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Biocuration:DecipheringthedraftgenomeofAsianCitrusPsyllidonegeneatatime
PrashantSHosmani,MirellaFlores-Gonzalez,TomD’elia,WayneHunter,InternationalPsyllidAnnotationConsortium,SusanBrown,
BoyceThompsonInstitute,Ithaca,NY
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Acknowledgements
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Genome Annotation
Targetforinterdictionmolecules
IdentificationoftargetsforinterdictionwithOmicsisdependentongenomeandannotation
quality.
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D.citri genomev1.1highlyfragmentedandmisassembledgenome
Source Library Count
Illumina Paired-end 99.7millIllumina 2kbMate-pair 35.1millIllumina 5kbMate-pair 30millIllumina 10kbMate-pair 30millPacbio 2.7mill
Genome Diaci1.1
Contigs 161,988TotalLength 485MbLongest 1,098,238Shortest 201Ns 19,337,167
Dataavailability:www.Citrusgreening.org andAgDataCommonshttps://data.nal.usda.gov/dataset/diaphorina-citri-genome-assembly-diaci-11_3494
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ComprehensiveMCOTtranscriptome
Dataavailability:www.Citrusgreening.org (BlastandFTP)andAgDataCommonshttps://data.nal.usda.gov/dataset/diaphorina-citri-mcot-transcriptome_3495
MCOT
MAKER Cufflinks
Oases Trinity
Denovotranscriptome
Genome-basedannotation
MCOT v1.0 set has 30,562 proteins
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MCOTtranscriptomecontainsmoresinglecopygenemarkers
Annotation assessment using BUSCO v2 with 1066 single copy markers from Arthopoda.
MCOT v1.0 contains 1039/1066 (97.5%) complete BUSCO
PreprintSaha etalbiorxiv.org
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GenomeAnnotationpipeline
AutomatedAnnotationPipeline
StructuralannotationMAKERandNCBIgenomeannotationpipelines
Functionalannotation
Manualcuration
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ManualcurationworkflowOrthologs
Structural assessment
GenomesearchviaBlastandBLAT
Structural curation ofgenemodel
Qualitycontrolandreview
Functional curationGenereportPeerreviewFinalreport
Multiplesequence alignment
Identifyconserved domains MCOTv1.0transcriptome
OfficialGeneSet(OGS)Validatestructural features,namingconventionand
descriptions
Ortholog fromrelatedspeciesApolloGenomeAnnotationEditori5kWorkspace@NALhttps://i5k.nal.usda.gov
Phase1- 530 genescuratedin
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Manuallycuratedgenesshowimprovedgenestructure
AnnotationEditDistance(AED)measurescongruenceofapredictedgenemodelwiththeRNAseqevidencesupportingit.AEDscoresrangebetween0and1,0=>perfectsupportingevidence1=>lackofanysupportingevidence
0%
10%
20%
30%
40%
50%
60%
70%
NCBIv100 Curated MAKER MCOT_mapped
Percentageofgeneswith<0.5AEDscore
PreprintSaha etalbiorxiv.org
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ReducedimmunepathwayinD.citri
Arpetal.2016Front.PhysiolPreprintSaha etalbiorxiv.org
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PreprintatbioRxiv andunderreview
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ImprovedGenomeDiaci v1.9.NowAvailable!
70XcoveragewithPacbio
Poster- P7.1SuryaSaha
Genomeversions Diaci v1.1 Diaci v1.9
Numberofcontigs 161,988 8,352
Totalbases 485Mb 591.7MbLongest 1,098,238bp 2,096,698bp
Shortest 201 bp 1,547bp
Averagelength 2,998bp 70,849bp
N50 34,407bp 92,630bpN’s 19,337,167 0
Dataavailability:www.Citrusgreening.org (BLASTandFTP)andAgDataCommonshttps://data.nal.usda.gov/dataset/diaphorina-citri-genome-assembly-diaci-19_3496
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Available tools:Host, Vector and Pathogen(s)Blast DatabasesJbrowse – Genome BrowserMetabolic Pathway DatabasesFTP siteNews, Publications, LinksSocial Media
New tool availablePsyllid Expression Network (PEN)
Poster- P9.2Mirella
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Expressioncube Expressionimages
Psyllid Expression Network (PEN)Poster- P9.2Mirella
Gene
s
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Summary
• Genomicresourceswillenablefasterandmoreaccuratetargetdiscovery.
• ComprehensiveMCOTtranscriptomeisanalternativetotheexistinggenomicannotations.
• UndergraduateandcommunitybasedmanualcurationhasimprovedD.citri annotationfor530genes.
• Improvedgenomeassembly(Diaci v1.9)isavailable.
• www.CitrusGreening.org,a systemsbiologyresource
• PEN - PsyllidExpressionNetworktovisualizeexpressionpatterns
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Thankyou!Pleaseprovidefeedbackandnominategenesfor
manualcurationathttps://citrusgreening.org/contact/form
