Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces(Pseudogymnoascus) destructans


previous item | next item

Citation
Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces(Pseudogymnoascus) destructans

Material Information

Title:
Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces(Pseudogymnoascus) destructans
Series Title:
American Society for Microbiology Journals
Creator:
Chibucos, Marcus C
Crabtree, Jonatha
Nagaraj, Sushma
Chaturvedi, Sudha
Chaturvedi, Vishnu
Publication Date:
Language:
English

Subjects

Subjects / Keywords:
Geomyces Pannorum ( local )
Dichotomy ( local )
Proteins ( local )
Genomes ( local )
Saprobic And Pathogenic Attributes ( local )
Genre:
serial ( sobekcm )

Notes

Abstract:
We report the draft genome sequences of Geomyces pannorum sensu latoand Geomyces (Pseudogymnoascus) destructans. G. pannorum has a larger proteome than G. destructans, containing more proteins with ascribed enzymatic functions. This dichotomy in the genomes of related psychrophilic fungi is a valuable target for defining their distinct saprobic and pathogenic attributes.
Original Version:
American Society for Microbiology Journals, Vol. 1, no. 6 (2013-11-03).

Record Information

Source Institution:
University of South Florida Library
Holding Location:
University of South Florida
Rights Management:
This object is protected by copyright, and is made available here for research and educational purposes. Permission to reuse, publish, or reproduce the object beyond the bounds of Fair Use or other exemptions to copyright law must be obtained from the copyright holder.
Resource Identifier:
K26-00082 ( USFLDC: LOCAL DOI )
k26.82 ( USFLDC: LOCAL Handle )

USFLDC Membership

Aggregations:
University of South Florida
Karst Information Portal

Postcard Information

Format:
serial

Downloads

This item is only available as the following downloads:


Full Text

PAGE 1

DraftGenomeSequencesofHumanPathogenicFungus Geomyces pannorumSensuLato andBatWhiteNoseSyndromePathogen Geomyces ( Pseudogymnoascus ) destructans MarcusC.Chibucos ,a,b JonathanCrabtree ,a SushmaNagaraj ,a SudhaChaturvedi ,c,d VishnuChaturvedi c,dInstituteforGenomeSciences,UniversityofMarylandSchoolofMedicine,Baltimore,Maryland,USAa;DepartmentofMicrobiologyandImmunology,Universityof MarylandSchoolofMedicine,Baltimore,Maryland,USAb;MycologyLaboratory,WadsworthCenter,NewYorkStateDepartmentofHealth,Albany,NewYork,USAc; DepartmentofBiomedicalSciences,SchoolofPublicHealth,UniversityatAlbany,Albany,NewYork,USAdWereportthedraftgenomesequencesof Geomycespannorumsensulato and Geomyces(Pseudogymnoascus)destructans . G.pannorum hasalargerproteomethan G.destructans ,containingmoreproteinswithascribedenzymaticfunctions.ThisdichotomyinthegenomesofrelatedpsychrophilicfungiisavaluabletargetfordeÞningtheirdistinctsaprobicandpathogenicattributes. Received 3November2013 Accepted 26November2013 Published 19December2013 Citation ChibucosMC,CrabtreeJ,NagarajS,ChaturvediS,ChaturvediV.2013.Draftgenomesequencesofhumanpathogenicfungus Geomycespannorumsensulato andbat whitenosesyndromepathogen Geomyces ( Pseudogymnoascus ) destructans .GenomeAnnounc.1(6):e01045-13.doi:10.1128/genomeA.01045-13. Copyright ©2013Chibucosetal.Thisisanopen-accessarticledistributedunderthetermsofthe CreativeCommonsAttribution3.0Unportedlicense . AddresscorrespondencetoMarcusC.Chibucos,mchibucos@som.umaryland.edu,orVishnuChaturvedi,vishnu@wadsworth.org. G eomycespannorum isasoil-dwellingfunguscommonin colderpartsoftheworld( 1–3 ). G.pannorum israrelyimplicatedinthehumandiseasegeomycosis,whichmanifestsasskin andnailinfections( 4–6 ). Geomycesdestructans istheetiologic agentofbatgeomycosisorwhitenosesyndrome(WNS)( 7 , 8 ). G.destructans isrestrictedtocavesandminesintheUnitedStates andEurope( 9 , 10 ). G.pannorumsensulato representsaspecies complex,while G.destructans wasrecentlyreclassiedas Pseudogymnoascusdestructans ( 2 , 9 ).Astaxonomyisinastateofux, G.destructans and G.pannorum willbeusedastheorganism namesthroughoutthiswork.Bothfungiareadaptedtoapsychrophilicrange(4°to15°C)andexpressenzymesimplicatedinfungal virulence( 1 , 3 , 8 , 11 ).Thestudyofthebiologyandpathogenicity ofpsychrophilicfungiisinitsinfancyduetoalackofexperimental tools.Thisisalsotrueforothereukaryotesinhabitingcolderparts oftheearth. GenomicDNAfrom G.pannorum M1372and G.destructans M1379wasobtainedbyphenol-chloroformextractionofpulverizedfungalmycelia.TheIlluminaHiSeq2000wasusedfor 100-basepaired-endsequencing.Theassembliesweregeneratedusingfourprograms,subsampling89millionreadsfor G.pannorum and88millionreadsfor G.destructans .Optimal assembliesrepresenting100 coveragefor G.pannorum and 150 coveragefor G.destructans weregeneratedwith MaSuRCAversion1.9.2( 12 ).The G.pannorum assemblyis 29.47Mb,withaG Ccontentof50.5%,andcomprises856 scaffoldsranginginlengthfrom300basesto839kb(average, 34.4kb;median,7.9kb;N50,105kb). G.destructans is 30.49Mb,withaG Ccontentof49.8%,andwasassembled into5,008scaffoldsoflength108basesto234kb(average, 6.1kb;median,1.8kb;N50,19.2kb).Fifty-twopercentofthe G.destructans referenceDNAsharessimilaritywith G.pannorum queryDNA,with45%ofitbeingidentical.Acustom ab initio genepredictionpipelinegenerated9,689 G.pannorum proteinsand7,967 G.destructans proteins.Thedifferencein thecodingdensity,whichis48%for G.pannorum and37%for G.destructans ,isattributabletothesmallernumberofproteins andnumerousrepeats(25.8%ofthegenome)in G.destructans thanin G.pannorum (5.40%repeats).CEGMApredicted 96.7%ofthe458conservedgenesin G.destructans and98.3% in G.pannorum ( 13 ).FunctionalannotationwithBLAST againstUniProt( 14 )andHMMsearchesagainstTIGRfams/ Pfams( 15 , 16 )yieldedGeneOntologyannotations( 17 )for 62.3%ofthe G.destructans proteinsand63.1%ofthe G.pannorum proteins.ECassignmentsweregivento2,052 G.destructans proteins(25.8%)and2,734 G.pannorum proteins (28.2%).Thus, G.pannorum containsmoreproteinsthan G.destructans ,includingmorewithascribedenzymaticfunctions.Thisdichotomyinthegenomesofrelatedpsychrophilic fungiisavaluabletargetfordeningtheirdistinctsaprobicand pathogenicattributes. Nucleotidesequenceaccessionnumbers. The G.(Pseudogymnoascus)destructans whole-genomeshotgunprojecthas beendepositedatDDBJ/EMBL/GenBankundertheaccession no. AYKP00000000 .Theversiondescribedinthispaperis AYKP01000000.The G.pannorum whole-genomeshotgunprojecthasbeendepositedatDDBJ/EMBL/GenBankundertheaccessionno. AYKR00000000 .Theversiondescribedinthispaperis AYKR01000000.ACKNOWLEDGMENTSThisstudywaspartlysupportedwithfundsfromtheNationalScience Foundation(toV.C.andS.C.).FurthersupportcamefromOwenWhite, InstituteforGenomeSciences(IGS),Baltimore,MD. WearegratefultoMichelleGiglio,AnupMahurkar,andOwenWhite ofIGSforgenerousaccesstothecomputationalinfrastructure,andto JoshuaOrvisforrunningthefunctionalannotationpipeline. GenomeAnnouncements November/December2013Volume1Issue6e01045-13 genomea.asm.org 1

PAGE 2

REFERENCES1. MarshallWA. 1998.Aerialtransportofkeratinaceoussubstrateanddistributionofthefungus Geomycespannorum inAntarcticsoils.Microb. Ecol. 36: 212–219. 2. deHoogGS,GuarroJ,GenéJ,FiguerasMJ. 2009.Atlasofclinicalfungi, 3rdedition(pilotversion).CBS/UniversitatRoviraiVirgli,Utrecht,the Netherlands. 3. KochkinaGA,IvanushkinaNE,AkimovVN,Gilichinski DA,OzerskaiaSM. 2007.Halo-andpsychrotolerant Geomyces fungifromArctic cryopegsandmarinedeposits.Mikrobiologiia 76: 39–47.(ArticleinRussian.) 4. Christen-ZaechS,PatelS,ManciniAJ. 2008.Recurrentcutaneous Geomycespannorum infectioninthreebrotherswithichthyosis.J.Am.Acad. Dermatol. 58: S112–S113. 5. GianniC,CarettaG,RomanoC. 2003.Skininfectiondueto Geomyces pannorum var. pannorum .Mycoses 46: 430–432. 6. ZelenkováH. 2006. Geomycespannorum asapossiblecausativeagentof dermatomycosisandonychomycosisintwopatients.ActaDermatovenerol.Croat. 14: 21–25. 7. BlehertDS,HicksAC,BehrM,MeteyerCU,Berlowski-ZierBM, BucklesEL,ColemanJT,DarlingSR,GargasA,NiverR,Okoniewski JC,RuddRJ,StoneWB. 2009.Batwhite-nosesyndrome:anemerging fungalpathogen?Science 323: 227.doi: 10.1126/science.1163874 . 8. ChaturvediV,SpringerDJ,BehrMJ,RamaniR,LiX,PeckMK,RenP, BoppDJ,WoodB,SamsonoffWA,ButchkoskiCM,HicksAC,Stone WB,RuddRJ,ChaturvediS. 2010.Morphologicalandmolecularcharacterizationsofpsychrophilicfungus Geomycesdestructans fromNew Yorkbatswithwhitenosesyndrome(WNS).PLoSOne 5: e10783.doi: 10 .1371/journal.pone.0010783 . 9. MinnisAM,LindnerDL. 2013.Phylogeneticevaluationof Geomyces and alliesrevealsnocloserelativesof Pseudogymnoascusdestructans ,comb. nov.,inbathibernaculaofeasternNorthAmerica.FungalBiol. 117: 638–649. 10. PuechmailleSJ,WibbeltG,KornV,FullerH,ForgetF,MühldorferK, KurthA,BogdanowiczW,BorelC,BoschT,CherezyT,DrebetM, GörfölT,HaarsmaAJ,HerhausF,HallartG,HammerM,JungmannC, LeBrisY,LutsarL,MasingM,MulkensB,PassiorK,StarrachM, WojtaszewskiA,ZöphelU,TeelingEC. 2011.Pan-Europeandistributionofwhite-nosesyndromefungus( Geomycesdestructans )notassociatedwithmassmortality.PLoSOne 6: e19167.doi: 10.1371/journal.pone. 0019167 . 11. MarchisioVF,FusconiA,RigoS. 1994.Keratinolysisanditsmorphologicalexpressioninhairdigestionbyairbornefungi.Mycopathologia 127: 103–115. 12. ZiminAV,MarçaisG,PuiuD,RobertsM,SalzbergSL,YorkeJA. 2013. TheMaSuRCAgenomeassembler.Bioinformatics 29: 2669–2677. 13. ParraG,BradnamK,KorfI. 2007.CEGMA:apipelinetoaccurately annotatecoregenesineukaryoticgenomes.Bioinformatics 23: 1061–1067. 14. UniProtConsortium. 2013.UpdateonactivitiesattheUniversalProtein Resource(UniProt)in2013.NucleicAcidsRes. 41: D43–D47.doi: 10.109 3/nar/gks1068 . 15. PuntaM,CoggillPC,EberhardtRY,MistryJ,TateJ,BoursnellC,Pang N,ForslundK,CericG,ClementsJ,HegerA,HolmL,Sonnhammer EL,EddySR,BatemanA,FinnRD. 2012.ThePfamproteinfamilies database.NucleicAcidsRes. 40: D290–D301. 16. HaftDH,SelengutJD,WhiteO. 2003.TheTIGRfamsdatabaseofproteinfamilies.NucleicAcidsRes. 31: 371–373. 17. GeneOntologyConsortium,BlakeJA,DolanM,DrabkinH,HillDP, LiN,SitnikovD,BridgesS,BurgessS,BuzaT,McCarthyF,Peddinti D,PillaiL,CarbonS,DietzeH,IrelandA,LewisSE,MungallCJ, GaudetP,ChrisholmRL,FeyP,KibbeWA,BasuS,SiegeleDA, McIntoshBK,RenfroDP,ZweifelAE,HuJC,BrownNH,TweedieS, Alam-FaruqueY,ApweilerR,AuchinchlossA,AxelsenK,BelyB, BlatterM-,BonillaC,BouguerleretL,BoutetE,BreuzaL,BridgeA, ChanWM,ChavaliG,CoudertE,DimmerE,EstreicherA,Famiglietti L,FeuermannM,GosA,Gruaz-GumowskiN,etal. 2013.Geneontologyannotationsandresources.NucleicAcidsRes. 41: D530–D535.doi: 10.1093/nar/gks1050 .Chibucosetal. GenomeAnnouncements 2 genomea.asm.org November/December2013Volume1Issue6e01045-13


printinsert_linkshareget_appmore_horiz

Download Options

close


  • info Info

    There are only PDFs associated with this resource.

  • link PDF(s)



Cite this item close

APA

Cras ut cursus ante, a fringilla nunc. Mauris lorem nunc, cursus sit amet enim ac, vehicula vestibulum mi. Mauris viverra nisl vel enim faucibus porta. Praesent sit amet ornare diam, non finibus nulla.

MLA

Cras efficitur magna et sapien varius, luctus ullamcorper dolor convallis. Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Fusce sit amet justo ut erat laoreet congue sed a ante.

CHICAGO

Phasellus ornare in augue eu imperdiet. Donec malesuada sapien ante, at vehicula orci tempor molestie. Proin vitae urna elit. Pellentesque vitae nisi et diam euismod malesuada aliquet non erat.

WIKIPEDIA

Nunc fringilla dolor ut dictum placerat. Proin ac neque rutrum, consectetur ligula id, laoreet ligula. Nulla lorem massa, consectetur vitae consequat in, lobortis at dolor. Nunc sed leo odio.