Genomes from three strains of Kocuria rosea were sequenced. K. rosea ATCC 186, the type strain, was 3,958,612 bp in length with a total G+C content of 72.70%. When assembled, K. rosea ATCC 516 was 3,862,128 bp with a 72.82% G+C content. K. rosea ATCC 49321 was 4,018,783 bp in size with a 72.49% G+C content

Goen, Abigail E.

MacLea, Kyle S.

Trachtenberg, Ariel M.

Genome Announcements

English

ABSTRACT
          
            Genomes from three strains of
            Kocuria rosea
            were sequenced.
            K. rosea
            ATCC 186, the type strain, was 3,958,612 bp in length with a total G+C content of 72.70%. When assembled,
            K. rosea
            ATCC 516 was 3,862,128 bp with a 72.82% G+C content.
            K. rosea
            ATCC 49321 was 4,018,783 bp in size with a 72.49% G+C content.
          </jats:p

Ariel M. Trachtenberg

Abigail E. Goen

Kyle S. MacLea

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Genome Sequences for Three Strains of Kocuria rosea, Including the Type Strain

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University of New HampshireUniversity of New Hampshire Scholars' RepositoryLife Sciences Faculty Scholarship Life Sciences6-21-2018Genome Sequences for Three Strains of Kocuriarosea, Including the Type StrainAriel M. TrachtenbergUniversity of New Hampshire, ManchesterAbigail E. GoenUniversity 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 CitationTrachtenberg, A.M.*, Goen, A.E.*, and MacLea, K.S. Genome Sequences for Three Strains of Kocuria rosea, Including the Type Strain.Genome Announc, 6(25):e00594-18; doi: 10.1128/genomeA.00594-18, 2018. http://genomea.asm.org/content/6/25/e00594-18.fullGenome Sequences for Three Strains of Kocuria rosea,Including the Type StrainAriel M. Trachtenberg,a Abigail E. Goen,a Kyle S. MacLeaa,b,caBiology Program, University of New Hampshire, Manchester, New Hampshire, USAbBiotechnology Program, University of New Hampshire, Manchester, New Hampshire, USAcDepartment of Life Sciences, University of New Hampshire, Manchester, New Hampshire, USAABSTRACT Genomes from three strains of Kocuria rosea were sequenced. K. roseaATCC 186, the type strain, was 3,958,612 bp in length with a total GC content of72.70%. When assembled, K. rosea ATCC 516 was 3,862,128 bp with a 72.82% GCcontent. K. rosea ATCC 49321 was 4,018,783 bp in size with a 72.49% GC content.The Actinobacteria include a large number of terrestrial and aquatic bacteria, includ-ing important soil microbes and pathogens. Kocuria rosea is a Gram-positiveactinobacterium originally appreciated as a pigmented environmental isolate (1, 2) andlater noted as an underappreciated human pathogen (3–10), potential bioremediatorin the elimination of azo dyes and other chemicals (11), and producer of importantcompounds (12). Several strains of K. rosea were originally known under other baso-nyms (1, 13, 14) but are now grouped together in the same genus and species. To verifythese taxonomic assignments to the K. rosea species and to provide a platform forcomparison among the environmental, commensal, and pathogenic strains of thespecies, a sequencing project was undertaken to genomically evaluate three distinctstrains of K. rosea.K. rosea ATCC 186T, ATCC 516, and ATCC 49321 were obtained from the ATCC(Manassas, VA, USA) in lyophilized form and rehydrated. Cultures were grown at 26°Con nutrient or brain heart infusion medium from isolated colonies of each strain, withcareful attention on keeping each strain pure and separate. The QIAamp DNA minikit(Qiagen, Valencia, CA, USA) was used to isolate genomic DNA (gDNA) from singlecolonies grown in broth culture according to the manufacturer’s instructions. PuriﬁedgDNA was fragmented, adapter tagged using the Nextera DNA library prep kit (Illumina,San Diego, CA, USA), and sequenced with an Illumina HiSeq 2500 instrument at theHubbard Center for Genome Studies (Durham, NH, USA). The resulting 250-bp paired-end read sequences were bioinformatically trimmed using Trimmomatic (15) prior toassembly and gene analysis.Assembly and annotation of each genome were undertaken using SPAdes v. 3.11.1and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) process (16). Type strainATCC 186 had a genome size of 3,958,612 bp with a GC content of 72.70%. The otherstrains had similar sizes and GC contents; K. rosea ATCC 516 was 3,862,128 bp with aGC content of 72.82%, and strain ATCC 49321 was 4,018,783 bp in size with a GCcontent of 72.49%. A total of 3,564 to 3,718 genes were identiﬁed in each of thethree strains by the PGAP. RNA genes, including rRNA, tRNAs, noncoding (ncRNAs), and84 to 100 pseudogenes were found in each strain. No clustered regularly interspacedshort palindromic repeat (CRISPR) arrays were found. A total of 162 nonidenticalreductases were found in the three strains, consistent with the noted observation ofhigh K. rosea reductase activity in decolorization and detoxiﬁcation of azo dyes, whichis of potential use in cleanup and bioremediation (11). Comparisons among the strainsequences using average nucleotide identity (ANI) on the EzBioCloud portal (17)Received 24 May 2018 Accepted 24 May2018 Published 21 June 2018Citation Trachtenberg AM, Goen AE, MacLeaKS. 2018. Genome sequences for three strainsof Kocuria rosea, including the type strain.Genome Announc 6:e00594-18. https://doi.org/10.1128/genomeA.00594-18.Copyright © 2018 Trachtenberg et al. This isan open-access article distributed under theterms of the Creative Commons Attribution 4.0International license.Address correspondence to Kyle S. MacLea,Kyle.MacLea@UNH.edu.PROKARYOTEScrossmVolume 6 Issue 25 e00594-18 genomea.asm.org 1 on June 28, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from support their assignment to the same species, as each strain had greater than 98% ANIcompared with the other two strains in any dyad combination. The genome sequencesgenerated in this study should prove useful in the comparison of these strains withother K. rosea isolates with environmental, commensal, and pathogenic origins.Accession number(s). The Kocuria rosea whole-genome shotgun (WGS) projectswere deposited under the GenBank accession numbers QFBJ00000000 (ATCC 186T),QFBK00000000 (ATCC 516), and QFBL00000000 (ATCC 49321). The versions described inthis paper are the ﬁrst versions, QFBJ01000000, QFBK01000000, and QFBL01000000,respectively.ACKNOWLEDGMENTSSequencing and bioinformatics analysis were undertaken at the Hubbard Center forGenome Studies at UNH, supported by NH-INBRE, with the kind assistance of KelleyThomas, Toni Westbrook, and Stephen Simpson. K. S. M. acknowledges new laboratorymember Elliott F. MacLea for 6months of helpful discussions. This work was a project of theMicrobiology Education through Genome Annotation-New Hampshire (MEGA-NH) pro-gram.The Department of Life Sciences at UNH Manchester provided funds for purchasingthe bacterial strains. Sequencing costs were supported by New Hampshire-INBREthrough Institutional Development Award (IDeA) P20GM103506 from the NationalInstitute of General Medical Sciences of the NIH. The funders had no role in studydesign, data collection and interpretation, or the decision to submit the work forpublication.REFERENCES1. 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Endocar-ditis by Kocuria rosea in an immunocompetent child. Braz J Infect Dis19:82–84. https://doi.org/10.1016/j.bjid.2014.09.007.6. Ananieva MM, Faustova MO, Basarab IO, Loban’ GA. 2017. Kocuria rosea,Kocuria kristinae, Leuconostoc mesenteroides as caries-causing repre-sentatives of oral microﬂora. Wiad Lek 70:296–298.7. Gunaseelan P, Suresh G, Raghavan V, Varadarajan S. 2017. Native valveendocarditis caused by Kocuria rosea complicated by peripheral mycoticaneurysm in an elderly host. J Postgrad Med 63:135. https://doi.org/10.4103/jpgm.JPGM_441_16.8. Dotis J, Printza N, Papachristou F. 2012. Peritonitis attributable to Kocuriarosea in a pediatric peritoneal dialysis patient. Perit Dial Int 32:577–578.https://doi.org/10.3747/pdi.2011.00300.9. Srinivasa KH, Agrawal N, Agarwal A, Manjunath CN. 2013. Dancingvegetations: Kocuria rosea endocarditis. Case Rep 2013:bcr2013010339.https://doi.org/10.1136/bcr-2013-010339.10. Lee MK, Choi SH, Ryu DW. 2013. Descending necrotizing mediastinitiscaused by Kocuria rosea: a case report. BMC Infect Dis 13:475. https://doi.org/10.1186/1471-2334-13-475.11. Parshetti GK, Telke AA, Kalyani DC, Govindwar SP. 2010. Decolorization anddetoxiﬁcation of sulfonated azo dye methyl orange by Kocuria rosea MTCC1532. J Hazard Mater 176:503–509. https://doi.org/10.1016/j.jhazmat.2009.11.058.12. Gu D, Jiao Y, Wu J, Liu Z, Chen Q. 2017. Optimization of EPS productionand characterization by a halophilic bacterium, Kocuria rosea ZJUQHfrom Chaka Salt Lake with response surface methodology. Molecules22:814. https://doi.org/10.3390/molecules22050814.13. Tindall BJ, Schumann P, Stackebrandt E. 2000. The status of the genusPelczaria (Poston 1994) and the species Pelczaria aurantia (Poston 1994).Request for an opinion. Int J Syst Evol Microbiol 50:1695–1696. https://doi.org/10.1099/00207713-50-4-1695.14. Schumann P, Tindall BJ, Mendrock U, Kramer I, Stackebrandt E. 2000.Pelczaria aurantia ATCC 49321(T) (DSM 12801(T)) is a strain of Kocuriarosea (Flügge 1886) Stackebrandt et al. 1995. Int J Syst Evol Microbiol50:1421–1424. https://doi.org/10.1099/00207713-50-4-1421.15. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a ﬂexible trimmer forIllumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170.16. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W. 2013.Prokaryotic Genome Annotation Pipeline. National Center for Biotech-nology Information (US), Bethesda, MD.17. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y, Seo H, Chun J. 2017. IntroducingEzBioCloud: a taxonomically united database of 16S rRNA gene se-quences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755.Trachtenberg et al.Volume 6 Issue 25 e00594-18 genomea.asm.org 2 on June 28, 2018 by UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://genomea.asm.org/Downloaded from 

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Genome Sequences for Three Strains of Kocuria rosea, Including the Type Strain

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