Draft genome sequence of Vitellibacter aquimaris D-24T isolated from seawater

brazilian journal of microbiology49(2018)10–12

h ttp : / / w w w . b j m i c r o b i o l . c o m . b r /

Genome

Announcement

Draft

genome

sequence

of

Vitellibacter

aquimaris

D-24

T

isolated

from

seawater

Suganthi

Thevarajoo

_,

_Chitra

_Selvaratnam

_,

_Kok-Gan

_Chan

_,

Kian

Mau

Goh

_,

_Chun

_Shiong

_Chong

a_{UniversitiTeknologiMalaysia,FacultyofBiosciencesandMedicalEngineering,Skudai,Johor,Malaysia}

b_{UniversityofMalaya,InstituteofBiologicalSciences,DivisionofGeneticsandMolecularBiology,KualaLumpur,Malaysia}

a

r

t

i

c

l

e

i

n

f

o

Received26October2016 Accepted28March2017 Availableonline19July2017 AssociateEditor:JohnMcCulloch

Keywords: Vitellibacteraquimaris Genomesequence Denitrification Proteases

a

b

s

t

r

a

c

t

VitellibacteraquimarisD-24T_(=KCTC42708T_=DSM101732T_{),ahalophilicmarinebacterium,}

wasisolatedfromseawatercollectedfromDesarubeach,Malaysia.Here,wepresentthe draftgenomesequenceofD-24T_{withagenomesizeofapproximately3.1MbpandG+C}

contentof39.93%. Thegenome ofD-24T _{containsgenesinvolvedin reducinga potent}

greenhousegas(N2O)intheenvironmentandthedegradationofproteinaceouscompounds.

Genomeavailabilitywillprovideinsightsintopotentialbiotechnologicalandenvironmental applicationsofthisbacterium.

©2017SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.Thisis anopenaccessarticleundertheCCBY-NC-NDlicense(http://creativecommons.org/

licenses/by-nc-nd/4.0/).

Over the last few decades, marine microorganisms have received considerable attention for their applications in biotechnology. Prime focus has been given on identifica-tion of halophilic enzymes with potential applications.1,2

Halophilic enzymes boast unique properties such as the sustainabilityatextremerangesofsaltconcentration, temper-ature,pH,andorganicsolvents.3,4_{Characterizationofmarine}

bacteriathroughtheirgenomesequencehasprovidedgreat opportunities formining and identifying of enzymes with biotechnologicalimportance.

∗ _{Correspondingauthor.}

E-mail:cschong@utm.my(C.S.Chong).

VitellibacteraquimarisD-24T_{,previouslyisolatedfrom}

sea-water,wasconfirmedasanewspeciesingenusVitellibacter.5

This bacterium isa Gram negative, rod-shape and yellow-orangepigmentedbacterium.Inthisstudy,wereportthedraft genomeofV.aquimarisD-24T_.

V. aquimaris D-24T _{wasgrown inMarine Broth 2216(BD}

Difco)andthegenomicDNAwasextractedusingtheDNeasy Blood and Tissue kit (Qiagen,Hilden, Germany) per manu-facturerinstructions.ThegenomeoftheV.aquimarisD-24T

sequence was generated using pair-end sequencing in an

https://doi.org/10.1016/j.bjm.2017.03.013

1517-8382/©2017SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.ThisisanopenaccessarticleundertheCC BY-NC-NDlicense(http://creativecommons.org/licenses/by-nc-nd/4.0/).

brazilian journal of microbiology49(2018)10–12

11

Table1–GenomefeaturesofVitellibacteraquimaris

D-24T_.

Attributes Values

Genomesize 3,147,268bp

G+Ccontent 39.93%

Numberofcontigs 66

Proteincodinggenes 2790

rRNAgenes 7

tRNAgenes 35

Pseudogenes 134

Frameshiftedgenes 8

Geneswithsignalpeptides 376

Geneswithtransmembranehelices 727

Illumina MiSeq sequencing platform (Illumina, California, USA).DenovoassemblywasperformedusingIDBA-UDversion 1.0.9,6obtaining66contigswithaN50contiglengthof439,587.

GenomeannotationswerecarriedoutusingNCBIProkaryotic Genome Annotation Pipeline 2.87 _{and Integrated Microbial}

GenomesExpertReview(IMG-ER).8_{Proteincodingsequences}

were predicted by using GeneMarkS+ version 2.8 with the best-placed reference protein method9 _{and Prodigal,}10

respectively.

Thedraft genomeofV. aquimaris D-24T _{is comprisedof}

3,147,268nucleotideswith ameanG+C contentof39.93%. Atotalof2967geneswerepredicted,ofwhich2790(94.03%) protein-codinggeneswere assigned with putative function or hypotheticalproteins. The genome consistsof three 5S

rRNA, one 16S rRNA, one 23 rRNA, and 35 tRNA genes

(Table 1). The genome V. aquimaris D-24T _{contains genes}

encodedfornitritereductase (nirK)(WP045079976.1),nitric oxidereductasesubunitB(norB)(WP062619270.1),nitricoxide reductase subunit C (norC) (WP062619272.1), and nitrous oxide reductase (nosZ) (WP062619280.1), all of which are involvedinthedenitrificationpathway(NO2−toN2).Nitrous

oxide (N2O) is a potent greenhouse gas which also

dam-ages the Earth’s ozone layer. Due to intensive agricultural and industrial practices, the release of this gas into the atmospherehasgreatlyincreased.11,12 _{Nitrous-oxide}

reduc-taseplaysanimportantrole incatalyzingthe reductionof nitrousoxidetonitrogen(N2).13Thenitrousoxidereductase

(nosZ)fromV. aquimarisD-24T _{isapromisingcandidatefor}

removingnitrousoxide,apotentgreenhousegas,from the environment.

Genome analysis also revealed a total of twelve genes encoded for proteases, including two metalloproteases (KXO00999.1;KXN98592.1);twoserineproteases(KXO01375.1; KXN97930.1); five proteases (KXO00989.1; KXO00819.1; KXN99950.1; KXN99951.1; KXO00100.1); two zinc metallo-proteases (KXO00568.1; KXN98177.1); and an acid protease (KXO00796.1). Genes encodingproteases were also present in the genome of another species of Vitellibacter.14 _The

draft genomesequence ofV. aquimaris D-24T _{willfacilitate}

understandinganddevelopmentofpotentialapplicationsof

Vitellibacterspecies.

TheWholeGenomeShotgunprojecthasbeen deposited

at DDBJ/EMBL/GenBank under the accession number

JRWG00000000. The first version (accession number

JRWG01000000)isdescribedinthispaper.

Conflicts

of

interest

Theauthorsdeclarenoconflictsofinterest.

Acknowledgments

This work was financially supported by Ministry of Edu-cation Malaysia (grant number: 4F265) and Universiti Teknologi Malaysia RU grants (grant number: 07H43 and

14H67). Suganthi Thevarajoo and Chitra Selvaratnam

acknowledge the PhD Zamalah scholarship from

Uni-versiti Teknologi Malaysia. Kok-Gan Chan acknowledges the University of Malaya High Impact Research Grants (UM.C/625/1/HIR/MOHE/CHAN/01, GrantNo.A-000001-50001 andUM-MOHEHIRGrantUM.C/625/1/HIR/MOHE/CHAN/14/1, no.H-50001-A000027).

r

e

f

e

r

e

n

c

e

s

1.DalmasoGZL,FerreiraD,VermelhoAB.Marine

extremophiles:asourceofhydrolasesforbiotechnological

applications.MarDrugs.2015;13(4):1925–1965.

2.GomesJ,SteinerW.Thebiocatalyticpotentialof

extremophilesandextremozymes.FoodTechnolBiotechnol.

2004;42(4):223–235.

3.KumarS,KaranR,KapoorS,SinghS,KhareS.Screeningand

isolationofhalophilicbacteriaproducingindustrially

importantenzymes.BrazJMicrobiol.2012;43(4):1595–1603.

4.MorenoM,PérezD,GarcíaMT,MelladoE.Halophilicbacteria

asasourceofnovelhydrolyticenzymes.Life.2013;3(1):

38–51.

5.ThevarajooS,SelvaratnamC,GohKM,etal.Vitellibacter

aquimarissp.nov.,amarinebacteriumisolatedfromsea

water.IntJSystEvolMicrobiol.2016;66(9):3662–3668.

6.PengY,LeungHC,YiuS-M,ChinFY.IDBA-UD:adenovo

assemblerforsingle-cellandmetagenomicsequencingdata

withhighlyunevendepth.Bioinformatics.2012;28:1420–1428.

7.AngiuoliSV,GussmanA,KlimkeW,etal.Towardanonline

repositoryofstandardoperatingprocedures(SOPs)for

(meta)genomicannotation.OMICS.2008;12:137–141.

8.MarkowitzVM,MavromatisK,IvanovaNN,ChenI-MA,Chu

K,KyrpidesNC.IMGER:asystemformicrobialgenome

annotationexpertreviewandcuration.Bioinformatics.

2009;25(17):2271–2278.

9.BesemerJ,BorodovskyM.GeneMark:websoftwareforgene

findinginprokaryotes,eukaryotesandviruses.NucleicAcids

Res.2005;33:W451–W454.

10.HyattD,ChenG-L,LoCascioPF,LandML,LarimerFW,Hauser

LJ.Prodigal:prokaryoticgenerecognitionandtranslation

initiationsiteidentification.BMCBioinf.2010;11:119.

11.ZumftWG,KroneckPM.Respiratorytransformationof

nitrousoxide(N2O)todinitrogenbyBacteriaandArchaea.

12

12.JonesCM,GrafDR,BruD,PhilippotL,HallinS.The

unaccountedyetabundantnitrousoxide-reducingmicrobial

community:apotentialnitrousoxidesink.ISMEJ.

2013;7:417–426.

13.PauletaSR,Dell’AcquaS,MouraI.Nitrousoxidereductase.

CoordChemRev.2013;257:332–349.

14.ThevarajooS,SelvaratnamC,ChanK-G,GohKM,ChongCS.

DraftgenomesequenceofVitellibactervladivostokensisKMM

3516T_{:aprotease-producingbacterium.MarGen.}