U.S. Department of Energy Office of Biological and Environmental Research

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Assembling Individual Genomes from Complex Metagenomics Sequencing Samples
Published: October 27, 2011
Posted: August 21, 2012

Microbes in nature often live in communities containing many different species. Identifying the mix of species is necessary for many studies of microbes for energy and environmental missions. Genome sequencing of an entire community (determining the metagenome) is often the best means of discovering which species are in a given community. However, it is a major challenge to pull out and assemble the whole genomes of the individual microbes comprising the community. Although many of the species are difficult to culture in a laboratory, they often contain a wealth of novel capabilities that must be characterized to enable understanding of the processes that take place in a community. Researchers at the DOE Joint Genome Institute have shown, through simulations and analysis of reference microbial communities, that extracting and assembling single genotypes requires 20X sequencing coverage. Their results also suggest that a higher coverage of sequencing will not enhance the assembly of individual organism. This result will help researchers plan metagenomic sequencing experiments for a wide range of DOE-relevant microbial communities.

Reference: Luo, C., D. Tsementzi, N. Kyrpides, and K. Konstantinidis. 2012. "Individual Genome Assembly from Complex Community Short Read Metagenomic Datasets," ISME Journal 6, 898-901. DOI: 10.1038/ismej.2011.147. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: Computational Biology, Bioinformatics, Modeling

Division: SC-23.2 Biological Systems Science Division, BER

 

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