Draft genome sequence of Streptomyces sp strain F1, a potential source for glycoside hydrolases isolated from Brazilian soil B G D F i RQ1 D H a C b C a A R A A A K A G S D S I S k t b h 1 u 1 2 3 4 5[.]
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h tt p : / / w w w b j m i c r o b i o l c o m b r /
Ricardo Rodrigues de Meloa,b,1, Gabriela Felix Persinotia,1,
Q1
Douglas Antonio Alvaredo Paixãoa, Fábio Márcio Squinaa, Roberto Rullera, ∗,
Helia Harumi Satob, ∗
aCentro Nacional de Pesquisa em Energia e Materiais (CNPEM), Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE),
Campinas, São Paulo, Brazil
bUniversidade Estadual de Campinas (UNICAMP), Faculdade de Engenharia de Alimentos, Departamento de Ciência de Alimentos,
Campinas, São Paulo, Brazil
a r t i c l e i n f o
Article history:
Received26September2016
Accepted22November2016
Availableonlinexxx
AssociateEditor:JohnMcCulloch
Keywords:
Actinobacteria
Glycosidehydrolases
Streptomyces
Draftgenomesequence
Soilbacteria
a b s t r a c t Here,weshowthedraftgenomesequenceofStreptomycessp.F1,astrainisolatedfrom soilwithgreatpotentialforsecretionofhydrolyticenzymesusedtodeconstructcellulosic biomass.ThedraftgenomeassemblyofStreptomycessp.strainF1has87contigswitha totalgenomesizeof8,162,446bpandG+C72.63%.Preliminarygenomeanalysisidentified
327proteinsasCarbohydrate-ActiveEnzymes,being141glycosidehydrolasesorganizedin
46distinctfamilies.Thisdraftgenomeinformationprovidesnewinsightsonthekeygenes encodinghydrolyticenzymesinvolvedinbiomassdeconstructionemployedbysoilbacteria
©2017PublishedbyElsevierEditoraLtda.onbehalfofSociedadeBrasileirade Microbiologia.ThisisanopenaccessarticleundertheCCBY-NC-NDlicense(http://
creativecommons.org/licenses/by-nc-nd/4.0/)
Introduction
StreptomycesspeciesareaerobicGram-positivebacteriabest
knownindustriallyasproducersofnaturalantibiotics,1 but
theyarealsorecognizedfortheircapacitytoutilizecellulosic
biomass.2Phylogenetically,Streptomycesisthelargestgenus
∗ Corresponding authors.
E-mails:roberto.ruller@bioetanol.org.br(R.Ruller),heliah@fea.unicamp.br(H.H.Sato)
1 Theseauthorscontributedequallytothiswork
oftheActinobacteriaphylum.Duringtheirlifetime,thesesoil bacteriaareabletodifferentiate,produceaerialmyceliaand
awide varietyofsecondarymetabolites.3 Althoughalarge number ofStreptomycesspeciescangrowonplantbiomass, understanding of key genes encoding hydrolytic enzymes involved in biomass degrading by Streptomycesis currently limited to afew soil-isolates.2,4–7 Streptomycessp strain F1
http://dx.doi.org/10.1016/j.bjm.2016.11.010
1517-8382/©2017PublishedbyElsevierEditoraLtda.onbehalfofSociedadeBrasileiradeMicrobiologia.Thisisanopenaccessarticle undertheCCBY-NC-NDlicense(http://creativecommons.org/licenses/by-nc-nd/4.0/)
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Table 1 – Summary of genome features ofStreptomyces
sp F1.
Features
wasisolatedfromsoilcontainingdecomposingorganicmatter
collectedinCampinas,SãoPaulo,Brazil.Thisisolatedstrain
showedabilitytogrowinculturemediumcontaining
cellu-lose orhemicelluloseassole carbonsource,and tosecrete
extracellularenzymesbelongingtotheglycosidehydrolases
(GHs)families.Glycosidehydrolasesareagroupofenzymes
thatplayanimportantroleintheconversionoflignocellulosic
biomassintosmallchemicalbuildingblocks,whichcanthen
beusedtoproducebiofuelsandotherimportant
intermedi-arymolecules.8Here,weshowthedraftgenomesequenceof
Streptomycessp.F1,toidentifyGHsfamily membersand to
improveunderstandingofnaturalbiomassutilizationbysoil
bacteria
Genomic DNA extraction from Streptomyces sp F1 was
carried out using FastDNA SPIN Kit for soil (MP
Biomedi-cals,Irvine,CA)accordingtothemanufacturer’sinstructions
The genome was sequenced by whole genome shotgun
sequencingusing the IlluminaHiSeq 2500System atCTBE
Sequencing and RoboticsNGS facility, generating8,147,881
pairedendreads(2×100bp).Readswerepreprocessedwith
Trimmomatic,9toremovelow-qualityandadaptersequences
andwereassembledusingSpadesversion3.6.10Thegenome
sizewasestimatedtobe8,205,272,withapproximately100×
coverage.ThedraftgenomeassemblyofStreptomycessp.F1
has87 contigs,8,162,446bpinlengthwithG+Ccontent of
72.63%(Table1 anN50of259,843bp,andthelargestcontig
was664,709bp.Genomecompletenesswasevaluatedusing
CheckM,11 which revealed that theassembly is100%
com-plete, considering460 markergenes from Streptomycetaceae
family
Streptomyces sp.F1 showed highest 16S rDNA sequence
similarity with Streptomyces misionensis strain JCM 4497 In
silicoDNA–DNAhybridization(DDH)12andAverageNucleotide
Identity/Alignmentfraction(gANI/AF)13valuesofStreptomyces
sp.F1comparedtoStreptomyces misionensisDSM40306,were
94.2%and99.4%/0.99,respectively,suggestingthatstrainF1
maybeclassifiedasStreptomyces misionensis.
Streptomyces sp F1 genome was annotated using
IMG-JGIMicrobialGenomeAnnotationPipeline (img.jgi.doe.gov)
It has been predicted to include 7494 genes, being 7397
protein-coding genes, 9 rRNA (5S (6), 16S (1), 23S (2)), and
66tRNAgenes(Table1 AccordingtoIMGfunctional
anno-tation,4453geneswereclassifiedinto COGcategories,5816
inPFAMproteinfamilies,1542inTIGRFAMfamilies,and714
in Transporter Classification Further classification
accord-ing to dbCAN showed that 327 proteins were classified as
Carbohydrate-Active Enzymes, being 141 glycoside
hydro-lasesorganizedin46distinct families.Thecurrentgenome
assembly providesapreliminarylandscape ofthe genomic andmetaboliccapabilitiesofStreptomycessp.F1
Nucleotide sequence accession number
ThewholegenomesequencesofStreptomycessp.F1havebeen deposited at DDBJ/EMBL/GenBankunder accession number FKJI00000000
Conflict of interest
Theauthorsdeclarenoconflictsofinterest
Acknowledgements
The authors gratefully acknowledgethe Brazilian National Q2
Council for Scientific and Technological Development (CNPq) for their financial support and fellowships, and CNPEM-CTBE for the use of Sequencing and Robotics NGS facility
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