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Operated by Los Alamos National Security, LLC for the U.S. Department of Energy's NNSA
UNCLASSIFIED
Blake HovdeAlgae Biomass Summit
Oct 25th, 2016
Greenhouse: an omics resource for algal feedstocks
ABBB, June 2016
SEQUENCINGPLATFORMS/METHODS
Greenhouse 2
GREENHOUSE.LANL.GOV
ABBB, June 2016
• Buildfundamentalknowledgeofalgalbiology
• Informrationalegeneticengineering(andbreeding)strategies
• Cultivationdiagnostics,monitoring,cropprotection
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Whyisomicsdatauseful?
Greenhouse
ABBB, June 2016
• Curationof“Algal”omicsinformation
• Currentlythereisnosingleresourceforresearcherstoaccessalgalspecificomicsdata
• Combinesgenomicsinformationfrommultipleresources
• FunctionalityincludesBLASTsearchesagainstgenome-specificdatabases
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WhyisGreenhouseuseful?
Greenhouse
ABBB, June 2016
GREENHOUSE.LANL.GOV
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• Greenhouseisacentralizedwebsitetodisplayandsharesequence-baseddatarelevanttotheimprovementandadvancementofalgalbiofuelfeedstocks.
• Currentlyrepresentsover30publishedalgalspecies,whichisthelargestalgalgenomecollectionavailableonline
Wearealwayslookingtoaddmoregenomes!Greenhouse
ABBB, June 2016
• Foreachalga– Speciesinformation– Genomestats– Downloads– othermeta-databasedonavailability
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Analgalomicsresource
Greenhouse
ABBB, June 2016
• Abilitytohostpublishedorunpublishedspeciesspecificdata– Biomassandlipidprofiles,culturemonitoring(contamination)
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Collectingmetadata
Greenhouse
ABBB, June 2016
AlgalBLAST
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• BLASTandGenomeBrowsersforallalgalspeciesintheGreenhousedatabase
Greenhouse
ABBB, June 2016
• GenomebrowsingwithannotationvisualizationviaJbrowse
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Genomebrowsing
Greenhouse
ABBB, June 2016
AdditionalOmicsResources
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• Additionalomicsresourcesforalgalresearchers
Greenhouse
• Wearehappytoaddsuggestedresources!
ABBB, June 2016
SEQUENCINGPLATFORMS/METHODS
• Greenhouseutilizesausermanagementsystemwhichallowsgroupsofuserstoaccessprivatedatasets:
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UserManagementSystem
ABBB, June 2016
SEQUENCINGPLATFORMS/METHODS
• Currentinternalandexternalgenome/transcriptomecollaborations:– NREL– CUNY– LANL
• Genomes,annotationsandotheruploadeddatacanbehosted
• Notlimitedtogenomicdata
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UserManagementSystem– Privatedata
ABBB, June 2016
SEQUENCINGPLATFORMS/METHODS
Greenhouse 13
NRELGenomes
NNA 4C12 14F2
Quality Draft Draft Draft
Size(Mbp) 14.4 40.7 69.5
Contigs* 31 278 424
N50 1.1 Mb 617kb 781kb
Max 1.5 Mb 2.7Mb 3.3Mb
NRELGenomeProjectsdelivered
*>5kbpcutoff
ABBB, June 2016
Strain 1230 1230 1228 1412 1412v2 1412v3Quality Draft Improved
DraftImprovedDraft
HQDraft
ImprovedDraft
ImprovedDraft
Platforms Illumina Illumina+Pacbio
Opgen+Pacbio
Illumina PacBio PacBio +Illumina
Size 56.2Mb 59.7Mb 61Mb 59.3 57.6 57.8
Scaffolds/Chromosomes
N.D. N.D. 13/12 N.D. N.D N.D
Contigs 10042 22 64 5949 154 65
N50 10.8kb 3818 kb 2395kb 19.5kb 674 kb 2025 kb
Max 75kb 5.1Mb 4.56Mb 122kb 1.9Mb 5.4Mb
C.sorokinianaGENOMEIMPROVEMENTS
14Greenhouse
ABBB, June 2016 Greenhouse
SEQUENCINGPLATFORMS/METHODSPacBioSequencingImprovements
YuliyaKunde,ShawnStarkenburg
ABBB, June 2016
ASSEMBLYQUALITYMETRICS• BUSCODatasetscurrentlyavailable:
– Eukaryotes(429genes)– Fungi(~1300genes)– Bacteria,Vertebrates,Metazoans,Arthropods,Plants
• SpecieswithinaBUSCOdatabaseshouldhit>90%ofBUSCO’s
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BUSCO– BenchmarkingUniversalSingleCopyOrthologs
No“Algae”BUSCOyet!
Greenhouse
"Eukaryotic"BUSCOssearched:429C.sorokiniana1228 300 22 21 108C.sorokiniana1230 285 20 34 110C.sorokiniana1412 285 20 29 115ANC_14F2_NREL 278 18 43 108C.subellipsoideaC-169 273 17 54 102C.variabilis 270 15 42 117
ABBB, June 2016
SEQUENCINGPLATFORMS/METHODS
• Integrationofotheromicsdata:– Transcriptomics– Proteomics– Metagenomics
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AdditionalGreenhousefunctionality
ABBB, June 2016
PathwayCentricIntegrationofOmicsData
Greenhouse
ABBB, June 2016
SEQUENCINGPLATFORMS/METHODS
• CurrentlyutilizeQIIMEfor16Sculturediagnostics
• FutureimplementationofGOTTCHA– afastandaccuratestrainlevel identificationtool
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CultivationDiagnostics
PaulLi,PatrickChain
ABBB, June 2016 Greenhouse 20
FutureGreenhouseFeatures
INTEGRATEDOMICsPATHWAYVIEWERCULTIVATIONDIAGNOSTICS ALGALGENOME
ANNOTATIONPIPELINE
UTEXCultureCollection
PREDATORGENOMES
ABBB, June 2016
Multi-omicsPathwayViewer
Greenhouse
Integratedomicspathwayviewer
ABBB, June 2016
SEQUENCINGPLATFORMS/METHODS
• Websiteislive:publicaccessandaccountregistrationavailableat:GREENHOUSE.LANL.GOV
• Registeranaccount!– toseeallpublicallyavailablegenomes– Stayuptodateonnewfeatures
• Sendmissinggenomesornewgenomestome,BlakeHovde:[email protected]
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Summary
ABBB, June 2016
SEQUENCINGPLATFORMS/METHODS• Funding:DOE-BETO
• Websitesupport:YanXu,PaulLi,ShawnStarkenburg
• LANLSequencingandAssembly:YuliyaKunde,KarenDavenport
• GOTTCHA:PaulLi,PatrickChain
• Genomesequencing/assemblycollaborations:MichaelGuarnieri- NREL
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Acknowledgements
