ABSTRACT
          
            We sequenced a naturally competent bacterial isolate, WY10, cultured from a Wyoming soil sample. Sequence analysis revealed that WY10 is a novel strain of
            Bacillus simplex
            . To our knowledge, WY10 is the first
            B. simplex
            strain to be characterized as naturally competent for DNA uptake by transformation.
          </jats:p

Adhya, Sankar L

Bliskovsky, Valery V

Dantas, Gautam

Keen, Eric C

Genome Announcements

English

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Washington University School of MedicineDigital Commons@BeckerOpen Access Publications2017Draft genome sequence of the naturally competentBacillus simplex strain WY10Eric C. KeenWashington University School of Medicine in St. LouisValery V. BliskovskyNational Institutes of HealthSankar L. AdhyaNational Institutes of HealthGautam DantasWashington University School of Medicine in St. LouisFollow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubsThis Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in OpenAccess Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact engeszer@wustl.edu.Recommended CitationKeen, Eric C.; Bliskovsky, Valery V.; Adhya, Sankar L.; and Dantas, Gautam, ,"Draft genome sequence of the naturally competentBacillus simplex strain WY10." Genome Announcements.5,46. e01295-17. (2017).https://digitalcommons.wustl.edu/open_access_pubs/6418Draft Genome Sequence of the NaturallyCompetent Bacillus simplex Strain WY10Eric C. Keen,a Valery V. Bliskovsky,b Sankar L. Adhya,c Gautam Dantasa,d,e,fThe Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine,St. Louis, Missouri, USAa; CCR Genomics Core, National Cancer Institute, National Institutes of Health, Bethesda,Maryland, USAb; Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, NationalInstitutes of Health, Bethesda, Maryland, USAc; Department of Pathology & Immunology, Washington UniversitySchool of Medicine, St. Louis, Missouri, USAd; Department of Molecular Microbiology, Washington University Schoolof Medicine, St. Louis, Missouri, USAe; Department of Biomedical Engineering, Washington University in St. Louis, St.Louis, Missouri, USAfABSTRACT We sequenced a naturally competent bacterial isolate, WY10, culturedfrom a Wyoming soil sample. Sequence analysis revealed that WY10 is a novel strainof Bacillus simplex. To our knowledge, WY10 is the ﬁrst B. simplex strain to be char-acterized as naturally competent for DNA uptake by transformation.The Gram-positive bacterial genus Bacillus comprises dozens of species and includesobligate human pathogens (B. anthracis), facultative human pathogens (B. cereus),and nonpathogenic model organisms (B. subtilis) (1). Various Bacillus species are ubiquitousin soils and other natural environments, and some strains are notable for their naturalcompetence for DNA uptake in vitro and in situ (2). As part of a previously publishedstudy (3), we obtained a bacterial isolate from a soil sample collected in Cheyenne, WY,USA, which formed mucoid off-white colonies on LB plates and spontaneously took upexogenous plasmid DNA in liquid culture. 16S rRNA proﬁling placed this isolate, thencalled WY10, within Bacillus; here, we report that WY10 constitutes a novel strain ofBacillus simplex.DNA was extracted from a WY10 overnight culture with phenol-chloroform, pro-cessed into sequencing libraries (Nextera XT kit; Illumina), and sequenced using 2 250 paired-end reads (MiSeq; Illumina). The resulting 4,066,400 paired-end reads weretrimmed of Illumina adapters and human-like sequences with Trimmomatic (4) andDeconseq (5), respectively. The remaining 3,924,890 reads (96.5% of original) wereassembled with SPAdes (6), yielding a draft genome assembly of 117 contigs (largestcontig  1,148,191 bp; N50  322,734 bp) and 106 scaffolds. All 81 scaffolds 200 bp,comprising 40.3% GC content across 5,516,951 bp, were functionally annotated withRapid Annotations using Subsystems Technology (RAST) (7). RAST identiﬁed 78 RNAsand 5,739 coding sequences, 44% of which could be functionally categorized. Becauseindividual WY10 scaffolds displayed the greatest sequence similarity by BLASTn toB. simplex, JSpeciesWS (8) was used to calculate average nucleotide identity (ANI) basedon MUMmer (9) between the WY10 draft genome sequence and all existing B. simplexgenomes. WY10 shares 93.7% and 90.9% ANI with two completely sequenced B. simplexstrains, DSM 1321 and SH-B26, respectively, and 85.9% to 97.3% ANI (median ANI 96.7%) with nine additional B. simplex whole-genome shotgun assemblies. Thus, WY10does not represent a unique type species (conventionally95% ANI [10]) of Bacillus butrather a novel strain of B. simplex.We recently reported that certain bacteriophages, dubbed “superspreaders,” do notefﬁciently degrade bacterial plasmids during infection and instead release intact plas-mid DNA upon lysis, thereby promoting horizontal gene transfer by transformation (3).In this previous work, WY10 was shown to acquire and manifest antibiotic resistance viaReceived 17 October 2017 Accepted 23October 2017 Published 16 November 2017Citation Keen EC, Bliskovsky VV, Adhya SL,Dantas G. 2017. Draft genome sequence of thenaturally competent Bacillus simplex strainWY10. Genome Announc 5:e01295-17. https://doi.org/10.1128/genomeA.01295-17.Copyright © 2017 Keen et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Eric C. Keen,e.keen@wustl.edu.PROKARYOTEScrossmVolume 5 Issue 46 e01295-17 genomea.asm.org 1 on December 23, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from the uptake of phage-released plasmid DNA. Here, we announce the draft genomesequence of WY10 and its placement within B. simplex. To our knowledge, WY10 is theﬁrst B. simplex strain to be functionally characterized as naturally competent and theﬁrst Gram-positive bacterium to demonstrate compatibility with the Escherichia coliplasmid p (R6K origin) (11). The draft genome sequence of B. simplex WY10 willfacilitate further analysis of phage-mediated plasmid transformation and, by extension,horizontal gene transfer and bacterial evolution.Accession number(s). This whole-genome shotgun project has been deposited inDDBJ/ENA/GenBank under the accession number NWQJ00000000. The version de-scribed in this paper is the ﬁrst version, NWQJ01000000.ACKNOWLEDGMENTSWe thank Robert Potter, Alaric D’Souza, and Andrew Gasparrini for discussion andSteve Shema, Eric Martin, and Brian Koebbe for technical assistance.This research was supported by the Intramural Research Program of the NationalCancer Institute and by a National Science Foundation Graduate Research Fellowship(DGE-1143945) to E.C.K. The funders had no role in the study design, data collection andinterpretation, or the decision to submit the work for publication.REFERENCES1. Bhandari V, Ahmod NZ, Shah HN, Gupta RS. 2013. Molecular signaturesfor Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereusclades in molecular terms and proposal to limit the placement of newspecies into the genus Bacillus. Int J Syst Evol Microbiol 63:2712–2726.https://doi.org/10.1099/ijs.0.048488-0.2. Kovács AT, Smits WK, Miron´czuk AM, Kuipers OP. 2009. Ubiquitous latecompetence genes in Bacillus species indicate the presence of functionalDNA uptake machineries. Environ Microbiol 11:1911–1922. https://doi.org/10.1111/j.1462-2920.2009.01937.x.3. Keen EC, Bliskovsky VV, Malagon F, Baker JD, Prince JS, Klaus JS, AdhyaSL. 2017. Novel “superspreader” bacteriophages promote horizontalgene transfer by transformation. mBio 8:e02115-16. https://doi.org/10.1128/mBio.02115-16.4. 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. Schmieder R, Edwards R. 2011. Fast identiﬁcation and removal of se-quence contamination from genomic and metagenomic datasets. PLoSOne 6:e17288. https://doi.org/10.1371/journal.pone.0017288.6. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV,Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a newgenome assembly algorithm and its applications to single-cell sequenc-ing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021.7. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K,Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL,Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD,Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008.The RAST server: rapid annotations using subsystems technology. BMCGenomics 9:75. https://doi.org/10.1186/1471-2164-9-75.8. Richter M, Rosselló-Móra R, Glöckner FO, Peplies J. 2016. JSpeciesWS: aweb server for prokaryotic species circumscription based on pairwisegenome comparison. Bioinformatics 32:929–931. https://doi.org/10.1093/bioinformatics/btv681.9. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C,Salzberg SL. 2004. Versatile and open software for comparing largegenomes. Genome Biol 5:R12. https://doi.org/10.1186/gb-2004-5-2-r12.10. Richter M, Rosselló-Móra R. 2009. Shifting the genomic gold standardfor the prokaryotic species deﬁnition. Proc Natl Acad Sci U S A 106:19126–19131. https://doi.org/10.1073/pnas.0906412106.11. Srivastava P, Chattoraj DK. 2007. Selective chromosome ampliﬁcation inVibrio cholerae. Mol Microbiol 66:1016–1028. https://doi.org/10.1111/j.1365-2958.2007.05973.x.Keen et al.Volume 5 Issue 46 e01295-17 genomea.asm.org 2 on December 23, 2017 by Washington University in St. Louishttp://genomea.asm.org/Downloaded from 

Draft genome sequence of the naturally competent Bacillus simplex strain WY10

Eric C. Keen

Valery V. Bliskovsky

Sankar L. Adhya

Gautam Dantas

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Draft Genome Sequence of the Naturally Competent Bacillus simplex Strain WY10

https://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article=7417&amp;context=open_access_pubs

Draft genome sequence of the naturally competent Bacillus simplex strain WY10

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