Single cell genome analysis of an uncultured heterotrophic stramenopile

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


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Biodiversity
  • Computational Biology
  • Genomics*
  • Phylogeny
  • Proteome
  • Proteomics
  • RNA, Ribosomal, 18S / genetics
  • Seawater
  • Single-Cell Analysis*
  • Stramenopiles / classification
  • Stramenopiles / genetics*
  • Stramenopiles / metabolism


  • Proteome
  • RNA, Ribosomal, 18S