The aerobic phenol-degrading Gram-negative rod Oceanimonas baumannii ATCC 700832T was first isolated from estuary mud from the River Wear, United Kingdom, in 1983. Information on the draft genome sequence for O. baumannii ATCC 700832T is included in this announcement. The predicted genome size is 3,809,332 bp, with 55.88% G+C content

Brennan, Marc A.

MacLea, Kyle S.

McClelland, William D.

Trachtenberg, Ariel M.

English

UNH Scholars' Repository

University of New HampshireUniversity of New Hampshire Scholars' RepositoryLife Sciences Faculty Scholarship Life Sciences9-1-2017Draft Genome Sequence of the Marine BacteriumOceanimonas baumannii ATCC 700832TWilliam D. McClellandUniversity of New Hampshire, ManchesterAriel M. TrachtenbergUniversity of New Hampshire, ManchesterMarc A. BrennanUniversity of New Hampshire, ManchesterKyle S. MacLeaUniversity of New Hampshire, Manchester, kyle.maclea@unh.eduFollow this and additional works at: https://scholars.unh.edu/unhmbiology_facpubThis Article is brought to you for free and open access by the Life Sciences at University of New Hampshire Scholars' Repository. It has been acceptedfor inclusion in Life Sciences Faculty Scholarship by an authorized administrator of University of New Hampshire Scholars' Repository. For moreinformation, please contact nicole.hentz@unh.edu.Recommended CitationMcClelland, W.D., Trachtenberg, A.M., Brennan, M.A., and MacLea, K.S. Draft Genome Sequence of the Marine BacteriumOceanimonas baumannii ATCC 700832T. Genome Announc, 5:e01007-17; doi:10.1128/genomeA.01007-17, 2017.Draft Genome Sequence of the MarineBacterium Oceanimonas baumannii ATCC700832TWilliam D. McClelland,a Ariel M. Trachtenberg,a Marc A. Brennan,bKyle S. MacLeaa,b,cBiology Program, University of New Hampshire, Manchester, New Hampshire, USAa; Biotechnology Program,University of New Hampshire, Manchester, New Hampshire, USAb; Department of Life Sciences, University ofNew Hampshire, Manchester, New Hampshire, USAcABSTRACT The aerobic phenol-degrading Gram-negative rod Oceanimonas bau-mannii ATCC 700832T was ﬁrst isolated from estuary mud from the River Wear,United Kingdom, in 1983. Information on the draft genome sequence for O. bau-mannii ATCC 700832T is included in this announcement. The predicted genome sizeis 3,809,332 bp, with 55.88% GC content.Oceanimonas baumannii strain GB6T (ATCC 700832T) is an aerobic Gram-negativerod that displays up to four polar ﬂagella and can readily grow on minimal saltsmedium supplemented with phenol (1). It was isolated in 1998 from estuary mud at themouth of the River Wear in Sunderland, United Kingdom (1). At the time of its discovery,Brown et al. found that O. baumannii should be classiﬁed in a new genus calledOceanomonas (1), later corrected in spelling to Oceanimonas (2), along with the typestrain for this new genus, (Pseudomonas) doudorofﬁi ATCC 27123, now called Oceani-monas doudorofﬁi (1).O. baumannii is a chemoorganotrophic gammaproteobacterium and has a require-ment for sodium. It can grow at NaCl levels of up to 7% (wt/vol) (1) or 12% (3). Itsabsolute requirement for NaCl is 0.15% (wt/vol) (3), and it grows at temperaturesbetween 10°C and 30°C (1). O. baumannii can be grown on glycerol, D-galactose, caprate,malate, citrate, ethanol, betaine, sarcosine, phenol, succinate, L-alanine, L-proline, andL-glutamate (1).O. baumannii ATCC 700832T was purchased from the ATCC (Manassas, VA, USA) inlyophilized form. It was rehydrated and then cultured in marine broth or agar (ATCCmedium 2216) under conditions of 26°C for 48 h at atmospheric pressure. A singlecolony was picked and cultured in log-phase growth to obtain genomic DNA (gDNA),using the Genomic-tip 500/G kit (Qiagen, Valencia, CA, USA). gDNA was fragmented,tagged with adapters using the Nextera DNA library prep kit (Illumina, San Diego, CA,USA), and sequenced on an Illumina HiSeq 2500. Two hundred ﬁfty-base-pair paired-end reads were generated at the Hubbard Center for Genome Studies (Durham, NH,USA), and Trimmomatic (4) was used for bioinformatic trimming and removal ofadapter sequences prior to gene analysis.The O. baumannii genome was assembled using SPAdes version 3.8.0 (5) from2,790,420 reads, with an average length of 899 bp, into 70 contigs (after removal ofsmall low-quality contigs). The total genome length was 3,809,332 bp, and we calcu-lated an average coverage of 80. The largest contig found was 408,079 bp, with aGC content of 55.88% and an N50 value of 232,731 bp. The GC content is in closeagreement with that published by Brown et al., at 54% (1). The genome was annotatedwith the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) process (6). PGAP foundReceived 12 August 2017 Accepted 15August 2017 Published 7 September 2017CitationMcClelland WD, Trachtenberg AM,Brennan MA, MacLea KS. 2017. Draft genomesequence of the marine bacteriumOceanimonas baumannii ATCC 700832T.Genome Announc 5:e01007-17. https://doi.org/10.1128/genomeA.01007-17.Copyright © 2017 McClelland et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to Kyle S. MacLea,kyle.maclea@unh.edu.PROKARYOTEScrossmVolume 5 Issue 36 e01007-17 genomea.asm.org 1 on June 19, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from a total of 3,651 genes, 3,498 coding sequences (CDSs), 98 RNA genes, 55 pseudogenes,and 1 clustered regularly interspaced short palindromic repeat (CRISPR) array.Accession number(s). This whole-genome shotgun project has been deposited atDDBJ/ENA/GenBank under the accession no. NQJF00000000. The version described inthis paper is version NQJF01000000.ACKNOWLEDGMENTSSequencing and bioinformatics analyses were undertaken at the Hubbard Center forGenome Studies at UNH with the kind assistance of Kelley Thomas, Jordan Ramsdell,and Stephen Simpson. K.S.M. acknowledges Annabelle MacLea and Duncan MacLea forhelpful discussions. This work was a project of the Microbiology Education throughGenome Annotation–New Hampshire (MEGA-NH) program.The Department of Life Sciences at UNH Manchester provided funds for sequencing.The funders had no role in the study design, data collection, or interpretation or thedecision to submit the work for publication.REFERENCES1. Brown GR, Sutcliffe IC, Cummings SP. 2001. Reclassiﬁcation of [Pseudomo-nas] doudorofﬁi (Baumann et al. 1983) into the genus Oceanomonas gen.nov. as Oceanomonas doudorofﬁi comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumanniisp. nov. Int J Syst Evol Microbiol 51:67–72. https://doi.org/10.1099/00207713-51-1-67.2. International Journal of Systematic and Evolutionary Microbiology. 2001.Notiﬁcation that new names and new combinations have appeared involume 51, part 1, of the IJSEM. Int J Syst Evol Microbiol 51:269. https://doi.org/10.1099/00207713-51-2-269.3. Brown GR, Sutcliffe IC, Bendell D, Cummings SP. 2000. The modiﬁcation ofthe membrane of Oceanimonas baumannii when subjected to both os-motic and organic solvent stress. FEMS Microbiol Lett 189:149–154.https://doi.org/10.1111/j.1574-6968.2000.tb09221.x.4. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a ﬂexible trimmer forIllumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170.5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, LesinVM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N,Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome as-sembly algorithm and its applications to single-cell sequencing. J ComputBiol 19:455–477. https://doi.org/10.1089/cmb.2012.0021.6. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W. 2013.Prokaryotic Genome Annotation Pipeline. National Center for Biotechnol-ogy Information, Bethesda, MD.McClelland et al.Volume 5 Issue 36 e01007-17 genomea.asm.org 2 on June 19, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from 

Draft Genome Sequence of the Marine Bacterium Oceanimonas baumannii ATCC 700832T

https://scholars.unh.edu/cgi/viewcontent.cgi?article=1014&context=unhmbiology_facpub

Draft Genome Sequence of the Marine Bacterium Oceanimonas baumannii ATCC 700832T

Abstract

Similar works

Full text

Available Versions

UNH Scholars' Repository