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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC AND BIOLOGICAL DETERMINANTS OF RESPIRATORY DISEASES OF RUMINANTS

Location: Genetics, Breeding, & Animal Health

Title: Reducing assembly complexity of microbial genomes with single-molecule sequencing

Authors
item Koren, Sergey -
item Harhay, Gregory
item Smith, Timothy
item Bono, James
item Harhay, Dayna
item McVey, D Scott
item Radune, Diana -
item Bergman, Nicholas -
item Phillippy, Adam -

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 22, 2013
Publication Date: September 13, 2013
Citation: Koren, S., Harhay, G.P., Smith, T.P.L., Bono, J.L., Harhay, D.M., McVey, D.S., Radune, D., Bergman, N.H., Phillippy, A.M. 2013. Reducing assembly complexity of microbial genomes with single-molecule sequencing. Genome Biology. 14:R101. DOI: 10.1186/GB-2013-14-9-R101.

Interpretive Summary: The sequencing and assembly of bacterial genomes is an important first step in understanding bacterial mechanisms of survival, reproduction, and their impact on agricultural systems. This manuscript describes an approach or “recipe” for performing bacterial genome sequencing and assembly, as well as the technical and biological requirements that result in complete chromosomal assembly.

Technical Abstract: Genome assembly algorithms cannot fully reconstruct microbial chromosomes from the DNA reads output by first or second-generation sequencing instruments. Therefore, most genomes are left unfinished due to the significant resources required to manually close gaps left in the draft assemblies. Single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem. To measure the benefit of single-molecule sequencing on microbial genome assembly, we analyzed the repeat complexity of 2,267 previously finished bacteria and archaea, and sequenced the genomes of six bacteria. Our results demonstrate that current single-molecule sequencing can close more than 70% of known bacterial and archaeal genomes at finished-grade quality using only a single library. In addition, this single-library approach shows comparable accuracy to hybrid assemblies of multiple technologies. This drastically reduces the cost of microbial finishing to below $2,000 per genome, and enables high-fidelity, population-scale studies of core-genomes, pan-genomes and chromosomal organization.

Last Modified: 7/22/2014
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