Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution
Single-cell genetic analysis is an essential method to investigate the biodiversity and evolutionary ecology of marine protists. In protist groups that do not reproduce under laboratory conditions, this approach provides the only means to directly associate molecular sequences with cell morphology....
Published in: | Frontiers in Marine Science |
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Main Authors: | , , , , , , , , , |
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Language: | English |
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2016
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Online Access: | https://risweb.st-andrews.ac.uk/portal/en/researchoutput/methodology-for-singlecell-genetic-analysis-of-planktonic-foraminifera-for-studies-of-protist-diversity-and-evolution(479c1024-cf23-4436-ad04-a40001ef8d6d).html https://doi.org/10.3389/fmars.2016.00255 https://research-repository.st-andrews.ac.uk/bitstream/10023/10126/1/Darling_2016_FMS_PlanktonicForaminifera_CC.pdf |
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ftunstandrewcris:oai:risweb.st-andrews.ac.uk:publications/479c1024-cf23-4436-ad04-a40001ef8d6d 2023-05-15T18:00:26+02:00 Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution Weiner, Agnes K M Morard, Raphael Weinkauf, Manuel F. G. Darling, Kate F. André, Aurore Quillévéré, Frédéric Ujiie, Yurika Douady, Christophe J. de Vargas, Colomban Kucera, Michal 2016-12-15 application/pdf https://risweb.st-andrews.ac.uk/portal/en/researchoutput/methodology-for-singlecell-genetic-analysis-of-planktonic-foraminifera-for-studies-of-protist-diversity-and-evolution(479c1024-cf23-4436-ad04-a40001ef8d6d).html https://doi.org/10.3389/fmars.2016.00255 https://research-repository.st-andrews.ac.uk/bitstream/10023/10126/1/Darling_2016_FMS_PlanktonicForaminifera_CC.pdf eng eng info:eu-repo/semantics/openAccess Weiner , A K M , Morard , R , Weinkauf , M F G , Darling , K F , André , A , Quillévéré , F , Ujiie , Y , Douady , C J , de Vargas , C & Kucera , M 2016 , ' Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution ' , Frontiers in Marine Science , vol. 3 , 255 . https://doi.org/10.3389/fmars.2016.00255 Comparability Cryptic diversity Foraminifera Laboratory protocols Methods Protists Single-cell genetics Standardization article 2016 ftunstandrewcris https://doi.org/10.3389/fmars.2016.00255 2022-10-13T15:26:10Z Single-cell genetic analysis is an essential method to investigate the biodiversity and evolutionary ecology of marine protists. In protist groups that do not reproduce under laboratory conditions, this approach provides the only means to directly associate molecular sequences with cell morphology. The resulting unambiguous taxonomic identification of the DNA sequences is a prerequisite for barcoding and analyses of environmental metagenomic data. Extensive single-cell genetic studies have been carried out on planktonic foraminifera over the past 20 years to elucidate their phylogeny, cryptic diversity, biogeography, and the relationship between genetic and morphological variability. In the course of these investigations, it has become evident that genetic analysis at the individual specimen level is confronted by innumerable challenges ranging from the negligible amount of DNA present in the single cell to the substantial amount of DNA contamination introduced by endosymbionts or food particles. Consequently, a range of methods has been developed and applied throughout the years for the genetic analysis of planktonic foraminifera in order to enhance DNA amplification success rates. Yet, the description of these methods in the literature rarely occurred with equivalent levels of detail and the different approaches have never been compared in terms of their efficiency and reproducibility. Here, aiming at a standardization of methods, we provide a comprehensive review of all methods that have been employed for the single-cell genetic analysis of planktonic foraminifera. We compile data on success rates of DNA amplification and use these to evaluate the effects of key parameters associated with the methods of sample collection, storage and extraction of single-cell DNA. We show that the chosen methods influence the success rates of single-cell genetic studies, but the differences between them are not sufficient to hinder comparisons between studies carried out by different methods. The review thus not only provides ... Article in Journal/Newspaper Planktonic foraminifera University of St Andrews: Research Portal Frontiers in Marine Science 3 |
institution |
Open Polar |
collection |
University of St Andrews: Research Portal |
op_collection_id |
ftunstandrewcris |
language |
English |
topic |
Comparability Cryptic diversity Foraminifera Laboratory protocols Methods Protists Single-cell genetics Standardization |
spellingShingle |
Comparability Cryptic diversity Foraminifera Laboratory protocols Methods Protists Single-cell genetics Standardization Weiner, Agnes K M Morard, Raphael Weinkauf, Manuel F. G. Darling, Kate F. André, Aurore Quillévéré, Frédéric Ujiie, Yurika Douady, Christophe J. de Vargas, Colomban Kucera, Michal Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution |
topic_facet |
Comparability Cryptic diversity Foraminifera Laboratory protocols Methods Protists Single-cell genetics Standardization |
description |
Single-cell genetic analysis is an essential method to investigate the biodiversity and evolutionary ecology of marine protists. In protist groups that do not reproduce under laboratory conditions, this approach provides the only means to directly associate molecular sequences with cell morphology. The resulting unambiguous taxonomic identification of the DNA sequences is a prerequisite for barcoding and analyses of environmental metagenomic data. Extensive single-cell genetic studies have been carried out on planktonic foraminifera over the past 20 years to elucidate their phylogeny, cryptic diversity, biogeography, and the relationship between genetic and morphological variability. In the course of these investigations, it has become evident that genetic analysis at the individual specimen level is confronted by innumerable challenges ranging from the negligible amount of DNA present in the single cell to the substantial amount of DNA contamination introduced by endosymbionts or food particles. Consequently, a range of methods has been developed and applied throughout the years for the genetic analysis of planktonic foraminifera in order to enhance DNA amplification success rates. Yet, the description of these methods in the literature rarely occurred with equivalent levels of detail and the different approaches have never been compared in terms of their efficiency and reproducibility. Here, aiming at a standardization of methods, we provide a comprehensive review of all methods that have been employed for the single-cell genetic analysis of planktonic foraminifera. We compile data on success rates of DNA amplification and use these to evaluate the effects of key parameters associated with the methods of sample collection, storage and extraction of single-cell DNA. We show that the chosen methods influence the success rates of single-cell genetic studies, but the differences between them are not sufficient to hinder comparisons between studies carried out by different methods. The review thus not only provides ... |
format |
Article in Journal/Newspaper |
author |
Weiner, Agnes K M Morard, Raphael Weinkauf, Manuel F. G. Darling, Kate F. André, Aurore Quillévéré, Frédéric Ujiie, Yurika Douady, Christophe J. de Vargas, Colomban Kucera, Michal |
author_facet |
Weiner, Agnes K M Morard, Raphael Weinkauf, Manuel F. G. Darling, Kate F. André, Aurore Quillévéré, Frédéric Ujiie, Yurika Douady, Christophe J. de Vargas, Colomban Kucera, Michal |
author_sort |
Weiner, Agnes K M |
title |
Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution |
title_short |
Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution |
title_full |
Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution |
title_fullStr |
Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution |
title_full_unstemmed |
Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution |
title_sort |
methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution |
publishDate |
2016 |
url |
https://risweb.st-andrews.ac.uk/portal/en/researchoutput/methodology-for-singlecell-genetic-analysis-of-planktonic-foraminifera-for-studies-of-protist-diversity-and-evolution(479c1024-cf23-4436-ad04-a40001ef8d6d).html https://doi.org/10.3389/fmars.2016.00255 https://research-repository.st-andrews.ac.uk/bitstream/10023/10126/1/Darling_2016_FMS_PlanktonicForaminifera_CC.pdf |
genre |
Planktonic foraminifera |
genre_facet |
Planktonic foraminifera |
op_source |
Weiner , A K M , Morard , R , Weinkauf , M F G , Darling , K F , André , A , Quillévéré , F , Ujiie , Y , Douady , C J , de Vargas , C & Kucera , M 2016 , ' Methodology for single-cell genetic analysis of planktonic foraminifera for studies of protist diversity and evolution ' , Frontiers in Marine Science , vol. 3 , 255 . https://doi.org/10.3389/fmars.2016.00255 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.3389/fmars.2016.00255 |
container_title |
Frontiers in Marine Science |
container_volume |
3 |
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1766169532147171328 |