Genome Sequences of Three Atypical Xanthomonas campestris pv. campestris Strains, CN14, CN15, and CN16.

Xanthomonas campestris pv. campestris is the causal agent of black rot on Brassicaceae. The draft genome sequences of three strains (CN14, CN15, and CN16) that are highly aggressive on Arabidopsis have been determined. These genome sequences present an unexpected genomic diversity in X. campestris pv. campestris, which will be valuable for comparative analyses.

GENOME ANNOUNCEMENT

Xanthomonas campestris pv. campestris is the causal agent of black rot on a wide range of Brassicaceae, including vegetable crops (e.g., cabbages and radish) and weeds (e.g., Arabidopsis thaliana) (1). Seven genomic clades (A to G) of X. campestris pv. campestris have been defined (2). As yet, genomic resources are available for only clades A and C (3–6). Interestingly, clade G strains seem to represent ancestral X. campestris pv. campestris strains that have not been described so far (2).

X. campestris pv. campestris CN14, CN15, and CN16 are clade G strains that have been isolated in 2003 in Guilin, China, on Brassica juncea var. foliosa, Brassica rapa subsp. chinensis, and Brassica rapa subsp. pekinensis, respectively (7). These three strains cause typical black rot disease symptoms on cabbages and Arabidopsis (2, 7). Shotgun sequencing of genomic DNA was performed on a HiSeq 2000 Illumina platform. For strains CN14, CN15, and CN16, 2,512,066, 12,943,052, and 13,937,309 paired-end reads of 85, 101, and 101 bp were obtained and correspond to 86-, 521-, and 561-fold coverage, respectively. Genome assembly was performed using a combination of SOAPdenovo (8) and Velvet (9) assemblers and yielded 165, 73, and 80 contigs of >500 bp and an N50 of 74,016, 214,266, and 195,559 bp, respectively. The average contig sizes are 30,240, 68,756, and 62,722 bp, the largest being 181,633, 466,491, and 407,991 bp long, for a total genome size of 4,989,674, 5,019,206, and 5,017,785 bp for strains CN14, CN15, and CN16, respectively. Next, 155, 67, and 75 of those contigs were organized into 8, 7, and 7 pseudomolecules, respectively. The largest one corresponds to the chromosome (4,908,255, 4,920,230, and 4,928,563 bp, respectively; 65% G+C content for all) based on X. campestris pv. campestris strain 8004 chromosomal organization. Remaining pseudomolecules match to known Xanthomonas plasmid sequences and should account for the ca. 20-kb and 50-kb endogenous plasmids found in each strain (2). Genome analysis of the CN14, CN15, and CN16 genomes confirmed the presence of at least 22, 22, and 23 type III-secreted proteins, respectively (2). Due to their highly repetitive nature, transcription activator-like effector sequences could not be assembled and are not represented in the final assemblies. Annotation transfer was performed using RATT (10) with X. campestris pv. campestris strains B100, 8004, and ATCC 33913 as references. De novo annotation was performed on remaining areas using FrameD (11) and manually inspected. In strains CN14, CN15, and CN16, 4,733, 4,800, and 4,793 coding sequences (CDSs), 53, 52, and 52 tRNA genes, and 3, 4, and 4 rRNA genes could be identified, respectively.

Phylogenetic analyses based on the core genome shared with the 5 X. campestris pv. campestris genomes (3–6, 12) and X. campestris pv. raphani strain 756C were performed using UNUS (13). This analysis shows that the three clade G strains are most closely related to other X. campestris pv. campestris strains but assemble into a novel phylogenetic group of X. campestris pv. campestris. Using orthoMCL (percent match cutoff = 80, BLAST parameter F = false) (14), CN14, CN15, and CN16 share 3,635, 3,648, and 3,646 CDSs with the 3 X. campestris pv. campestris reference genomes, while Xca5 shares 3,711 CDSs with those three strains (4). In conclusion, the CN14, CN15, and CN16 genomes significantly contribute to our knowledge of intraspecific genomic diversity in X. campestris pv. campestris.

Nucleotide sequence accession numbers.

The annotated whole-genome shotgun sequences of CN14, CN15, and CN16 have been deposited at NCBI under the accession no. AQOP00000000, AQOO00000000, and AQON00000000, respectively.