Genome Sequence of the Rice Pathogen Dickeya zeae Strain ZJU1202

Abstract

Dickeya zeae is a phytopathogenic bacterium causing soft rot diseases in a wide range of economically important crops. Here we present the draft genome sequence of strain ZJU1202, which is the causal agent of rice foot rot in China. The draft genome will contribute to epidemiological and comparative genomic studies and the quarantine of this devastating phytopathogen.

GENOME ANNOUNCEMENT

Dickeya zeae, formerly Erwinia chrysanthemi, is a facultative aerobic/anaerobic phytopathogenic bacterium that causes soft rot diseases in a wide range of plant species, including many economically important crops (4). In rice, this pathogen can cause bacterial foot rot and has been reported in many Asian countries, in particular, China. The disease often starts at the ligules, where the leaves join the sheaths (9, 10, 11). The characteristic symptom is a dark brown sheath rot; as it extends, the leaf blades yellow, die, and drop off. Gradually the nodes, culms, crowns, and roots become infected and decay. As rice seeds and soil contaminated with this pathogen are important sources of the primary inoculums and a means of dissemination of the pathogen to new areas (9, 10, 11), this pathogen has been gaining increasing attention in China.

We sequenced and annotated the draft genome of D. zeae strain ZJU1202, a strain isolated from diseased rice in Guangdong Province, China, in 2012. Genomic DNA was isolated with a Wizard genomic DNA purification kit (Promega, Madison, WI), and sequencing was performed using an Illumina HiSeq 2000 sequencing system. The whole-genome sequencing approach resulted in 6,410,708 high-quality filtered reads with an average paired-end read length of 100 bp and 140-fold sequencing coverage, on average. Quality filtered reads were assembled in silico with SOAPdenovo and the GapCloser program (6). On the basis of the reference genome of D. zeae strain Ech1591 (http://genome.jgi-psf.org/dicda/dicda.info.html) isolated from a maize leaf, a draft genome of ZJU1202 was generated. Functional annotation was done by analyzing results obtained from the RAST (rapid annotation using subsystem technology) server (2), BLAST (1), tRNAscan-SE 1.21 (7), and RNAmmer 1.2 (5).

Here we present the draft genome sequence of strain ZJU1202, which comprises 4,606,930 bp and has a G+C content of 53.3%. The draft genome was assembled into 188 contigs. A total of 4,111 genes were predicted using GLIMMER (8). The draft sequence contains 16 5S rRNAs genes, 2 16S rRNA genes, 3 copies of 23S rRNA genes, and 67 tRNAs. Furthermore, 82.2% of the open reading frames (ORFs) have orthologs in the reference strain D. zeae Ech1591 (BLASTP E-value 1E-20), but 588 ORFs were not found in the released genomes of members of the genus Dickeya.

Functional annotation revealed pathogenicity-related genes, including those for a type 6 secretion system gene cluster or Hcp and a Vgr-like protein, type 3 and 4 secretion systems, Hrp protein, and flagellin, in strain ZJU1202. These genes are virulence associated in many phytopathogenic Gram-negative bacteria (3). Meanwhile, several multidrug resistance efflux pumps, the multidrug transporter MdtB, and ABC transporter subunits were identified.

Overall, the genome sequence of D. zeae provides an important data resource for epidemiological and comparative genomic studies and for quarantine measures against this devastating phytopathogen.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number AJVN00000000. The version described in this paper is the first version, AJVN01000000.