Search tips
Search criteria 


Logo of genannJournal InfoAuthorsPermissionsJournals.ASM.orggenomeA ArticleGenome Announcements
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.


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.


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.


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.


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.


1. Farrar K, Bryant D, Cope-Selby N 2014. Understanding and engineering beneficial plant–microbe interactions: plant growth promotion in energy crops. Plant Biotechnol J 12:1193–1206. doi:.10.1111/pbi.12279 [PMC free article] [PubMed] [Cross Ref]
2. Bhattacharyya PN, Jha DK. 2012. Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol 28:1327–1350. doi:.10.1007/s11274-011-0979-9 [PubMed] [Cross Ref]
3. Siddiqui ZA, Akhtar MS 2008. Effects of fertilizers, AM fungus and plant growth promoting rhizobacterium on the growth of tomato and on the reproduction of root-knot nematode Meloidogyne incognita. J Plant Interact 3:263–271. doi:.10.1080/17429140802272717 [Cross Ref]
4. Akhtar MS, Siddiqui ZA. 2007. Biocontrol of a chickpea root-rot disease complex with Glomus intraradices, Pseudomonas putida and Paenibacillus polymyxa. Australas Plant Pathol 36:175–180. doi:.10.1071/AP07006 [Cross Ref]
5. Wemheuer F, Wemheuer B, Kretzschmar D, Pfeiffer B, Herzog S, Daniel R, Vidal S. 2016. Impact of grassland management regimes on bacterial endophyte diversity differs with grass species. Lett Appl Microbiol 62:323–329. doi:.10.1111/lam.12551 [PubMed] [Cross Ref]
6. Bolger AM, Lohse M, Usadel B 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:.10.1093/bioinformatics/btu170 [PMC free article] [PubMed] [Cross Ref]
7. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:.10.1089/cmb.2012.0021 [PMC free article] [PubMed] [Cross Ref]
8. García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A 2012. Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics 28:2678–2679. doi:.10.1093/bioinformatics/bts503 [PubMed] [Cross Ref]
9. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi:.10.1093/bioinformatics/btu153 [PubMed] [Cross Ref]
10. Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E. 2015. Phylogenomics and systematics in Pseudomonas. Front Microbiol 6:214. doi:.10.3389/fmicb.2015.00214 [PMC free article] [PubMed] [Cross Ref]
11. Franklin FC, Bagdasarian M, Bagdasarian MM, Timmis KN. 1981. Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc Natl Acad Sci U S A 78:7458–7462. doi:.10.1073/pnas.78.12.7458 [PubMed] [Cross Ref]
12. Molina L, Ramos C, Duque E, Ronchel MC, García JM, Wyke L, Ramos JL 2000. Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions. Soil Biol Biochem 32:315–321. doi:.10.1016/S0038-0717(99)00156-X [Cross Ref]
13. Kanehisa M, Sato Y, Morishima K 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. doi:.10.1016/j.jmb.2015.11.006 [PubMed] [Cross Ref]
14. Huber B, Feldmann F, Köthe M, Vandamme P, Wopperer J, Riedel K, Eberl L. 2004. Identification of a novel virulence factor in Burkholderia cenocepacia H111 required for efficient slow killing of Caenorhabditis elegans. Infect Immun 72:7220–7230. doi:.10.1128/IAI.72.12.7220-7230.2004 [PMC free article] [PubMed] [Cross Ref]
15. Péchy-Tarr M, Bruck DJ, Maurhofer M, Fischer E, Vogne C, Henkels MD, Donahue KM, Grunder J, Loper JE, Keel C. 2008. Molecular analysis of a novel gene cluster encoding an insect toxin in plant‐associated strains of Pseudomonas fluorescens. Environ Microbiol 10:2368–2386. doi:.10.1111/j.1462-2920.2008.01662.x [PubMed] [Cross Ref]
16. Rangel LI, Henkels MD, Shaffer BT, Walker FL, Davis EW, Stockwell VO, Bruck D, Taylor BJ, Loper JE 2016. Characterization of toxin complex gene clusters and insect toxicity of bacteria representing four subgroups of Pseudomonas fluorescens. PLoS One 11:e0161120. doi:.10.1371/journal.pone.0161120 [PMC free article] [PubMed] [Cross Ref]
17. Kupferschmied P, Péchy-Tarr M, Imperiali N, Maurhofer M, Keel C 2014. Domain shuffling in a sensor protein contributed to the evolution of insect pathogenicity in plant-beneficial Pseudomonasprotegens. PLoS Pathog 10:e1003964. doi:.10.1371/journal.ppat.1003964 [PMC free article] [PubMed] [Cross Ref]
18. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH. 2015. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43:W237–W243. doi:.10.1093/nar/gkv437 [PMC free article] [PubMed] [Cross Ref]
19. Stintzi A, Cornelis P, Hohnadel D, Meyer JM, Dean C, Poole K, Kourambas S, Krishnapillai V. 1996. Novel pyoverdine biosynthesis gene(s) of Pseudomonas aeruginosa PAO. Microbiology 142:1181–1190. doi:.10.1099/13500872-142-5-1181 [PubMed] [Cross Ref]
20. Jimenez PN, Koch G, Thompson JA, Xavier KB, Cool RH, Quax WJ 2012. The multiple signaling systems regulating virulence in Pseudomonas aeruginosa. Microbiol Mol Biol Rev 76:46–65. doi:.10.1128/MMBR.05007-11 [PMC free article] [PubMed] [Cross Ref]

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