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Open Access Highly Accessed Methodology article

Rapid quantification of sequence repeats to resolve the size, structure and contents of bacterial genomes

David Williams1, William L Trimble2, Meghan Shilts1, Folker Meyer23 and Howard Ochman1*

Author Affiliations

1 Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA

2 Institute for Genomics & Systems Biology, University of Chicago, 5800 S Ellis Ave, Chicago, Illinois 60637, USA

3 Mathematics & Computer Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA

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BMC Genomics 2013, 14:537  doi:10.1186/1471-2164-14-537

Published: 8 August 2013

Abstract

Background

The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly analyzing the abundances of distinct k-mers among reads.

Results

The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes.

Conclusions

Application of these procedures, based solely on k-mer abundances in short read data sets, allows aspects of genome structure to be resolved that are not apparent from conventional short read assemblies. This knowledge of the repetitive content of genomes provides insights into genome evolution and diversity.

Keywords:
K-mer; Genome assembly; Repetitive elements; Bacterial evolution