Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes
Vendrami D, Shah A, Telesca L, Hoffman J. Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes. MARINE GENOMICS . 2016;27:17-23. Transcriptional profiling not only provides insights into patterns of gene express...
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2016
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ftubbiepub:oai:pub.uni-bielefeld.de:2905163 2023-05-15T15:58:10+02:00 Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes Vendrami, David Shah, Abhijeet Telesca, Luca Hoffman, Joseph 2016 https://pub.uni-bielefeld.de/record/2905163 eng eng Elsevier Science BV info:eu-repo/semantics/altIdentifier/doi/10.1016/j.margen.2015.12.009 info:eu-repo/semantics/altIdentifier/issn/1874-7787 info:eu-repo/semantics/altIdentifier/issn/1876-7478 info:eu-repo/semantics/altIdentifier/wos/000379376100004 info:eu-repo/semantics/altIdentifier/pmid/26806806 https://pub.uni-bielefeld.de/record/2905163 info:eu-repo/semantics/closedAccess Crassostrea gigas Mya truncata Mytilus edulis Pecten maximus Non-model organism http://purl.org/coar/resource_type/c_6501 info:eu-repo/semantics/article doc-type:article text 2016 ftubbiepub https://doi.org/10.1016/j.margen.2015.12.009 2022-02-08T22:36:07Z Vendrami D, Shah A, Telesca L, Hoffman J. Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes. MARINE GENOMICS . 2016;27:17-23. Transcriptional profiling not only provides insights into patterns of gene expression, but also generates sequences that can be mined for molecular markers, which in turn can be used for population genetic studies. As part of a large-scale effort to better understand how commercially important European shellfish species may respond to ocean acidification, we therefore mined the transcriptomes of four species (the Pacific oyster Crassostrea gigas, the blue mussel Mytilus edulis, the great scallop Pecten maximus and the blunt gaper Mya truncata) for single nucleotide polymorphisms (SNPs). Illumina data for C. gigas, M. edulis and P. maximus and 454 data for M. truncata were interrogated using GATK and SWAP454 respectively to identify between 8267 and 47,159 high quality SNPs per species (total = 121,053 SNPs residing within 34,716 different contigs). We then annotated the-transcripts containing SNPs to reveal homology to diverse genes. Finally, as oceanic pH affects the ability of organisms to incorporate calcium carbonate, we honed in on genes implicated in the biomineralization process to identify a total of 1899 SNPs in 157 genes. These provide good candidates for biomarkers with which to study patterns of selection in natural or experimental populations. (C) 2016 Elsevier B.V. All rights reserved. Article in Journal/Newspaper Crassostrea gigas Ocean acidification Pacific oyster PUB - Publications at Bielefeld University Pacific Marine Genomics 27 17 23 |
institution |
Open Polar |
collection |
PUB - Publications at Bielefeld University |
op_collection_id |
ftubbiepub |
language |
English |
topic |
Crassostrea gigas Mya truncata Mytilus edulis Pecten maximus Non-model organism |
spellingShingle |
Crassostrea gigas Mya truncata Mytilus edulis Pecten maximus Non-model organism Vendrami, David Shah, Abhijeet Telesca, Luca Hoffman, Joseph Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes |
topic_facet |
Crassostrea gigas Mya truncata Mytilus edulis Pecten maximus Non-model organism |
description |
Vendrami D, Shah A, Telesca L, Hoffman J. Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes. MARINE GENOMICS . 2016;27:17-23. Transcriptional profiling not only provides insights into patterns of gene expression, but also generates sequences that can be mined for molecular markers, which in turn can be used for population genetic studies. As part of a large-scale effort to better understand how commercially important European shellfish species may respond to ocean acidification, we therefore mined the transcriptomes of four species (the Pacific oyster Crassostrea gigas, the blue mussel Mytilus edulis, the great scallop Pecten maximus and the blunt gaper Mya truncata) for single nucleotide polymorphisms (SNPs). Illumina data for C. gigas, M. edulis and P. maximus and 454 data for M. truncata were interrogated using GATK and SWAP454 respectively to identify between 8267 and 47,159 high quality SNPs per species (total = 121,053 SNPs residing within 34,716 different contigs). We then annotated the-transcripts containing SNPs to reveal homology to diverse genes. Finally, as oceanic pH affects the ability of organisms to incorporate calcium carbonate, we honed in on genes implicated in the biomineralization process to identify a total of 1899 SNPs in 157 genes. These provide good candidates for biomarkers with which to study patterns of selection in natural or experimental populations. (C) 2016 Elsevier B.V. All rights reserved. |
format |
Article in Journal/Newspaper |
author |
Vendrami, David Shah, Abhijeet Telesca, Luca Hoffman, Joseph |
author_facet |
Vendrami, David Shah, Abhijeet Telesca, Luca Hoffman, Joseph |
author_sort |
Vendrami, David |
title |
Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes |
title_short |
Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes |
title_full |
Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes |
title_fullStr |
Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes |
title_full_unstemmed |
Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes |
title_sort |
mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms within biomineralization genes |
publisher |
Elsevier Science BV |
publishDate |
2016 |
url |
https://pub.uni-bielefeld.de/record/2905163 |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Ocean acidification Pacific oyster |
genre_facet |
Crassostrea gigas Ocean acidification Pacific oyster |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.margen.2015.12.009 info:eu-repo/semantics/altIdentifier/issn/1874-7787 info:eu-repo/semantics/altIdentifier/issn/1876-7478 info:eu-repo/semantics/altIdentifier/wos/000379376100004 info:eu-repo/semantics/altIdentifier/pmid/26806806 https://pub.uni-bielefeld.de/record/2905163 |
op_rights |
info:eu-repo/semantics/closedAccess |
op_doi |
https://doi.org/10.1016/j.margen.2015.12.009 |
container_title |
Marine Genomics |
container_volume |
27 |
container_start_page |
17 |
op_container_end_page |
23 |
_version_ |
1766393900081086464 |