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Draft Genome Sequence of Pseudomonas Moraviensis Strain Devor Implicates Metabolic Versatility and Bioremediation Potential

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Draft Genome Sequence of Pseudomonas Moraviensis Strain Devor Implicates Metabolic Versatility and Bioremediation Potential Genomics Data 9 (2016) 154–159 Contents lists available at ScienceDirect Genomics Data journal homepage: www.elsevier.com/locate/gdata Draft genome sequence of Pseudomonas moraviensis strain Devor implicates metabolic versatility and bioremediation potential Neil T. Miller a,DannyFullera,M.B.Cougera, Mark Bagazinski a,PhilipBoynea, Robert C. Devor a, Radwa A. Hanafy a, Connie Budd a, Donald P. French b, Wouter D. Hoff a, Noha Youssef a,⁎ a Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States b Department of Integrative Biology, Oklahoma State University, Stillwater, OK, United States article info abstract Article history: Pseudomonas moraviensis is a predominant member of soil environments. We here report on the genomic Received 19 July 2016 analysis of Pseudomonas moraviensis strain Devor that was isolated from a gate at Oklahoma State University, Accepted 2 August 2016 Stillwater, OK, USA. The partial genome of Pseudomonas moraviensis strain Devor consists of 6016489 bp of Available online 4 August 2016 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 Keywords: of fructose, xylose, mannose and all amino acids with the exception of tryptophan and valine, implying that Pseudomonas moraviensis Draft genome sequence the organism is a versatile heterotroph. The genome of P. moraviensis strain Devor was rich in transporters Detailed analysis and, based on COG analysis, did not cluster closely with P. moraviensis R28-S genome, the only previous report Student Initiated Microbial Discovery (SIMD) of a P. moraviensis genome with a native mercury resistance plasmid. project © 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license Metabolic versatility (http://creativecommons.org/licenses/by-nc-nd/4.0/). 1. Introduction 2. Materials and methods The strain Devor was isolated from an outdoor gate located on 2.1. Genome project history Oklahoma State University (OSU) campus in Stillwater, OK. The isola- tion process was part of the Student Initiated Microbial Discovery Pseudomonas moraviensis strain Devor was isolated with the aim of (SIMD) project at OSU (introduced in [1]). The organism was isolated sequencing its genome as part of an undergraduate project at OSU. by an undergraduate student (RCD) during an introductory microbiolo- The project is funded by the Howard Hughes Medical Institute and gy lab course, and analyzed by a team of undergraduate (MB and PB) aims at improving undergraduate student involvement in authentic and graduate students (NTM and DF). The genus Pseudomonas is research. Isolation of the strain, and analysis of the sequenced genome known to be phylogenetically and physiologically diverse. Members were performed by undergraduate students in an introductory microbi- are ubiquitously found in soil and water systems, with the potential to ology course, and an upper division microbial genomics class, respec- utilize a broad range of organic compounds [2–12]. Resistance for tively. The quality draft assembly and annotation were completed in heavy metal has also been shown for some strains [13]. Genomic analy- 2015–2016. Table 1 shows the genome project information. sis of members belonging to the genus Pseudomonas can contribute to our understanding of the molecular mechanisms of the biodegradation 2.2. Growth conditions and genomic DNA preparation of organic compounds, including environmental pollutants, and could potentially contribute to bioremediation efforts in multiple environ- Pseudomonas moraviensis strain Devor was grown overnight at 30 °C fi ments. Here we report on the draft genomic sequence, and the rst on tryptic soy agar plates, and genomic DNA was isolated using the detailed analysis of a Pseudomonas moraviensis strain. MPBio PowerSoil® DNA extraction kit according to manufacturer's in- structions. 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 ⁎ Corresponding author at: 1110 S Innovation way, Stillwater, OK 74074, United States. acid (PTA; 2% w/v) was then added to the grid followed by a 45-s E-mail address: [email protected] (N. Youssef). incubation. Excess PTA was wicked off and the grid was allowed to http://dx.doi.org/10.1016/j.gdata.2016.08.004 2213-5960/© 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). N.T. Miller et al. / Genomics Data 9 (2016) 154–159 155 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 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 Fig. 1. Negative stain TEM micrograph of Pseudomonas moraviensis strain Devor. 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 Within the genus Pseudomonas, 163 species are described with project is deposited in GOLD (Genomes On-Line Database) and this validly published names. Strain Devor shares 77.8%–99.8% 16S rRNA Whole Genome Shotgun (WGS) project has been deposited in GenBank gene identities with other species in the Pseudomonas genus as follows: under the accession MAYQ00000000. The version described in this paper P. abietaniphilia (97.7%) type strain ATCC 700689T, P. aeruginosa (94.7%) is version MAYQ01000000. type strain ATCC 10145T, P. aestusnigri (95.5%) VGXO14T, P. agarici (98%) type strain ATCC 25941T, P. alcaligenes (95.8%) type strain ATCC 14909T, 2.4. Genome annotation P. alcalophilia (96.5%) type strain AL15-21T, P. amygdali (96.6%) type strain ATCC 33614T, P. anguilliseptica (94.7%) type strain ATCC 33660T, Gene models were created using the prokaryotic gene calling soft- P. antarctica (97.3%) type strain DSM 15318T, P. argentinensis (97.6%) ware package Prodigal [15]. A total of 5473 gene models were predicted type strain CH01T, P. arsenicoxydans (97.7%) type strain VC-1T, P. asplenii with an average gene size of 1002 bp. Predicted protein sequences were (97.7%) type strain ATCC 23835T, P. asturiensis (97.1%) type strain LPPA annotated using a combination of NCBI Blast C++ homology search, 221T, P. asuensis (95.8%) type strain CP 155-2T, P. azotifigens (93.9%) type and HMMER 3.0 [16] hmmscan against the PFAM [17] 26.0 database. strain ATCC BAA-1049T, P. azotoformans (98.1%) type strain CCUG Additional functional annotations were carried out through the 12536T, P. baetica (99.2%) type strain a390T, P. balearica (95%) type Integrated Microbial Genomes Expert Review (IMG-ER) platform. strain DSM 6083T, P. bauzanensis (95%) type strain DSM 22558T, P. benzenivorans (96.9%) type strain DSM 8628T, P. borbori (96.1%) 2.5. Comparative genomics type strain DSM 17834, P. brassicacearum (97.1%) type strain DSM 13227T, P. brenneri (97.8%) type strain DSM 15294, P. caeni (93.8%) We compared the genome of Pseudomonas moraviensis strain Devor type strain HY-14T, P. cannabina (97.8%) type strain CFBP 2341T, P. to 13 closely related genomes (IMG genome IDs: 2619619019, carboxydohydrogena (77.8%) type strain ATCC 29978T, P. caricapapayae 2654587541, 2603880217, 2561511156, 2639762619, 2636416187, (97.7%) type strain ATCC 33615T, P. cedrina (98.2%) type strain 2639762638, 2639762633, 2597489942, 2639762506, 2517572232, DSM 17516T, P. chengduensis (96.6%) type strain DSM 26382, 2639762618, 2556921015) using the “Genome clustering” function on P. chloritidismutans (96.6%) type strain ATCC BAA-443T, P. chlororaphis the IMG-ER analysis platform based on the COG profile. We also used (97.9%) type strain ATCC 9446T, P. cichorii (96.8%) type strain ATCC principal component analysis to compare the genomes based on several 10857T, P. citronellosis (94.4%) type strain ATCC 13674T, P. coleopterorum genomic features including the genome size, the number of genes, (97.8%) type strain LMG 28558T, P. composti (96.7%) type strain C2T, the number of transporters identified, the GC content, the number of P. congealans (97.7%) type strain DSM 14939T, P. corrugata (97.7%) non-coding bases, the number of genes belonging to COG categories, type strain ATCC 29736T, P. constantinii (97.4%) type strain PS 3aT, P. as well as the number of genes belonging to each COG category. The cremoricolorata (97.1%) type strain DSM 17059T, P. cuatrocienegasensis PCA analysis was conducted using the “princomp” function in the labdsv (96.5%) type strain LMG 24676T, P. deceptionensis (97.2%) type strain library of R [18]. The results were visualized using a biplot, where M1T, P. delhiensis (94.3%) type strain RLD-1T, P. duriflava (94.7%) type genomes were represented by stars and genomic features or COG strain HR2T, P. elongata (89.3%) type strain ATCC 10144T, P. endophytica categories used for comparison were represented by arrows. (97.3%) type strain BSTT44T, P. entomophila (97.7%) type strain L48T, P. extremaustralis (97.3%) type strain DSM 17835T, P. extremorientalis 3. Results and discussion (97.5%) type strain KMM 3447T, P. ficuserectae (97.6%) type strain ATCC 35104T, P. flavescens (96.5%) type strain ATCC 51555T, 3.1.
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