PFR 2 :a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution
Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstruction...
Published in: | Molecular Ecology Resources |
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Main Authors: | , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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2015
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Online Access: | https://risweb.st-andrews.ac.uk/portal/en/researchoutput/pfr2(a9c44088-b567-4a0b-8a22-dcc3d1f10887).html https://doi.org/10.1111/1755-0998.12410 http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12410/suppinfo |
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ftunstandrewcris:oai:risweb.st-andrews.ac.uk:publications/a9c44088-b567-4a0b-8a22-dcc3d1f10887 2023-05-15T18:00:14+02:00 PFR 2 :a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution Morard, R. Darling, K.F. Mahé, F. Audic, S. Ujiié, Y. Weiner, A.K.M. André, A. Seears, H.A. Wade, C.M. Quillévéré, F. Douady, C.J. Escarguel, G. de Garidel-Thoron, T. Siccha, M. Kucera, M. de Vargas, C. 2015 https://risweb.st-andrews.ac.uk/portal/en/researchoutput/pfr2(a9c44088-b567-4a0b-8a22-dcc3d1f10887).html https://doi.org/10.1111/1755-0998.12410 http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12410/suppinfo eng eng info:eu-repo/semantics/restrictedAccess Morard , R , Darling , K F , Mahé , F , Audic , S , Ujiié , Y , Weiner , A K M , André , A , Seears , H A , Wade , C M , Quillévéré , F , Douady , C J , Escarguel , G , de Garidel-Thoron , T , Siccha , M , Kucera , M & de Vargas , C 2015 , ' PFR 2 : a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution ' , Molecular Ecology Resources . https://doi.org/10.1111/1755-0998.12410 18S ribosomal DNA Genetic diversity Molecular ecology Molecular taxonomy Planktonic foraminifera Sequence database article 2015 ftunstandrewcris https://doi.org/10.1111/1755-0998.12410 2021-12-26T14:26:24Z Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR 2 , the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR 2 website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent. Article in Journal/Newspaper Planktonic foraminifera University of St Andrews: Research Portal Molecular Ecology Resources 15 6 1472 1485 |
institution |
Open Polar |
collection |
University of St Andrews: Research Portal |
op_collection_id |
ftunstandrewcris |
language |
English |
topic |
18S ribosomal DNA Genetic diversity Molecular ecology Molecular taxonomy Planktonic foraminifera Sequence database |
spellingShingle |
18S ribosomal DNA Genetic diversity Molecular ecology Molecular taxonomy Planktonic foraminifera Sequence database Morard, R. Darling, K.F. Mahé, F. Audic, S. Ujiié, Y. Weiner, A.K.M. André, A. Seears, H.A. Wade, C.M. Quillévéré, F. Douady, C.J. Escarguel, G. de Garidel-Thoron, T. Siccha, M. Kucera, M. de Vargas, C. PFR 2 :a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution |
topic_facet |
18S ribosomal DNA Genetic diversity Molecular ecology Molecular taxonomy Planktonic foraminifera Sequence database |
description |
Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR 2 , the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR 2 website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent. |
format |
Article in Journal/Newspaper |
author |
Morard, R. Darling, K.F. Mahé, F. Audic, S. Ujiié, Y. Weiner, A.K.M. André, A. Seears, H.A. Wade, C.M. Quillévéré, F. Douady, C.J. Escarguel, G. de Garidel-Thoron, T. Siccha, M. Kucera, M. de Vargas, C. |
author_facet |
Morard, R. Darling, K.F. Mahé, F. Audic, S. Ujiié, Y. Weiner, A.K.M. André, A. Seears, H.A. Wade, C.M. Quillévéré, F. Douady, C.J. Escarguel, G. de Garidel-Thoron, T. Siccha, M. Kucera, M. de Vargas, C. |
author_sort |
Morard, R. |
title |
PFR 2 :a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution |
title_short |
PFR 2 :a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution |
title_full |
PFR 2 :a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution |
title_fullStr |
PFR 2 :a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution |
title_full_unstemmed |
PFR 2 :a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution |
title_sort |
pfr 2 :a curated database of planktonic foraminifera 18s ribosomal dna as a resource for studies of plankton ecology, biogeography and evolution |
publishDate |
2015 |
url |
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/pfr2(a9c44088-b567-4a0b-8a22-dcc3d1f10887).html https://doi.org/10.1111/1755-0998.12410 http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12410/suppinfo |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_source |
Morard , R , Darling , K F , Mahé , F , Audic , S , Ujiié , Y , Weiner , A K M , André , A , Seears , H A , Wade , C M , Quillévéré , F , Douady , C J , Escarguel , G , de Garidel-Thoron , T , Siccha , M , Kucera , M & de Vargas , C 2015 , ' PFR 2 : a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution ' , Molecular Ecology Resources . https://doi.org/10.1111/1755-0998.12410 |
op_rights |
info:eu-repo/semantics/restrictedAccess |
op_doi |
https://doi.org/10.1111/1755-0998.12410 |
container_title |
Molecular Ecology Resources |
container_volume |
15 |
container_issue |
6 |
container_start_page |
1472 |
op_container_end_page |
1485 |
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1766169244593029120 |