Limits...
Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites

View Article: PubMed Central - PubMed

ABSTRACT

Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the order Pseudomonadales and the family Pseudomonadaceae. We isolated strain P3B5 from the phyllosphere of basil plants (Ocimum basilicum L.). Here we describe the physiology of this microorganism, its full genome sequence, and detailed annotation. The 6.95 Mbp genome contains 6071 predicted protein coding sequences and 96 RNA coding sequences. P. citronellolis has been the subject of many studies including the investigation of long-chain aliphatic compounds and terpene degradation. Plant leaves are covered by long-chain aliphates making up a waxy layer that is associated with the leaf cuticle. In addition, basil leaves are known to contain high amounts of terpenoid substances, hinting to a potential nutrient niche that might be exploited by P. citronellolis. Furthermore, the isolated strain exhibited resistance to several antibiotics. To evaluate the potential of this strain as source of transferable antibiotic resistance genes on raw consumed herbs we therefore investigated if those resistances are encoded on mobile genetic elements. The availability of the genome will be helpful for comparative genomics of the phylogenetically broad pseudomonads, in particular with the sequence of the P. citronellolis type strain PRJDB205 not yet publicly available. The genome is discussed with respect to a phyllosphere related lifestyle, aliphate and terpenoid degradation, and antibiotic resistance.

Electronic supplementary material: The online version of this article (doi:10.1186/s40793-016-0190-6) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Circular map of the Pseudomonas citronellolis P3B5 genome, generated using CGView [70]. Starting from the outmost circle moving inwards, the following tracks are shown: (1) predicted protein coding genes on forward strand colored according to COG categories, (2) CDS (black), tRNA (green) and rRNA (orange) on forward strand, (3) CDS (black), tRNA (green) and rRNA (orange) on reverse strand, (4) predicted protein coding genes on reverse strand colored according to COG categories, (5) Intact prophages (red), incomplete prophages (light red), and genomic islands (blue), (6) GC content (black), (7) positive and negative GC skew (green and purple, respectively) and (8) genome region by mbp
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC5037603&req=5

Fig3: Circular map of the Pseudomonas citronellolis P3B5 genome, generated using CGView [70]. Starting from the outmost circle moving inwards, the following tracks are shown: (1) predicted protein coding genes on forward strand colored according to COG categories, (2) CDS (black), tRNA (green) and rRNA (orange) on forward strand, (3) CDS (black), tRNA (green) and rRNA (orange) on reverse strand, (4) predicted protein coding genes on reverse strand colored according to COG categories, (5) Intact prophages (red), incomplete prophages (light red), and genomic islands (blue), (6) GC content (black), (7) positive and negative GC skew (green and purple, respectively) and (8) genome region by mbp

Mentions: The properties of the complete genome sequence of P. citronellolis P3B5 are summarized in Table 3. The average GC content was 67.11 %. Of the 6169 predicted genes, 6071 (98.41 %) were protein CDS of which 4762 genes had a function prediction. Genes without functional prediction by Prokka were annotated as “hypothetical protein”. Two pseudo genes (PcP3B5_29180 and PcP3B5_42810) were predicted by the NCBI annotation pipeline [39] and then incorporated into the Prokka annotation. Of the predicted protein coding genes, 5523 were assigned to COGs of 22 classes (Table 4, Fig. 3). Using the Pfam database, 5242 CDS were assigned to a protein family. Putative transmembrane domains were predicted for 1263 CDS. A signal peptide was predicted for 702 CDS. A total of 96 RNA genes were predicted including 15 rRNA (five complete rRNA operons each comprising a 23S, 16S and 5S rRNA gene), 76 tRNA, 1 tmRNA, and 4 ncRNA genes. Binding sites for cobalamin and thiamine pyrophosphate were predicted by the NCBI annotation pipeline. One CRISPR repeat was predicted by Prokka and further confirmed by CRISPRFinder [40] and PILER-CR [41]. However, no evidence for a Cas protein-coding gene was found in the genome. An analysis of putative prophages using PHAST [42] resulted in six hits in the genome, three of which were designated as intact prophages (PcP3B5_02970–PcP3B5_03410; PcP3B5_06890–PcP3B5_07120; PcP3B5_45940–PcP3B5_46520) and the other three as incomplete prophages (PcP3B5_40450–PcP3B5_40640; PcP3B5_40870–PcP3B5_41140; PcP3B5_46670–PcP3B5_46960). Genomic islands and ABR genes within genomic islands were predicted using IslandViewer 3 [43]. As references for genomic island analysis, the closely related genomes of P. knackmussii B13, P. denitrificansATCC 13867, P. aeruginosa PAO1, and P. stutzeriDSM 4166 were chosen.Table 3


Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites
Circular map of the Pseudomonas citronellolis P3B5 genome, generated using CGView [70]. Starting from the outmost circle moving inwards, the following tracks are shown: (1) predicted protein coding genes on forward strand colored according to COG categories, (2) CDS (black), tRNA (green) and rRNA (orange) on forward strand, (3) CDS (black), tRNA (green) and rRNA (orange) on reverse strand, (4) predicted protein coding genes on reverse strand colored according to COG categories, (5) Intact prophages (red), incomplete prophages (light red), and genomic islands (blue), (6) GC content (black), (7) positive and negative GC skew (green and purple, respectively) and (8) genome region by mbp
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5037603&req=5

Fig3: Circular map of the Pseudomonas citronellolis P3B5 genome, generated using CGView [70]. Starting from the outmost circle moving inwards, the following tracks are shown: (1) predicted protein coding genes on forward strand colored according to COG categories, (2) CDS (black), tRNA (green) and rRNA (orange) on forward strand, (3) CDS (black), tRNA (green) and rRNA (orange) on reverse strand, (4) predicted protein coding genes on reverse strand colored according to COG categories, (5) Intact prophages (red), incomplete prophages (light red), and genomic islands (blue), (6) GC content (black), (7) positive and negative GC skew (green and purple, respectively) and (8) genome region by mbp
Mentions: The properties of the complete genome sequence of P. citronellolis P3B5 are summarized in Table 3. The average GC content was 67.11 %. Of the 6169 predicted genes, 6071 (98.41 %) were protein CDS of which 4762 genes had a function prediction. Genes without functional prediction by Prokka were annotated as “hypothetical protein”. Two pseudo genes (PcP3B5_29180 and PcP3B5_42810) were predicted by the NCBI annotation pipeline [39] and then incorporated into the Prokka annotation. Of the predicted protein coding genes, 5523 were assigned to COGs of 22 classes (Table 4, Fig. 3). Using the Pfam database, 5242 CDS were assigned to a protein family. Putative transmembrane domains were predicted for 1263 CDS. A signal peptide was predicted for 702 CDS. A total of 96 RNA genes were predicted including 15 rRNA (five complete rRNA operons each comprising a 23S, 16S and 5S rRNA gene), 76 tRNA, 1 tmRNA, and 4 ncRNA genes. Binding sites for cobalamin and thiamine pyrophosphate were predicted by the NCBI annotation pipeline. One CRISPR repeat was predicted by Prokka and further confirmed by CRISPRFinder [40] and PILER-CR [41]. However, no evidence for a Cas protein-coding gene was found in the genome. An analysis of putative prophages using PHAST [42] resulted in six hits in the genome, three of which were designated as intact prophages (PcP3B5_02970–PcP3B5_03410; PcP3B5_06890–PcP3B5_07120; PcP3B5_45940–PcP3B5_46520) and the other three as incomplete prophages (PcP3B5_40450–PcP3B5_40640; PcP3B5_40870–PcP3B5_41140; PcP3B5_46670–PcP3B5_46960). Genomic islands and ABR genes within genomic islands were predicted using IslandViewer 3 [43]. As references for genomic island analysis, the closely related genomes of P. knackmussii B13, P. denitrificansATCC 13867, P. aeruginosa PAO1, and P. stutzeriDSM 4166 were chosen.Table 3

View Article: PubMed Central - PubMed

ABSTRACT

Pseudomonas citronellolis is a Gram negative, motile gammaproteobacterium belonging to the order Pseudomonadales and the family Pseudomonadaceae. We isolated strain P3B5 from the phyllosphere of basil plants (Ocimum basilicum L.). Here we describe the physiology of this microorganism, its full genome sequence, and detailed annotation. The 6.95 Mbp genome contains 6071 predicted protein coding sequences and 96 RNA coding sequences. P. citronellolis has been the subject of many studies including the investigation of long-chain aliphatic compounds and terpene degradation. Plant leaves are covered by long-chain aliphates making up a waxy layer that is associated with the leaf cuticle. In addition, basil leaves are known to contain high amounts of terpenoid substances, hinting to a potential nutrient niche that might be exploited by P. citronellolis. Furthermore, the isolated strain exhibited resistance to several antibiotics. To evaluate the potential of this strain as source of transferable antibiotic resistance genes on raw consumed herbs we therefore investigated if those resistances are encoded on mobile genetic elements. The availability of the genome will be helpful for comparative genomics of the phylogenetically broad pseudomonads, in particular with the sequence of the P. citronellolis type strain PRJDB205 not yet publicly available. The genome is discussed with respect to a phyllosphere related lifestyle, aliphate and terpenoid degradation, and antibiotic resistance.

Electronic supplementary material: The online version of this article (doi:10.1186/s40793-016-0190-6) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus