community resources for all y’all omics
TRANSCRIPT
www.citrusgreening.org
Community resources for all y’all Omics
Prashant S Hosmani1, Mirella Flores-Gonzalez1, Jodi L Humann2, Dorrie Main2, Susan J. Brown3, Lukas Mueller1 and Surya Saha1
1Boyce Thompson Institute; 2Washington State University; 3Kansas State University
[email protected] @SahaSurya
IRCHLB 2017Orlando, FL
www.Citrusgreening.org
www.citrusgreening.org
Acknowledgements
Kansas State University
Sue Brown
USDA/ARS
Wayne Hunter
Mueller Lab Main Lab
www.citrusgreening.org
Identification of targets for interdiction with Omics requires better genomics resources
Genome Annotation
Target for interdiction molecules
Pathway DatabasesExpression Networks
…….
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Current ACP assembly is fragmented and contains misassemblies
Scaffold N50: 109,898 bp (includes Ns)
Contig N50: 34,407bp
Whitefly scaffold N50: 3.23 Mbp!!
Genome Diaci1.1
Contigs 161,988
Total Length 485 Mb
Longest 1,098,238 bp
Shortest 201 bp
Ns 19,337,167 bp
Preprint: http://biorxiv.org/content/early/2017/01/09/099168
www.citrusgreening.org
Example of misassembly P450 CYP3167A1, 2 and 5 genes in Diaci 1.1
Preprint: http://biorxiv.org/content/early/2017/01/09/099168
www.citrusgreening.org
Long read Pacbio sequencing
70X coverage
Reads up to 50kb!!
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Interim assembly Diaci v1.9 is more contiguous
Pacbio RS II
Poster 7.1
Genome versions
Diaci v1.1 Diaci v1.9
Number of contigs
161,988 8,352
Total bases 485 Mb 591.7 Mb
Longest 1,098,238 bp 2,096,698 bp
Shortest 201 bp 1,547 bp
Averagelength
2,998 bp 70,849 bp
N50 34,407 bp 92,630 bp
N’s 19,337,167 0
Data availability: www.Citrusgreening.org (BLAST and FTP) and Ag Data Commonshttps://data.nal.usda.gov/dataset/diaphorina-citri-genome-assembly-diaci-19_3496
www.citrusgreening.org
New technology will help resolve assembly from mixed sample
Dovetail for long range scaffolding
Haplotyping contigs with 10X linked reads BioNano optical maps for chromosomal length scaffolding
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Metabolic Pathway Database Construction
Annotated Genome
e.g. C sinensis, D citri
PathoLogic
Software
Reference Pathway
Database (MetaCyc)
Reactions
Pathways
Compounds
Gene
productsGenes
Pathway/Genome
Database (CitrusCyc, DiaphorinaCyc)
Source: Peter Karp (SRI)
Predicts metabolic pathways
Predicts which genes code for missing enzymes in metabolic pathways
Infers transport reactions from transporter names
www.citrusgreening.org
C sinensis Cyc
C. Sinensis : http://pathways.citrusgenomedb.org/organism-summary?object=CSINENSIS_MLC clementina : http://pathways.citrusgenomedb.org/organism-summary?object=CCLEMENTINA_MLDiaphorina : http://ptools.citrusgreening.org/DIAPHORINA/organism-summary
C clementina Cyc Diaphorina Cyc
CitrusGenomeDB Poster 3.7
Pathway databases available for YOU
www.citrusgreening.org
C sinensis Cyc v3.0 cellular overviewhttp://pathways.citrusgenomedb.org/organism-summary?object=CSINENSIS_ML
Cellular Overview
Secondary metabolite biosynthesis Membrane pathways
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http://pathways.citrusgenomedb.org/organism-summary?object=CSINENSIS_ML
C sinensis Cyc photosynthesis pathway
www.citrusgreening.org
http://pathways.citrusgenomedb.org/organism-summary?object=CSINENSIS_ML
Genes in photosynthesis pathway
www.citrusgreening.org
http://pathways.citrusgenomedb.org/organism-summary?object=CSINENSIS_ML
C sinensis Cyc v3.0
Photosynthesis pathway
www.citrusgreening.org
http://pathways.citrusgenomedb.org/organism-summary?object=CSINENSIS_ML
C sinensis Cyc v3.0
Photosynthesis pathway
www.citrusgreening.org
DiaphorinaCyc pathway database Cellular overview with RNAseq data
Cellular Overview of Diaphorina citri overlaid with RNAseq expression counts
Based on NCBI v100
Membrane proteins
Secretory proteins
Membrane proteins
Kruse et al. (unpublished)
http://ptools.citrusgreening.org/overviewsWeb/celOv.shtml
www.citrusgreening.org
Poster 9.2
CitrusGreening.org
Host, Vector and Pathogen(s)
Blast Databases
Metabolic pathway databases
Jbrowse genome browser
Psyllid Expression Network
FTP site
News
Publications
Social Media
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Thank you!
Please provide feedback and nominate genes for manual curation at https://citrusgreening.org/contact/form
Slides: http://bit.ly/IRCHLB2017
@SahaSurya
• Interim ACP genome assembly Diaci v1.9 is asignificant improvement over the current version.
• DiaphorinaCyc and CitrusCyc pathway databasesallow exploration and discovery of global patterns inexpression and biochemical pathways.