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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
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Official URL: http://dx.doi.org/10.1111/j.1574-6941.2011.01072.x
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 | ||||
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| Subjects: | Q Science > QH Natural history > QH426 Genetics Q Science > QR Microbiology |
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| Divisions: | Faculty of 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: |
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| 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) |
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