Draft Genome Sequence of Pantoea anthophila Strain 11-2 from Hypersaline Lake Laysan, Hawaii.

Most Pantoea spp. have been isolated from plant sources or clinical samples. However, we cultivated Pantoea anthophila 11-2 from hypersaline water from the lake on Laysan, Northwestern Hawaiian Islands. Draft genome sequencing of 11-2 provides a molecular basis for studies in evolution and pathogenicity in Pantoea spp.

GENOME ANNOUNCEMENT

Pantoea spp. are Gram-negative bacteria generally isolated from agricultural or clinical samples, and marine sediment (1–3). Strain 11-2 from hypersaline Lake Laysan shared 100% nucleotide identity in its 16S rRNA gene with the 16S rRNA gene in Pantoea anthophila BD 871T (LMG 2558) from Impatiens balsamina (4–6). We report the draft genome sequence of P. anthophila 11-2.

Shotgun and 8-kb-span paired-end libraries prepared and sequenced in the Roche 454 GS FLX+ platform generated 126.7 Mb of shotgun sequences and 116.3 Mb of 8-kb-span paired-end sequences, providing ~50× genome coverage. Assembly was performed in Newbler 2.8 in a two-step strategy. Shotgun reads were assembled into contigs, after which paired-end reads were added to build 5 scaffolds containing 4,609,867 bp (N50 = 3,885,396 bp) and 16 contigs containing 4,600,679 bp assembled in the 5 scaffolds. Gap regions in scaffolds were estimated to cover ~9 kb. The genome’s G+C content is 56.8%.

The genome was annotated in the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (7) and the Rapid Annotation Using Subsystem Technology (RAST) server (8, 9). PGAP identified 4,069 protein-coding open reading frames, 67 tRNA coding regions, and 15 rRNA coding regions. RAST identified 502 function-related subsystems and 7 phage components, including 3 phage baseplate proteins, 2 phage packaging machineries, and 1 each of phage tail protein and phage tail fiber protein. Six virulence regulation components were also identified in the BarA-UvrY two-component regulatory system. Ten proteins in the type III secretion system (T3SS) apparatus, and 64 T3SS-related transcription regulators were predicted using BLASTp against the T3SS database (T3DB) (E < 1e−10) (10). Eleven diguanylate cyclases and nine diguanylate phosphodiesterases (E < 1e−10) were predicted, which synthesize and degrade the ubiquitous second messenger, cyclic-di-GMP, involved in bacterial morphology and biofilm formation. The N-terminal PAS domain and GAF domain sensors of several diguanylate cyclases and diguanylate phosphodiesterases were predicted by the SMART server (11). The draft genome sequence reported here provides a molecular basis for studies in pathogenicity and evolution of Pantoea spp.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JXXL00000000. The version described in this paper is version JXXL01000000.