RRC ID 61014
Author Lepere C, Demura M, Kawachi M, Romac S, Probert I, Vaulot D.
Title Whole-genome amplification (WGA) of marine photosynthetic eukaryote populations.
Journal FEMS Microbiol Ecol
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.
Volume 76(3)
Pages 513-23
Published 2011-6-1
DOI 10.1111/j.1574-6941.2011.01072.x
PMID 21348885
MeSH DNA, Plant / genetics Flow Cytometry Genes, rRNA Metagenomics / methods* Microalgae / genetics* Nucleic Acid Amplification Techniques / methods* Photosynthesis* Phylogeny Polymerase Chain Reaction Reproducibility of Results Seawater / microbiology Water Microbiology*
IF 4.098
Times Cited 38
Resource
Algae NIES-252 NIES-1411