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

Abstract

Clavibacter michiganensis subsp. 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. This 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 C. michiganensis subsp. sepedonicus and comparison with the genome sequences of related plant pathogens revealed a dramatic recent evolutionary history. The genome contains 106 insertion sequence elements, which appear to have been active in extensive rearrangement of the chromosome compared to that of Clavibacter michiganensis subsp. michiganensis. There are 110 pseudogenes with overrepresentation in functions associated with carbohydrate metabolism, transcriptional regulation, and pathogenicity. Genome comparisons also indicated that there is substantial gene content diversity within the species, probably due to differential gene acquisition and loss. These genomic features and evolutionary dating suggest that there was recent adaptation for life in a restricted niche where nutrient diversity and perhaps competition are low, correlated with a reduced ability to exploit previously occupied complex niches outside the plant. Toleration of factors such as multiplication and integration of insertion sequence elements, genome rearrangements, and functional disruption of many genes and operons seems to indicate that there has been general relaxation of selective pressure on a large proportion of the genome.

FIG. 1.

Circular diagram of the chromosome of C. michiganensis subsp. sepedonicus. The circles provide the following information (from the outermost circle to the innermost circle): circles 1 and 2, all CDSs (transcribed clockwise and anticlockwise) (dark blue, pathogenicity and adaptation; black, energy metabolism; red, information transfer; dark green, surface associated; cyan, degradation of large molecules; magenta, degradation of small molecules; yellow, central and intermediary metabolism; pale green, unknown; pale blue, regulators; orange, conserved hypothetical; brown, pseudogenes; pink, phage and IS elements; gray, miscellaneous); circle 3, putative laterally acquired CDSs; circle 4, CDSs not present in C. michiganensis subsp. michiganensis or L. xyli; circle 5, pseudogenes; circle 6, IS element transposases; circle 7, G+C content (window size, 10,000 bp); and circle 8, GC deviation (G − C/G + C; window size, 10,000 bp).

FIG. 2.

Alignment of chromosomes of C. michiganensis subsp. sepedonicus (Cms), C. michiganensis subsp. michiganensis (Cmm), and L. xyli subsp. xyli (Lxx). The diagram shows forward and reverse DNA strands (gray bars), and base coordinates with the positions of pat-1 homologues are indicated by vertical black lines. Similar regions that are more than 1,000 bases long are indicated by red (colinear) and blue (inverted) lines.

FIG. 3.

Bar chart of functional classes of all CDSs (open bars) and pseudogenes (shaded bars). Note the overrepresentation of pseudogenes in CDSs encoding transport and binding proteins, macromolecule degradation, small-molecule degradation, pathogenicity, and regulation.

FIG. 4.

Venn diagram showing numbers of shared and unique genes in the genomes of C. michiganensis subsp. sepedonicus (Cms), C. michiganensis subsp. michiganensis (Cmm), and L. xyli subsp. xyli (Lxx). The red numbers do not include the number of IS element transposases.

FIG. 5.

Dot plot amino acid alignment of the CMS0087 with CMM0090 (TomA) proteins. The axes show the amino acid residue, and the dots and lines indicate amino acid identity between the protein sequences. The plot was generated using Dotter (71). The Karlin/Altschul statistics for the sequences and score matrix are as follows: K = 0.129; Lambda = 0.301; expected MSP score in a 100 × 100 matrix, 23.817; expected residue score in MSP, 1.186; expected MSP length, 20.