JB Accepts, published online ahead of print on 11 January 2008

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J. Bacteriol. doi:10.1128/JB.01598-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Genome of the actinomycete plant pathogen Clavibacter michiganensis subspecies sepedonicus suggests recent niche adaptation

Stephen D. Bentley, Craig Corton, Susan E. Brown, Andrew Barron, Louise Clark, Jon Doggett, Barbara Harris, Doug Ormond, Michael A. Quail, Georgiana May, David Francis, Dennis Knudson, Julian Parkhill, and Carol A. Ishimaru^*

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK; Department of Biological Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523; Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108; Department of Horticulture and Crop Science Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691; Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108

Clavibacter michiganensis subspecies sepedonicus is a plant pathogenic bacterium and the causative agent of bacterial ring rot, a devastating agricultural disease under strict quarantine control and zero tolerance in the seed potato industry. The organism appears to be largely restricted to an endophytic lifestyle, proliferating within plant tissues and unable to persist in the absence of plant material. Analysis of the genome sequence of Clavibacter michiganensis subsp. sepedonicus and comparison with those of related plant-pathogens indicates a dramatic recent evolutionary history. The genome contains 106 insertion sequence elements, which appear to have been active in extensive rearrangement of the chromosome relative to that of Clavibacter michiganensis subsp. michiganensis. There are 110 pseudogenes with an over-representation in functions associated with carbohydrate metabolism, transcriptional regulation and pathogenicity. Genome comparisons also indicate substantial gene content diversity within the species probably due to differential gene acquisition and loss. These genomic features and evolutionary dating suggest recent adaptation for life within a restricted niche where nutrient diversity and perhaps competition is low, correlating with reduced ability to exploit formerly occupied complex niches outside of the plant. Toleration of factors such as multiplication and integration of insertion sequence elements, genome rearrangements and the functional disruption of many genes and operons seems to indicate a general relaxation of selective pressure on a large proportion of the genome.

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