
Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome |
title_fullStr |
Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome |
title_full_unstemmed |
Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome |
title_sort |
gene discovery in the antarctic fur seal (arctocephalus gazella) skin transcriptome |
publisher |
Wiley-Blackwell |
publishDate |
2011 |
url |
https://pub.uni-bielefeld.de/record/2307149 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
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/10.1111/j.1755-0998.2011.02999.x info:eu-repo/semantics/altIdentifier/issn/1755-098X info:eu-repo/semantics/altIdentifier/wos/000292478500012 info:eu-repo/semantics/altIdentifier/pmid/21466659 https://pub.uni-bielefeld.de/record/2307149 |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1111/j.1755-0998.2011.02999.x |
container_title |
Molecular Ecology Resources |
container_volume |
11 |
container_issue |
4 |
container_start_page |
703 |
op_container_end_page |
710 |
_version_ |
1766189084038922240 |