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Sci Rep. 2014 Apr 24;4:4780. doi: 10.1038/srep04780.

Single cell genome analysis of an uncultured heterotrophic stramenopile.

Author information

1
1] Department of Computer Science, Rutgers University, Piscataway, NJ 08854, USA [2] Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA.
2
Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA.
3
1] Department of Computer Science, Rutgers University, Piscataway, NJ 08854, USA [2] BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854, USA.
4
Department of Plant Biology and Pathology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
5
1] Faculty of Mathematics and Mechanics, Department of Statistical Modeling, Saint Petersburg State University, Universitetskiy 28, 198504, Stary Peterhof, Saint Petersburg, Russia [2] Algorithmic Biology Laboratory, Saint Petersburg Academic University, Khlopina 8/3, 194021, Saint Petersburg, Russia.
6
Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea.
7
Marine Ecosystem Research Division, Korea Institute of Ocean Science and Technology, Ansan 426-744, Korea.

Abstract

A broad swath of eukaryotic microbial biodiversity cannot be cultivated in the lab and is therefore inaccessible to conventional genome-wide comparative methods. One promising approach to study these lineages is single cell genomics (SCG), whereby an individual cell is captured from nature and genome data are produced from the amplified total DNA. Here we tested the efficacy of SCG to generate a draft genome assembly from a single sample, in this case a cell belonging to the broadly distributed MAST-4 uncultured marine stramenopiles. Using de novo gene prediction, we identified 6,996 protein-encoding genes in the MAST-4 genome. This genetic inventory was sufficient to place the cell within the ToL using multigene phylogenetics and provided preliminary insights into the complex evolutionary history of horizontal gene transfer (HGT) in the MAST-4 lineage.

PMID:
24759094
PMCID:
PMC3998028
DOI:
10.1038/srep04780
[Indexed for MEDLINE]
Free PMC Article
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