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Open Access Highly Accessed Methodology article

Microbial comparative pan-genomics using binomial mixture models

Lars Snipen1*, Trygve Almøy1 and David W Ussery2

Author Affiliations

1 Biostatistics, Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway

2 Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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BMC Genomics 2009, 10:385  doi:10.1186/1471-2164-10-385

Published: 19 August 2009

Abstract

Background

The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology.

Results

We estimate core- and pan-genome sizes for 16 different bacterial species. The results reveal a complex dependency structure for most species, manifested as heterogeneous detection probabilities. Estimated pan-genome sizes range from small (around 2600 gene families) in Buchnera aphidicola to large (around 43000 gene families) in Escherichia coli. Results for Echerichia coli show that as more data become available, a larger diversity is estimated, indicating an extensive pool of rarely occurring genes in the population.

Conclusion

Analyzing pan-genomics data with binomial mixture models is a way to handle dependencies between genomes, which we find is always present. A bottleneck in the estimation procedure is the annotation of rarely occurring genes.