Genome Sequence of the Rice Pathogen Pseudomonas fuscovaginae CB98818

Abstract

Pseudomonas fuscovaginae is a phytopathogenic bacterium causing bacterial sheath brown rot of cereal crops. Here, we present the draft genome sequence of P. fuscovaginae CB98818, originally isolated from a diseased rice plant in China. The draft genome will aid in epidemiological studies, comparative genomics, and quarantine of this broad-host-range pathogen.

GENOME ANNOUNCEMENT

Pseudomonas fuscovaginae belongs to the authentic rRNA group I of pseudomonads pathogenic toward several crop species, such as rice, maize, sorghum, and wheat (1, 4, 5). In rice, this pathogen can cause bacterial sheath brown rot and has been reported in many countries in Asia, Africa, the Americas, and Europe (4, 5, 10). Distinctive symptoms on rice plants are water-soaked, brown-black spots on the adaxial side of the flag leaf sheath, poor spike emergence, and sterility in severe cases (10–12). As P. fuscovaginae is a seed-borne and seed-transmitted pathogen of rice, the rice seeds contaminated with this pathogen are important sources of the primary inoculum and a means of dissemination of the pathogen to new areas (9–11). Therefore, this pathogen has been gaining increasing attention in China.

We sequenced and annotated the draft genome of P. fuscovaginae CB98818, a strain isolated from diseased rice in Zhejiang province, China, in our previous study (11). The genomic DNA, isolated with a Wizard genomic DNA purification kit (Promega, Madison, WI), was whole-genome sequenced by using Roche 454 GS FLX systems. A total of 437,333 reads were generated, with an average read length of 425 bp and coverage equivalent to about 200×. The sequence reads were de novo assembled using Geneious Pro v5.5.3 (3) and Newbler Assembler 2.7 (454 Life Science), resulting in a total of 263 contigs. Based on the most closely related reference genome of P. fuscovaginae UPB0736 (8), a draft genome of P. fuscovaginae CB98818 was generated. Functional annotation was conducted by merging the results obtained from the RAST (rapid annotation using subsystem technology) server (2), tRNAscan-SE 1.21 (7), and RNAmmer 1.2 (6).

Here we announce the draft genome sequence of P. fuscovaginae CB98818, which comprises 6,541,443 bp and has a G+C content of 61.4%. A total of 6,290 genes were predicted using Glimmer (9). The draft sequence contains 74 RNAs, including two 23S rRNA genes, seven 5S rRNA genes, and 65 tRNAs. Furthermore, 94.2% of the open reading frames (ORFs) have orthologs in the reference strain P. fuscovaginae CB98818 (BLASTP E value of 1E−20), but 372 ORFs were not found in the released genomes of members of the genus Pseudomonas.

P. fuscovaginae has the ability to produce three different types of phytotoxic metabolites, syringotoxin, fuscopeptin A, and fuscopeptin B, which are reported to be involved in producing the disease symptoms (8). Furthermore, functional annotation of P. fuscovaginae strain CB98818 revealed pathogenicity-related genes like type VI secretion system, type III and IV secretion system, Hcp- and VgR-like protein, Hrp protein, and flagellin. 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 also identified.

Overall, the genome sequence of P. fuscovaginae CB98818 will provide the basis for a better understanding of the molecular pathogenesis of rice bacterial sheath brown rot and is an important data resource for epidemiological studies, comparative genomics, and quarantine measures of this important phytopathogen.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number ALAQ00000000. The version described in this paper is the first version, ALAQ01000000.