The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice

Abstract

The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, a bacterium that causes bacterial blight in rice (Oryza sativa L.). The genome is comprised of a single, 4 941 439 bp, circular chromosome that is G + C rich (63.7%). The genome includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be assigned putative function. Orthologs for 80% of the predicted Xoo genes were found in the previously reported X.axonopodis pv. citri (Xac) and X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently specific to Xoo were identified. Xoo genes likely to be associated with pathogenesis include eight with similarity to Xanthomonas avirulence (avr) genes, a set of hypersensitive reaction and pathogenicity (hrp) genes, genes for exopolysaccharide production, and genes encoding extracellular plant cell wall-degrading enzymes. The presence of these genes provides insights into the interactions of this pathogen with its gramineous host.

Figure 1

Circular genome map of X.oryzae pv. oryzae str. KACC10331. Overall structure of the X.oryzae pv. oryzae genome. The putative origin of replication is at 0 kb. The outer scale indicates the coordinates (in base pair). Red symbols (character R) are positions of rRNA and blue symbols (character T) are tRNAs. The distribution of genes is shown on the first two rings within the scale. The next circle (green) shows G + C content and central circle (blue/red) shows GC-skew value. The window size of G + C content and GC-skew are 1000 nt.

Figure 2

Nucleotide alignments of Xoo (x-axis) versus Xac (y-axis), left; and Xoo (x-axis) versus Xcc (y-axis), right. Each point in the plot corresponds to an MUM of ≥25 bp.

Figure 3

Linear genomic comparisons of X.oryzae pv. oryzae with X.axonopodis pv. citri and X.campestris pv. campestris. Top, Xac; middle, Xoo; bottom, Xcc. The colored ticks represent the reading frames from top to bottom; +1 frame, +2 frame, +3 frame, a whole forward frame, a whole reverse frame, −1 frame, −2 frame and −3 frame. The red lines in between the genomes represent DNA:DNA similarities (BLASTN matches) between the two DNA sequences.

Figure 4

Comparisons of the hrp gene cluster of the three Xanthomonas species.