FN Archimer Export Format
PT J
TI Methodology for Single-Cell Genetic Analysis of Planktonic Foraminifera for Studies of Protist Diversity and Evolution
BT 
AF 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
AS 1:1,2;2:1;3:1,3;4:4,5;5:6;6:7;7:8;8:9,10;9:11,12;10:1;
FF 1:;2:;3:;4:;5:;6:;7:;8:;9:;10:;
C1 MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
   Department of Marine Biodiversity Research, Japan Agency for Marine Earth Science and Technology (JAMSTEC), Yokosuka, Japan
   Department of Earth Sciences, University of Geneva, Geneva, Switzerland
   School of GeoSciences, University of Edinburgh, Edinburgh, UK
   School of Geography and GeoSciences, University of St. Andrews, St. Andrews, UK
   UFR Sciences Exactes et Naturelles, Université de Reims-Champagne-Ardenne, Reims, France
   Centre Nationnal de la Recherche Scientifique (CNRS), École Normale Supérieure (ENS) de Lyon, University of Lyon, Villeurbanne, France
   Center for Advanced Marine Core Research, Kochi University, Kochi, Japan
   Laboratoire d'Ecologie des Hydrosystémes Naturels et Anthropisés, Univ Lyon, Université Lyon 1, CNRS UMR 5023, ENTPE, Villeurbanne, France
   Institut Universitaire de France, Paris, France
   Centre Nationnal de la Recherche Scientifique (CNRS), UMR 7144, Station Biologique de Roscoff, Roscoff, France
   Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Roscoff, France
C2 UNIV BREMEN, GERMANY
   JAMSTEC, JAPAN
   UNIV GENEVA, SWITZERLAND
   UNIV EDINBURGH, UK
   UNIV ST ANDREWS, UK
   UNIV REIMS, FRANCE
   CNRS LEGOS, FRANCE
   UNIV KOCHI, JAPAN
   UNIV LYON, FRANCE
   INST UNIV FRANCE, FRANCE
   CNRS, FRANCE
   UNIV PARIS 06, FRANCE
IN DOAJ
IF 5.247
TC 29
UR https://archimer.ifremer.fr/doc/00383/49460/49938.pdf
   https://archimer.ifremer.fr/doc/00383/49460/49939.xlsx
   https://archimer.ifremer.fr/doc/00383/49460/49940.xlsx
   https://archimer.ifremer.fr/doc/00383/49460/49941.xlsx
   https://archimer.ifremer.fr/doc/00383/49460/49942.pdf
   https://archimer.ifremer.fr/doc/00383/49460/49943.pdf
   https://archimer.ifremer.fr/doc/00383/49460/49944.pdf
LA English
DT Article
CR OISO - OCÉAN INDIEN SERVICE D'OBSERVATION
DE ;foraminifera;protists;single-cell genetics;cryptic diversity;comparability;methods;laboratory protocols;standardization
AB 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 a comprehensive reference with guidelines for future genetic studies on foraminifera, but it also establishes an important benchmark for investigations using existing single-cell datasets. The methods are widely applicable and the review may help to establish similar standard principles for their utilization in other protist groups. 
PY 2016
SO Frontiers In Marine Science
SN 2296-7745
PU Frontiers Media SA
VL 3
IS 255
UT 000457358000251
BP 1
EP 15
DI 10.3389/fmars.2016.00255
ID 49460
ER

EF