1/23/2018
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CASSAVAGENOME.ORG
Anestis GKANOGIANNIS
CIAT
CASSAVA FACTS
•Manihot esculenta Crantz (aka Cassava, Yuca, Manioc) •Feeds >500M
•rich in carbohydrates (85 %) •low in fat and proteins
•moderate levels of vitamins of Group B, vitamin C, potassium, magnesium, calcium, iron
•Industrial used for •starch (paper, wood, textiles, etc.) •bakery and food industry (flour, sweeteners, etc.) •ethanol (biofuel, distilleries) •livestock (pellets, leaves)
•Some other available resources •Phytozome (https://phytozome.jgi.doe.gov) •Cassavabase (https://cassavabase.org) •Cassava Genome Database (http://cassava.igs.umaryland.edu) •China Cassava Genome Database (http://www.cassava-genome.cn)
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CASSAVAGENOME.ORG – WHAT IT IS
• A web portal collecting Data and Tools for Cassava
• Targets around Cassava genetic research and gene discovery
• Data available
•Public published studies •Private and/or unpublished studies •Genomic, Transcriptomic, Phenotypic,
Metabolomic • Tools available •Searching/querying •Visualization •Analysis 4
CASSAVAGENOME.ORG – ARCHITECTURE
•Based on the Content Management System (CMS) Drupal with the Tripal module that interacts with the Chado database.
•Integration of other GMOD components and other tools underlying the hub, such as JBrowse, SNiPlay, Gigwa, Pathway Tools, CMAP Galaxy etc.
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CASSAVAGENOME.ORG – DATA
Status Type Technology Description Publication Samples Tools
public genomic WGS assembly/annotation V6 Prochnik et al, 2012 1 JBrowse, GeneSearch
public genomic WGS genetic variants Bredeson et al, 2016 61 JBrowse, SNiPlay, Gigwa
public genomic WGS genetic variants Ramu et al, 2017 241 JBrowse, SNiPlay, Gigwa
public genomic GBS genetic variants Soto et al, 2015 135 SNiPlay
private genomic WGS genetic variants CIAT in progress 45 JBrowse, SNiPlay, Gigwa
private genomic RADSeq genetic variants CIAT in progress 1300 JBrowse, SNiPlay, Gigwa
public transcript RNASeq response to Xanthomonas Munoz-Bodnar et al, 2014 12 (6*2) JBrowse, DiffExDB, daTALbase
public transcript RNASeq response to Xanthomonas Cohn et al, 2014 36 (12*3) JBrowse, DiffExDB, daTALbase
public transcript RNASeq gene expression atlas in tissues Wilson et al, 2017 33 (11*3) DiffExDB
public transcript RNASeq response to CBSD Maruthi et al, 2014 4 DiffExDB
public transcript RNASeq W14, KU50, ARG7 transcriptome Wang et al, 2014 12 (3*4) DiffExDB
public transcript RNASeq cold and drought stresses Wang et al, 2014 9 (3*3) DiffExDB
public transcript RNASeq response to mealybugs Wang et al, 2014 18 (6*3) DiffExDB
private transcript RNASeq response to White Fly in progress 16 (8*2) DiffExDB
private transcript RNASeq response to Xanthomonas (E. Ramirez) in progress 9 (3*3) DiffExDB, daTALbase
private transcript RNASeq response to Xanthomonas (R. Mora) in progress 15 (5*3) DiffExDB, daTALbase
public genomic GBS genetic map / markers Soto et al, 2015 16 (8*2) Quigmap
public genomic GBS QTL Soto et al, 2017 16 (8*2) Quigmap
public phenotypic GBS pest resistance (White fly, Green mite, Thrips) Parsa et al, 2014 477 PathostDB
public phenotypic GBS resistance to Xanthomonas Trujillo et al, 2014 90 (9*10) PathostDB
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7CASSAVAGENOME.ORG – TOOLS (SEARCHING)
TALs
targets
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CASSAVAGENOME.ORG – TOOLS (VISUALIZATION)
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CASSAVAGENOME.ORG – TOOLS (ANALYSIS)
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