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Genome Announc. 2017 March; 5(13): e00086-17.
Published online 2017 March 30. doi:  10.1128/genomeA.00086-17
PMCID: PMC5374236

Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L.

ABSTRACT

Pseudomonas putida GM4FR is an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. Functional annotation of the draft genome (7.1 Mb) revealed 6,272 predicted protein-encoding genes. The genome provides insights into the biocontrol and plant growth-promoting potential of P. putida GM4FR.

GENOME ANNOUNCEMENT

Beneficial plant-associated bacteria promote plant growth and health using a variety of mechanisms, including the production of phytohormones (1, 2). These bacteria can enhance the resistance of their host plant against biotic and abiotic stressors (2). Several members of the genus Pseudomonas are known as plant growth-promoting bacteria (2, 3). These include P. putida strains, which have been shown to act as efficient biocontrol agents against phytopathogens and nematodes (3, 4).

Here, we report the draft genome sequence of the endophyte P. putida GM4FR. This strain was isolated from surface-sterilized aerial tissues of healthy Festuca rubra L. plants. Samples were collected from the GrassMan experimental field (5). Genomic DNA of P. putida GM4FR was extracted using the MasterPure complete DNA purification kit (Epicentre, Madison, WI, USA). Obtained DNA was used to generate Illumina paired-end sequencing libraries. Sequencing was performed by employing a MiSeq system and the MiSeq reagent kit version 3 (600 cycles) as recommended by the manufacturer (Illumina, San Diego, CA, USA). Quality filtering using Trimmomatic version 0.32 (6) resulted in 5,419,862 paired-end reads. De novo genome assembly was performed with the SPAdes genome assembler version 3.8.0 (7). The assembly resulted in 79 contigs (>500 bp) and an average coverage of 144-fold. The assembly was validated and the read coverage determined with QualiMap version 2.1 (8).

The draft genome of P. putida strain GM4FR consists of 7,064,252 bp with an overall G+C content of 63.45%. Gene prediction and annotation were performed using Rapid Prokaryotic Genome Annotation (Prokka) (9). The draft genome harbored 10 rRNA genes, 55 tRNA genes, 2,867 protein-encoding genes with functional prediction, and 3,405 genes coding for hypothetical proteins. For phylogenetic classification of P. putida GM4FR, multilocus-sequence typing was performed according to Gomila et al. (10). The closest relative of the P. putida strain GM4FR is P. putida KT2440, which is a derivate of the soil isolate mt-2 (11) and able to colonize the rhizosphere of several important crop plants (12).

BlastKOALA (13) analysis of the GM4FR genome revealed a gene encoding for a putative nematicidal protein (AidA) (14). Additionally, putative genes encoding insecticidal proteins such as fitD/mcf (K19615) and tccC (K11021) were identified. These insecticidal toxins are known from plant-associated P. fluorescens and P. protegens providing protective effects for their host plants (15,17). An antiSMASH 3.0.5 (18) analysis predicted two bacteriocin gene clusters, an arylpolyene gene cluster, and a nonribosomal polyketide synthetase (NRPS) cluster with no or low (<35%) similarity to known clusters. From the identified NRPS cluster, 9% of genes showed similarities to a pyoverdine gene cluster of P. protegens and P. aeruginosa (19). Pyoverdines are important virulence factors such as fluorescent siderophores and required in pathogenesis (20).

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession MKZO00000000. The version described here is version MKZO01000000.

ACKNOWLEDGMENTS

We thank the Ministry of Science and Culture of Lower Saxony and the “Niedersächsisches Vorab” for funding as part of the Cluster of Excellence “Functional Biodiversity Research.” The funder had no role in the study design, data collection and interpretation, or the decision to submit the work for publication.

We thank Melanie Heinemann for technical support.

Footnotes

Citation Wemheuer F, Hollensteiner J, Poehlein A, Granzow S, Daniel R, Vidal S, Wemheuer B. 2017. Draft genome sequence of Pseudomonas putida strain GM4FR, an endophytic bacterium isolated from Festuca rubra L. Genome Announc 5:e00086-17. https://doi.org/10.1128/genomeA.00086-17.

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Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)