Genome Sequence of Pseudomonas chlororaphis GP72, a Root-Colonizing Biocontrol Strain

Abstract

Pseudomonas chlororaphis GP72 is a root-colonizing biocontrol strain isolated from a green pepper rhizosphere. It can produce several secondary metabolites to suppress phytopathogens. Here we present a 6.6-Mb assembly of its genome, which is the first genome sequence of the P. chlororaphis group and may provide insights into its antifungal activities.

GENOME ANNOUNCEMENT

Pseudomonas is a diverse genus with more than 60 species (5). Pseudomonas chlororaphis strains show broad antagonistic activities, mainly isolated from the plant rhizospheres (3, 14, 20). P. chlororaphis GP72 is a root-colonizing biocontrol rhizobacterium screened with the conserved probe of phenazine-1-carboxylic acid from a green pepper rhizosphere in eastern China (10). Strain GP72 has the capacity to colonize plant rhizosphere and can suppress several soilborne pathogens in vitro as determined previously (12). Previous studies confirmed that strain GP72 can produce well-characterized phenazine derivatives with high fungicidal activities: phenazine-1-carboxylic acid, 2-hydroxyphenazine, and the intermediate 2-hydroxyphenazine-1-carboxylic acid (7, 11). These phenazine derivatives could play important roles in Pseudomonas sp.-mediated biological control activities (22). However, no genetic component responsible has been identified from the genome sequence of a P. chlororaphis strain for the biological control activities.

The genome of P. chlororaphis GP72 was sequenced using the Illumina GAIIx platform and assembled into 347 contigs using Velvet 1.1.07 (24). The open reading frames were predicted using Glimmer 3.02 (4). The genome sequence of strain GP72 was annotated using the RAST server (2) and NCBI prokaryotic genomes automatic annotation pipeline (PGAAP). rRNA and tRNA genes were identified by RNAmmer 1.2 (8) and tRNAscan-SE (13), respectively. The metabolic pathways were examined through KAAS (KEGG automatic annotation server) (16). Comparative genome analysis was performed with WebACT (1) and mGenomeSubtractor (21).

The draft genome sequence of P. chlororaphis GP72 consists of 6,629,881 bases with a G+C content of 63.1%. The assembled genome has approximately 270-fold coverage with an N₅₀ scaffold size of 221 kb. There are 6,107 putative coding sequences (CDS) with 770 (12.6%) strain-specific CDS, 153 tRNA genes, and 4 rRNA operons. Genes encoding phenazine biosynthesis enzymes (phzIRABCDEFG) and a modifying enzyme (phzO) (7), and the reported regulator genes, such as rpeA and rpeB for two-component negative regulation and rpoN for positive regulation (11, 15), were annotated in the sequence. They play important roles in phenazine production or biological activities. Genes encoding pyrrolnitrin (prnABCD) (20) and hydrogen cyanide (hcnABC) (9) were also predicted. Moreover, a Pseudomonas fluorescens insecticidal toxin (19) gene cluster (fitABCDEFGH) was found in the genome. Hence, the characteristics contributing to environmental fitness for the antagonistic actions have been found in the genomic sequence of strain GP72. Additionally, in the genome sequence, there are pyoverdine and achromobactin gene clusters encoding iron acquisition systems (17) and multiple genes encoding antioxidative stress proteins, such as four catalases, 15 peroxidases, two superoxide dismutases, some oxidases (18), and two transcription factors: SoxR (23) and OxyR (6). Moreover, the sequence of strain GP72 shows the genes related to multidrug resistance mechanisms, such as the drug efflux pump systems, enzyme-mediated antibiotics resistance, and mobility. Therefore, the recently announced genome information for P. chlororaphis will allow further studies on control of agronomical pathogens and may provide insights into antifungal activities.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AHAY00000000. The version described in this paper is the first version, AHAY01000000.