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Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations

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Lepère, Cécile, Demura, Mikihide, Kawachi, Masanobu, Romac, Sarah, Probert, I. (Ian) and Vaulot, Daniel (2011) Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations. FEMS Microbiology Ecology, Volume 76 (Number 3). pp. 513-523. doi:10.1111/j.1574-6941.2011.01072.x ISSN 0168-6496.

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Official URL: http://dx.doi.org/10.1111/j.1574-6941.2011.01072.x

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Abstract

Metagenomics approaches have been developing rapidly in marine sciences. However, the application of these approaches to marine eukaryotes, and in particular to the smallest ones, is challenging because marine microbial communities are dominated by prokaryotes. One way to circumvent this problem is to separate eukaryotic cells using techniques such as single-cell pipetting or flow cytometry sorting. However, the number of cells that can be recovered by such techniques remains low and genetic material needs to be amplified before metagenomic sequencing can be undertaken. In this methodological study, we tested the application of whole-genome amplification (WGA) to photosynthetic eukaryotes. We performed various optimization steps both on a mixture of known microalgal strains and on natural photosynthetic eukaryote populations sorted by flow cytometry. rRNA genes were used as markers for assessing the efficiency of different protocols. Our data indicate that WGA is suitable for the amplification of photosynthetic eukaryote genomes, but that biases are induced, reducing the diversity of the initial population. Nonetheless, this approach appears to be suitable for obtaining metagenomics data on microbial eukaryotic communities.

Item Type: Journal Article
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QR Microbiology
Divisions: Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School
Library of Congress Subject Headings (LCSH): Microbial genomics, Gene amplification, Flow cytometry, RNA, Ribosomes, Eukaryotic cells -- Genetics, Marine microbiology
Journal or Publication Title: FEMS Microbiology Ecology
Publisher: Wiley-Blackwell Publishing Ltd.
ISSN: 0168-6496
Official Date: 2011
Dates:
DateEvent
2011Published
Volume: Volume 76
Number: Number 3
Page Range: pp. 513-523
DOI: 10.1111/j.1574-6941.2011.01072.x
Status: Peer Reviewed
Publication Status: Published
Funder: France. Agence nationale de la recherche (ANR), Japan. Kagaku Gijutsuchō [Japan Science and Technology Agency] (JST), Centre national de la recherche scientifique (France) (CNRS), Brittany (France), Seventh Framework Programme (European Commission) (FP7), European Union (EU)
Grant number: 06-BDIV-013 (ANR), 227799 (FP7)

Data sourced from Thomson Reuters' Web of Knowledge

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