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J Bacteriol. Feb 2012; 194(3): 724–725.
PMCID: PMC3264083

Draft Genome Sequences of the Pseudomonas fluorescens Biocontrol Strains Wayne1R and Wood1R

Abstract

Pseudomonas fluorescens strains Wayne1R and Wood1R have proven capacities to improve plant health. Here we report the draft genome sequences and automatic annotations of both strains. Genome comparisons reveal similarities with P. fluorescens strain Pf-5, reveal the novelty of Wood1R, and indicate some genes that may be related to biocontrol.

GENOME ANNOUNCEMENT

Pseudomonas fluorescens strains Wayne1R and Wood1R are rifampin-resistant variants of wild-type strains isolated from the rhizospheres of corn and soybeans (3). They harbor the phlD gene, which is essential for biosynthesis of 2,4-diacetylphloroglucinol (DAPG) in Pseudomonas spp. (2). Both strains can improve plant health under field conditions, a trait that appears to be common among phlD+ bacteria (8). Soybeans treated with Wayne1R have greater stands and yields in the field than those grown from untreated seeds (3). Also, seed treatment with Wood1R ameliorates nutrient stress of field-grown corn grown in acidic soil (6).

The genomic DNAs of Wayne1R and Wood1R were isolated, and libraries were prepared from sheared DNA fractions of ~300 bp using Illumina paired-end sample preparation kits. These were sequenced on a Genome Analyzer II (Illumina, San Diego, CA). The short-read sequences were assembled into assemblies with hash lengths of 37 nucleotides (nt) (Wayne1R) and 31 nt (Wood1R) and a minimum contig length of 300 nt using Velvet version 0.7.55 (9, 10). The assemblies were uploaded to an automated annotation platform, the rapid annotation using subsystems technology (RAST) server (1), and visualized with the SEED viewer (4).

The Wayne1R assembly has a total of 6,858,374 nt spread across 90 contigs. Some 6,228 protein-encoding genes (PEGs) were annotated on 75 contigs, with an average sequence coverage of ~20-fold. rRNA genes were not fully assembled. However, 52 tRNA sequences were identified. In the amino acid sequence-based comparisons to other Pseudomonas fluorescens strains in the public SEED database, 5,112 to 5,814 (82 to 93%) of the annotated PEGs of Wayne1R were mapped to the genomes of P. fluorescens strains Pf-5 (5), Pf0-1, and SBW25 (7), with an average DNA sequence identity of 74%. Of the 414, 1,079, and 1,116 PEGs predicted to be unique to Wayne1R when compared with Pf-5, Pf0-1, and SBW25, respectively, 117 (28.2%), 756 (70.0%), and 801 (71.8%) PEGs, respectively, were identified (i.e., not assigned as “hypothetical proteins”).

The Wood1R assembly has a total of 6,681,319 nt spread across 1,437 contigs. Some 5,897 PEGs were annotated on 1,304 contigs, with an average sequence coverage of ~13-fold. The assembly did not adequately reconstruct the rRNA genes, but 30 tRNA sequences were identified. In the amino acid sequence-based comparisons to other Pseudomonas fluorescens strains in the public SEED database, ~85% of the annotated PEGs of Wood1R were mapped to the genomes of Pf0-1, SBW25, and Pf-5, with an average DNA sequence identity of 74 to 77%. Of the 852, 914, and 916 PEGs predicted to be unique to Wood1R when compared with Pf0-1, SBW25, and Pf-5, respectively, 433 (48.9%), 475 (52.0%), and 459 (50.1%) PEGs, respectively, were identified.

The phlD genes in the Wayne1R and Wood1R genomes showed similarities of 99.6% and 78.4%, respectively, to the phlD gene in Pf-5 (PFL5957) (5). In keeping with the phlD-based classification of these strains, the plt cluster (pyoluteorin biosynthesis) was found in Wayne1R and the hcn locus (biosynthesis of hydrogen cyanide) was found in both Wayne1R and Wood1R.

ACKNOWLEDGMENTS

We are grateful to the whole MCIC sequencing and bioinformatics team at The Ohio State University, OARDC, for technical assistance.

This work was supported by a SEEDS grant from the Ohio Agricultural Research and Development Center and by the World Class University project of the National Research Foundation of Korea (grant no. R32-2009-000-20047-0).

REFERENCES

1. Aziz R, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. [PMC free article] [PubMed]
2. Bangera MG, Thomashow LS. 1999. Identification and characterization of a gene cluster for synthesis of the polyketide antibiotic 2,4-diacetylphloroglucinol from Pseudomonas fluorescens Q2-87. J. Bacteriol. 181:3155–3163 [PMC free article] [PubMed]
3. McSpadden Gardener BB, Gutierrez LJ, Joshi R, Edema R, Lutton E. 2005. Distribution and biocontrol potential of phlD+ pseudomonads in corn and soybean fields. Phytopathology 95:715–724 [PubMed]
4. Overbeek R, et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33:5691–5702 [PMC free article] [PubMed]
5. Paulsen IT, et al. 2005. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat. Biotechnol. 23:873–878 [PubMed]
6. Raudales RE, Stone E, McSpadden Gardener BB. 2009. Seed treatment with 2,4-diacetylphloroglucinol-producing pseudomonads improves crop health in low-pH soils by altering patterns of nutrient uptake. Phytopathology 99:506–511 [PubMed]
7. Silby M, et al. 2009. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol. 10:R51. [PMC free article] [PubMed]
8. Weller DM, Raaijmakers JM, Gardener BBM, Thomashow LS. 2002. Microbial populations responsible for specific soil suppressiveness to plant pathogens. Annu. Rev. Phytopathol. 40:309–348 [PubMed]
9. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829 [PMC free article] [PubMed]
10. Zerbino DR, McEwen GK, Margulies EH, Birney E. 2009. Pebble and Rock Band: heuristic resolution of repeats and scaffolding in the Velvet short-read de novo assembler. PLoS One 4:e8407. [PMC free article] [PubMed]

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