1. ¹Centre for Ecology and Hydrology-Oxford, Oxford, UK
2. ²Cardiff School of Biosciences, Cardiff University, Park Place, Cardiff, UK
3. ³Department of Plant Sciences, University of Oxford, Oxford, UK
4. ⁴Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK
5. ⁵Department of Microbiology, BIOMERIT Research Centre, BioSciences Institute, National University of Ireland, Cork, Ireland
6. ⁶Institute of Molecular Bioscience, Massey University, Auckland, New Zealand
7. ⁷Institute of Advanced Study, Massey University, Auckland, New Zealand
8. ⁸Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
9. ⁹School of Biosciences, University of Birmingham, Birmingham, UK

Correspondence: Professor MJ Bailey, Centre for Ecology and Hydrology-Oxford, Mansfield Road, Oxford OX1 3SR, UK. E-mail: mbailey@ceh.ac.uk

¹⁰These authors contributed equally to this work.

¹¹Current address: SIMBIOS Centre, University of Abertay Dundee, Bell Street, Dundee DD1 1HG, UK.

¹²Current address: Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.

Received 5 March 2007; Revised 22 May 2007; Accepted 22 May 2007; Published online 5 July 2007.

Abstract

The plasmid pQBR103 was found within Pseudomonas populations colonizing the leaf and root surfaces of sugar beet plants growing at Wytham, Oxfordshire, UK. At 425 kb it is the largest self-transmissible plasmid yet sequenced from the phytosphere. It is known to enhance the competitive fitness of its host, and parts of the plasmid are known to be actively transcribed in the plant environment. Analysis of the complete sequence of this plasmid predicts a coding sequence (CDS)-rich genome containing 478 CDSs and an exceptional degree of genetic novelty; 80% of predicted coding sequences cannot be ascribed a function and 60% are orphans. Of those to which function could be assigned, 40% bore greatest similarity to sequences from Pseudomonas spp, and the majority of the remainder showed similarity to other -proteobacterial genera and plasmids. pQBR103 has identifiable regions presumed responsible for replication and partitioning, but despite being tra⁺ lacks the full complement of any previously described conjugal transfer functions. The DNA sequence provided few insights into the functional significance of plant-induced transcriptional regions, but suggests that 14% of CDSs may be expressed (11 CDSs with functional annotation and 54 without), further highlighting the ecological importance of these novel CDSs. Comparative analysis indicates that pQBR103 shares significant regions of sequence with other plasmids isolated from sugar beet plants grown at the same geographic location. These plasmid sequences indicate there is more novelty in the mobile DNA pool accessible to phytosphere pseudomonas than is currently appreciated or understood.