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. 2016 Aug 4;9:154–159. doi: 10.1016/j.gdata.2016.08.004

Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential

Neil T Miller a, Danny Fuller a, MB Couger a, Mark Bagazinski a, Philip Boyne a, Robert C Devor a, Radwa A Hanafy a, Connie Budd a, Donald P French b, Wouter D Hoff a, Noha Youssef a,⁎
PMCID: PMC4993851  PMID: 27583206

Abstract

Pseudomonas moraviensis is a predominant member of soil environments. We here report on the genomic analysis of Pseudomonas moraviensis strain Devor that was isolated from a gate at Oklahoma State University, Stillwater, OK, USA. The partial genome of Pseudomonas moraviensis strain Devor consists of 6016489 bp of DNA with 5290 protein-coding genes and 66 RNA genes. This is the first detailed analysis of a P. moraviensis genome. Genomic analysis revealed metabolic versatility with genes involved in the metabolism and transport of fructose, xylose, mannose and all amino acids with the exception of tryptophan and valine, implying that the organism is a versatile heterotroph. The genome of P. moraviensis strain Devor was rich in transporters and, based on COG analysis, did not cluster closely with P. moraviensis R28-S genome, the only previous report of a P. moraviensis genome with a native mercury resistance plasmid.

Keywords: Pseudomonas moraviensis, Draft genome sequence, Detailed analysis, Student Initiated Microbial Discovery (SIMD) project, Metabolic versatility

1. Introduction

The strain Devor was isolated from an outdoor gate located on Oklahoma State University (OSU) campus in Stillwater, OK. The isolation process was part of the Student Initiated Microbial Discovery (SIMD) project at OSU (introduced in [1]). The organism was isolated by an undergraduate student (RCD) during an introductory microbiology lab course, and analyzed by a team of undergraduate (MB and PB) and graduate students (NTM and DF). The genus Pseudomonas is known to be phylogenetically and physiologically diverse. Members are ubiquitously found in soil and water systems, with the potential to utilize a broad range of organic compounds [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12]. Resistance for heavy metal has also been shown for some strains [13]. Genomic analysis of members belonging to the genus Pseudomonas can contribute to our understanding of the molecular mechanisms of the biodegradation of organic compounds, including environmental pollutants, and could potentially contribute to bioremediation efforts in multiple environments. Here we report on the draft genomic sequence, and the first detailed analysis of a Pseudomonas moraviensis strain.

2. Materials and methods

2.1. Genome project history

Pseudomonas moraviensis strain Devor was isolated with the aim of sequencing its genome as part of an undergraduate project at OSU. The project is funded by the Howard Hughes Medical Institute and aims at improving undergraduate student involvement in authentic research. Isolation of the strain, and analysis of the sequenced genome were performed by undergraduate students in an introductory microbiology course, and an upper division microbial genomics class, respectively. The quality draft assembly and annotation were completed in 2015–2016. Table 1 shows the genome project information.

Table 1.

Project information.

MIGS ID Property Term
MIGS 31 Finishing quality Draft
MIGS-28 Libraries used 2 × 300 paired end chemistry
MIGS 29 Sequencing platforms Illumina
MIGS 31.2 Fold coverage 300 ×
MIGS 30 Assemblers Velvet
MIGS 32 Gene calling method Prodigal
Genbank ID MAYQ00000000
GenBank date of release July 2016
GOLD ID Gp0126756
BIOPROJECT PRJNA327387
MIGS 13 Project relevance Environmental
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2.2. Growth conditions and genomic DNA preparation

Pseudomonas moraviensis strain Devor was grown overnight at 30 °C on tryptic soy agar plates, and genomic DNA was isolated using the MPBio PowerSoil® DNA extraction kit according to manufacturer's instructions. Negative stain TEM micrographs were obtained using the services of the Oklahoma State University Microscopy Lab. Briefly, the sample was placed on a carbon film TEM grid and allowed to incubate for 2 min, after which the excess liquid was wicked off. Phosphotungstic acid (PTA; 2% w/v) was then added to the grid followed by a 45-s incubation. Excess PTA was wicked off and the grid was allowed to dry before it was visualized using JOEL JEM-2100 transmission electron microscope.

2.3. Genome sequencing and assembly

The genome of Pseudomonas moraviensis strain Devor was sequenced at the University of Georgia Genomics Facility using the Illumina MiSeq platform 2 × 300 paired end chemistry. Average library insert size was 700 bp. The short read de Brujin graph assembly program Velvet [14] was used to assemble quality filtered sequence data using a kmer value of 101 bp and a minimum contig coverage value of 7 ×. The genome project is deposited in GOLD (Genomes On-Line Database) and this Whole Genome Shotgun (WGS) project has been deposited in GenBank under the accession MAYQ00000000. The version described in this paper is version MAYQ01000000.

2.4. Genome annotation

Gene models were created using the prokaryotic gene calling software package Prodigal [15]. A total of 5473 gene models were predicted with an average gene size of 1002 bp. Predicted protein sequences were annotated using a combination of NCBI Blast C ++ homology search, and HMMER 3.0 [16] hmmscan against the PFAM [17] 26.0 database. Additional functional annotations were carried out through the Integrated Microbial Genomes Expert Review (IMG-ER) platform.

2.5. Comparative genomics

We compared the genome of Pseudomonas moraviensis strain Devor to 13 closely related genomes (IMG genome IDs: 2619619019, 2654587541, 2603880217, 2561511156, 2639762619, 2636416187, 2639762638, 2639762633, 2597489942, 2639762506, 2517572232, 2639762618, 2556921015) using the “Genome clustering” function on the IMG-ER analysis platform based on the COG profile. We also used principal component analysis to compare the genomes based on several genomic features including the genome size, the number of genes, the number of transporters identified, the GC content, the number of non-coding bases, the number of genes belonging to COG categories, as well as the number of genes belonging to each COG category. The PCA analysis was conducted using the “princomp” function in the labdsv library of R [18]. The results were visualized using a biplot, where genomes were represented by stars and genomic features or COG categories used for comparison were represented by arrows.

3. Results and discussion

3.1. Classification and features

Cells of P. moraviensis strain Devor are Gram negative, motile, aerobic rods that are arranged as singles (Fig. 1). Colonies on TSA agar were orange.

Fig. 1.

Fig. 1

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Negative stain TEM micrograph of Pseudomonas moraviensis strain Devor.

Within the genus Pseudomonas, 163 species are described with validly published names. Strain Devor shares 77.8%–99.8% 16S rRNA gene identities with other species in the Pseudomonas genus as follows: P. abietaniphilia (97.7%) type strain ATCC 700689T, P. aeruginosa (94.7%) type strain ATCC 10145T, P. aestusnigri (95.5%) VGXO14T, P. agarici (98%) type strain ATCC 25941T, P. alcaligenes (95.8%) type strain ATCC 14909T, P. alcalophilia (96.5%) type strain AL15-21T, P. amygdali (96.6%) type strain ATCC 33614T, P. anguilliseptica (94.7%) type strain ATCC 33660T, P. antarctica (97.3%) type strain DSM 15318T, P. argentinensis (97.6%) type strain CH01T, P. arsenicoxydans (97.7%) type strain VC-1T, P. asplenii (97.7%) type strain ATCC 23835T, P. asturiensis (97.1%) type strain LPPA 221T, P. asuensis (95.8%) type strain CP 155-2T, P. azotifigens (93.9%) type strain ATCC BAA-1049T, P. azotoformans (98.1%) type strain CCUG 12536T, P. baetica (99.2%) type strain a390T, P. balearica (95%) type strain DSM 6083T, P. bauzanensis (95%) type strain DSM 22558T, P. benzenivorans (96.9%) type strain DSM 8628T, P. borbori (96.1%) type strain DSM 17834, P. brassicacearum (97.1%) type strain DSM 13227T, P. brenneri (97.8%) type strain DSM 15294, P. caeni (93.8%) type strain HY-14T, P. cannabina (97.8%) type strain CFBP 2341T, P. carboxydohydrogena (77.8%) type strain ATCC 29978T, P. caricapapayae (97.7%) type strain ATCC 33615T, P. cedrina (98.2%) type strain DSM 17516T, P. chengduensis (96.6%) type strain DSM 26382, P. chloritidismutans (96.6%) type strain ATCC BAA-443T, P. chlororaphis (97.9%) type strain ATCC 9446T, P. cichorii (96.8%) type strain ATCC 10857T, P. citronellosis (94.4%) type strain ATCC 13674T, P. coleopterorum (97.8%) type strain LMG 28558T, P. composti (96.7%) type strain C2T, P. congealans (97.7%) type strain DSM 14939T, P. corrugata (97.7%) type strain ATCC 29736T, P. constantinii (97.4%) type strain PS 3aT, P. cremoricolorata (97.1%) type strain DSM 17059T, P. cuatrocienegasensis (96.5%) type strain LMG 24676T, P. deceptionensis (97.2%) type strain M1T, P. delhiensis (94.3%) type strain RLD-1T, P. duriflava (94.7%) type strain HR2T, P. elongata (89.3%) type strain ATCC 10144T, P. endophytica (97.3%) type strain BSTT44T, P. entomophila (97.7%) type strain L48T, P. extremaustralis (97.3%) type strain DSM 17835T, P. extremorientalis (97.5%) type strain KMM 3447T, P. ficuserectae (97.6%) type strain ATCC 35104T, P. flavescens (96.5%) type strain ATCC 51555T, P. fluorescens (96.8%) type strain ATCC 13525T, P. formosensis (94.1%) type strain CC-CY503T, P. fragi (97.2%) type strain ATCC 4973T, P. frederiksbergensis (97.3%) type strain ATCC BAA-257T, P. fulva (98.6%) type strain ATCC 31418T, P. fuscovaginae (97.5%) type strain DSM 7231T, P. gessardii (98.2%) type strain CIP 105469T, P. graminis (98%) type strain DSM 11363T, P. granadensis (99.4%) type strain DSM 28040T, P. grimontii (97.4%) type strain ATCC BAA-140T, P. guangdongensis (95.1%) type strain SgZ-6T, P. guariconensis (97.2%) type strain PCAVU11T, P. guineae (95.5%) type strain M8T, P. helmanticensis (98.8%) type strain OHA11T, P. hussainii (93.8%) type strain CC-AMH-11T, P. indica (94.1%) type strain DSM 14015T, P. japonica (96.9%) type strain WLT, P. jessennii (99.3%) type strain ATCC 700870T, P. jinjuensis (95%) type strain Pss 26T, P. kilonensis (97.7%) type strain DSM 13647T, P. knackmussii (94.5%) type strain DSM 6978T, P. koreensis (99.8%) type strain Ps 9-14T, P. kunmingensis (96.3%) type strain DSM 25974T, P. kuykendallii (97.7%) type strain H2T, P. libanensis (98.2%) type strain CCUG 43190T, P. lini (97.7%) type strain DLE411JT, P. linyingensis (95%) type strain LYBRD3-7T, P. litoralis (94.8%) type strain 2SM5T, P. lundensis (97.5%) type strain ATCC 49968T, P. lurida (97.4%) type strain DSM 15835T, P. lutea (98.2%) type strain OK2T, P. luteola (95.6%) type strain ATCC 43273T, P. mandelii (97.8%) type strain ATCC 700871T, P. marginalis (97.2%) type strain ATCC 10844T, P. marincola (96%) type strain JCM 14761T, P. matsuisoli (93.8%) type strain CC-MHH0089, P. mediterranea (97%) type strain CFBP 5447T, P. mendocina (96.2%) type strain ATCC 25411T, P. meridiana (97.1%) type strain DSM 15319T, P. migulae (98.1%) type strain CCUG 43165T, P. mohnii (99.2%) type strain DSM 18327T, P. monteilii (97.8%) type strain ATCC 700476T, P. moorei (99.3%) type strain DSM 12647T, P. moraviensis (99.4%) type strain DSM 16007T, P. mosselii (97.6%) type strain ATCC BAA-99T, P. mucidolens (98.2%) type strain ATCC 4685T, P. multiresinivorans (94.8%) type strain ATCC 700690T, P. nitritireducens (94.8%) type strain WZBFD3-5A2T, P. nitroreducens (94.9%) type strain ATCC 33634T, P. oleovorans (94.4%) type strain ATCC 8062T, P. orientalis (97.1%) type strain DSM 17489T, P. oryzihabitans (97.3%) type strain ATCC 43272T, P. otitidis (95%) type strain ATCC BAA-1130T, P. pachastrellae (95.2%) type strain CCUG 46540T, P. palleroniana (97.4%) type strain CFBP 4389T, P. panacis (97.7%) type strain CG20106T, P. panipatensis (94.5%) type strain Esp-1, P. parafulva (98.6%) type strain DSM 17004T, P. pelagia (94.3%) CL-AP6T, P. peli (95.5%) type strain DSM 17833T, P. pertucinogena (93.3%) type strain ATCC 190T, P. pictorum (84.4%) type strain ATCC 23328T, P. plecoglossicida (97.7%) type strain ATCC 700383T, P. poae (97.2%) type strain DSM 14936T, P. pohangensis (95.7%) type strain DSM 17875T, P. prosekii (97.8%) type strain AN/28/1T, P. protegens (97%) type strain DSM 19095T, P. proteolytica (97.4%) type strain DSM 15321T, P. pseudoalcaligenes (96.9%) type strain ATCC 17440T, P. psychrophilia (97.1%) type strain E-3T, P. psychrotolerans (94.7%) type strain DSM 15758T, P. punonensis (97.7%) type strain LMT03T, P. putida (97.2%) type strain ATCC 12633T, P. reinekei (99.5%) type strain DSM 18361T, P. resinovorans (93.6%) type strain ATCC 14235T, P. rhizosphaerae (97.8%) type strain IH5T, P. rhodesiae (97.4%) type strain DSM 14020T, P. sabulinigri (94.9%) type strain J64T, P. sagittaria (94.8%) type strain CC-OPY-1T, P. salegens (94%) type strain GBPy5T, P. salina (94.3%) type strain XCD-X85T, P. salomonii (96.9%) type strain CFBP 2022T, P. saponiphilia (96.5%) type strain DSM 9751T, P. savastanoi (97.6%) type strain ATCC 13522T, P. segetis (96.3%) type strain FR1439T, P. seleniipraecipitans (97%) type strain CA5T, P. simiae (97.5%) type strain OLiT, P. soli (97.8%) type strain DSM 28043T, P. straminea (97%) type strain ATCC 33636T, P. stutzeri (96.4%) type strain ATCC 17588T, P. synxantha (98.1%) type strain ATCC 9890T, P. syringae (97.6%) type strain ATCC 19310T, P. taenensis (96.9%) type strain MS-3T, P. taetrolans (97.1%) type strain ATCC 4683T, P. taiwanensis (97.8%) type strain DSM 21245T, P. testosteroni (80.8%) type strain ATCC 11996T, P. thivervalensis (97.6%) type strain DSM 13194T, P. tolaasii (97.4%) type strain ATCC 33618T, P. toyotomiensis (96.5%) type strain HT-3T, P. tremae (97.8%) type strain CFBP 3229T, P. trivialis (97.1%) type strain DSM 14937T, P. tuomuerensis (95.2%) type strain 78-123, P. usmongensis (98.9%) type strain Ps 3-10T, P. vancouverensis (99.3%) type strain ATCC 700688T, P. veronii (97.6%) type strain ATCC 700272/700474T, P. viridiflava (96.2%) type strain ATCC 13223T, P. vranovensis (96.7%) type strain DSM 16006T, P. xanthomarina (96.5%) type strain CCUG 46543T, P. xiamenensis (93.5%) type strain C10-2T, P. xinjiangensis (94.5%) type strain S3-3T, P. yamanorum (98%) type strain DSM 26522T, P. zeshuii (95.4%) type strain BY-1T, P. zhaodongensis (96.6%) type strain DSM 27559T.

Phylogenetic analysis based on the 16S rRNA gene identified strain WW1 to be the closest taxonomic relative of Pseudomonas moraviensis strain Devor (Table 2, and Fig. 2).

Table 2.

Classification and general features of Pseudomonas moraviensis strain Devor [28].

MIGS ID Property Term Evidence codea
Classification Domain Bacteria TAS [9]
Phylum Proteobacteria TAS [9]
Class Gammaproteobacteria TAS [9]
Order Pseudomonadales TAS [9]
Family Pseudomonadaceae TAS [9]
Genus Pseudomonas TAS [9]
Species moraviensis TAS [9]
(Type) strain: Devor
Gram stain Negative TAS [9]
Cell shape Rod TAS [9]
Motility Motile TAS [9]
Sporulation Non-spore forming TAS [9]
Temperature range 4–35 °C TAS [9]
Optimum temperature 28–35 °C TAS [9]
pH range; optimum Unknown
Carbon source glycerol, l-arabinose, d-glucose, d-fructose, d-trehalose, d-lyxose, gluconate and 2-ketogluconate TAS [9]
MIGS-6 Habitat Soil/Gate IDA
MIGS-6.3 Salinity Unknown
MIGS-22 Oxygen requirement Aerobic IDA
MIGS-15 Biotic relationship Free living IDA
MIGS-14 Pathogenicity Non-pathogenic NAS
MIGS-4 Geographic location Stillwater, OK, USA IDA
MIGS-5 Sample collection March 2016 IDA
MIGS-4.1 Latitude 36.1157 IDA
MIGS-4.2 Longitude − 97.0586 IDA
MIGS-4.4 Altitude 1 M
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a

Evidence codes - IDA: Inferred from Direct Assay; TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [29].

Fig. 2.

Fig. 2

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A maximum likelihood phylogenetic tree constructed using multiple sequence alignments of 16S rRNA genes. “Pseudomonas moraviensis strain Devor” sequence is shown with in bold. Reference sequences are also shown and Genbank accession numbers are given in parentheses. The tree was obtained under “K2 + G” model with a variable site γ shape parameter of 0.05. “Pseudomonas aeruginosa 57 16S ribosomal RNA gene partial sequence” was used as the outgroup. Bootstrap values, in percent, are based on 100 replicates and are shown for branches with > 50% bootstrap support. Multiple sequence alignment, model selection, and maximum likelihood analysis were carried out in Mega [30].

Comparison to other Pseudomonas moraviensis sequenced genomes revealed that strain Devor shares 99% 16S rRNA sequence similarity to strain R28-S (Genbank accession number AYMZ00000000) [5].

3.2. Genome properties

The genome assembly process produced a contig N50 of 3,923,117 bp and a total genome size of 6,016,489 bp. The GC content was 60.0%. One hundred and eighty three RNA genes were identified including 3 ribosomal RNA and 63 tRNA genes. The ribosomal RNA operon showed an atypical organization, where 2 copies of 5S rRNA were present along with one copy of the 23S rRNA gene. Two copies each of the tRNAAla and the tRNAIle were present in the operon. The operon lacked a 16S rRNA gene. Of the 5473 genes detected, 5290 were protein-coding, of which 79.8% had a function prediction, 72.7% represented a COG functional category, and 11.3% were predicted to have a signal peptide. Using Psort [19], proteins were classified as 44.12% cytoplasmic, 1.06% extracellular, and 25.25% associated with the membrane. Based on the presence of 139 single copy genes [20], the genome is predicted to be 83.45% complete. Genome statistics are shown in Table 3. The distribution of genes into COG functional categories is shown in Table 4.

Table 3.

Genome statistics.

Attribute Value % of Total
Genome size (bp) 6,016,489 83.4
DNA coding (bp) 5,314,299 88.3
DNA G + C (bp) 3,609,956 60.0
DNA scaffolds 7 100
Total genes 5473 100
Protein coding genes 5290 96.6
RNA genes 183 3.3
Pseudo genes 0 0
Genes in internal clusters 1440 26.3
Genes with function prediction 4220 77.1
Genes assigned to COGs 3846 70.3
Genes with Pfam domains 4512 82.4
Genes with signal peptides 598 10.9
Genes with transmembrane helices 1208 22.1
CRISPR repeats 0 0
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Table 4.

Number of genes associated with general COG functional categories.

Code Value % age Description
J 236 5.40 Translation, ribosomal structure and biogenesis
A 2 0.05 RNA processing and modification
K 393 9.00 Transcription
L 124 2.84 Replication, recombination and repair
B 2 0.05 Chromatin structure and dynamics
D 40 0.92 Cell cycle control, cell division, chromosome partitioning
V 96 2.20 Defense mechanisms
T 286 6.55 Signal transduction mechanisms
M 270 6.18 Cell wall/membrane biogenesis
N 123 2.82 Cell motility
U 89 2.04 Intracellular trafficking and secretion
O 157 3.60 Posttranslational modification, protein turnover, chaperones
C 276 6.32 Energy production and conversion
G 230 5.27 Carbohydrate transport and metabolism
E 447 10.24 Amino acid transport and metabolism
F 96 2.20 Nucleotide transport and metabolism
H 206 4.72 Coenzyme transport and metabolism
I 213 4.88 Lipid transport and metabolism
P 253 5.79 Inorganic ion transport and metabolism
Q 121 2.77 Secondary metabolites biosynthesis, transport and catabolism
R 387 8.86 General function prediction only
S 263 6.02 Function unknown
– 1640 29.97 Not in COGs
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The total is based on the total number of protein coding genes in the genome.

3.3. Insights from the genome sequence

Genome analysis of Pseudomonas moraviensis strain Devor identified a Gram negative microorganism with typical cell wall structure, a peptidoglycan layer lacking pentaglycine bridges with diaminopimelic acid as the second amino acid in the peptide linkage. Genes encoding enzymes for the biosynthesis of the glycerophospholipids phosphatidylcholine, phosphatidyl-glycerophosphate, phosphatidyl-serine, and phosphatidyl ethanolamine were identified in the genome. The analysis also revealed the presence of genes encoding a complete flagellar assembly in line with the evidence for the presence of flagella in electron micrographs of the organism (Fig. 1). Extracellular structures including type IV pili and the Flp system, and some structural genes for the production of exopolysaccharides including a partial Yjb operon [21], as well as evidence for the biosynthesis of multiple nucleotide sugars were also found in the genome.

Further analysis suggested the capability to utilize xylose, fructose, mannose, glucose, all amino acids except valine and tryptophan, and fatty acids as carbon and energy sources. Almost complete to complete catabolic KEGG pathways were identified in the genome for each of the above carbon sources. A complete TCA cycle and electron transport chain with F-type ATPase subunits confirmed the aerobic nature of the microorganism. Facultative fermentation capability was also identified in the genome where genes for lactate and acetate fermentation were present. Comparison of the protein-coding genes against the transporter database [22] identified ABC and secondary transporters for several amino acids.

When compared against the virulence factor database [23], the genome of Pseudomonas moraviensis strain showed 1733 virulence factor hits (32.8% of the protein-coding genes). These included secretion systems (type I, type II, and type IV secretion systems) among others.

The Devor genome also encoded several proteins that suggest the potential for using this strain in bioremediation efforts. These included genes encoding for 4-hydroxybenzoate degradation to succinate, as well as genes encoding for the detoxification of the plant-secreted toxin nitronate and the industry-applied chelating agent nitriloacetate [24], [25], [26], [27]. Evidence for the capability of salvaging S from organo-S-compounds (e.g. taurine and alkanesulfonates) in cases of limiting inorganic S were also identified in the genome.

3.4. Insights from comparative genomics

We used the COG profile to compare the genome of Pseudomonas moraviensis strain Devor to 13 closely related genomes. The genome clustered with Pseudomonas moraviensis strain BS3668 (Fig. 3A), which was in agreement with the phylogenetic position of the isolate as Pseudomonas moraviensis (Fig. 2). We used genomic features including the genome size, the number of genes, the number of transporters identified, the GC content, the number of non-coding bases, the number of genes belonging to COG categories, as well as the number of genes belonging to each COG category to cluster Pseudomonas moraviensis strain Devor's genome in comparison to the 13 other closely related genomes. Results are shown in Fig. 3B. The genome Pseudomonas moraviensis strain Devor clustered close to the two P. moraviensis genomes, and the P. koorensis genome as well. This is consistent with its phylogeny as a P. moraviensis and as a member of the P. koorensis clade [9]. These genomes appear to be enriched in the number of transporters identified in the genome.

Fig. 3.

Fig. 3

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Comparative genomics of Pseudomonas moraviensis strain Devor and 13 closely related genomes. (A) COG profile clustering of the genomes compared in this study. (B) Principal component analysis biplot of the genomic features and COG category distribution in the genomes compared. Genomes are represented by stars. Arrows represent genomic features or COG categories used for comparison. The arrow directions follow the maximal abundance, and their lengths are proportional to the maximal rate of change between genomes. The first two components explained 75% of variation. Color coding: P. jessenei, brown; P. baetica, orange; P. umsongenesis, purple; P. morviensis, red; P. reineke, grey; P. fluorescens, green; P. koorensis, black; P. moorei, blue.

4. Conclusions

This study presents the genome sequence and annotation of Pseudomonas moraviensis strain Devor. The genome revealed metabolic versatility with suggested capability to degrade fatty acids, most amino acids, fructose, mannose, and xylose. Comparison to the virulence factor database identified 1733 genes in the genome with potential virulence-associated function including type I, type II, and type IV secretion systems. The genome also suggests the potential use in bioremediation efforts with evidence for degradation of 4-hydroxybenzoate, nitronate, and nitriloacetate. Comparative genomics using general genomic features and the COG function profile are in line with the phylogenetic position predicted based on the 16S rRNA gene sequence placing strain Devor with other P. moraviensis representatives.

Competing interests

All authors declare no competing interests.

Funding

This is Draft Genome #7 in the SIMD project supported in part by a grant from the Howard Hughes Medical Institute (1554854) through the Science Education Program. WDH acknowledges support by NSF grants MCB-1051590, MRI-1338097, and CHE-1412500.

Authors' contributions

NTM, DF, MB, PB, MBC, and NY contributed to the analysis. NTM, DF, WDH, DPF, and NY wrote the manuscript. RCD, CB, AR, and RAH performed the lab experiments.

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