Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants

Sophie Gaudriault¹^,2 , Sylvie Pages¹^,2 , Anne Lanois¹^,2 , Christine Laroui¹^,2 , Corinne Teyssier³ , Estelle Jumas-Bilak³ and Alain Givaudan¹^,2

¹INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France

²Université Montpellier 2, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France

³Université Montpellier 1, EA 3755, Laboratoire de Bactériologie-Virologie, 15, Avenue Charles Flahault, BP 14491, F-34060 Montpellier Cedex 5, France

author email corresponding author email

Genome Biology 2008, 9:R117doi:10.1186/gb-2008-9-7-r117


Published:	22 July 2008

Abstract

Background

The phenotypic consequences of large genomic architecture modifications within a clonal bacterial population are rarely evaluated because of the difficulties associated with using molecular approaches in a mixed population. Bacterial variants frequently arise among Photorhabdus luminescens, a nematode-symbiotic and insect-pathogenic bacterium. We therefore studied genome plasticity within Photorhabdus variants.

Results

We used a combination of macrorestriction and DNA microarray experiments to perform a comparative genomic study of different P. luminescens TT01 variants. Prolonged culturing of TT01 strain and a genomic variant, collected from the laboratory-maintained symbiotic nematode, generated bacterial lineages composed of primary and secondary phenotypic variants and colonial variants. The primary phenotypic variants exhibit several characteristics that are absent from the secondary forms. We identify substantial plasticity of the genome architecture of some variants, mediated mainly by deletions in the 'flexible' gene pool of the TT01 reference genome and also by genomic amplification. We show that the primary or secondary phenotypic variant status is independent from global genomic architecture and that the bacterial lineages are genomic lineages. We focused on two unusual genomic changes: a deletion at a new recombination hotspot composed of long approximate repeats; and a 275 kilobase single block duplication belonging to a new class of genomic duplications.

Conclusion

Our findings demonstrate that major genomic variations occur in Photorhabdus clonal populations. The phenotypic consequences of these genomic changes are cryptic. This study provides insight into the field of bacterial genome architecture and further elucidates the role played by clonal genomic variation in bacterial genome evolution.