Cataloging computationally putative resistance genes in grape and
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“ “ Cataloging Computationally Cataloging Computationally Putative Resistance Genes in Putative Resistance Genes in Grape and Their Grape and Their Corresponding Pathogenicity Corresponding Pathogenicity Genes” Genes” Bioinformatics Project Bioinformatics Project Dr. Yaqoub Ashhab Dr. Yaqoub Ashhab Amer Wazwaz & Murad Shneawer Amer Wazwaz & Murad Shneawer 26/5/2011 26/5/2011
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Transcript of Cataloging computationally putative resistance genes in grape and
““Cataloging Computationally Cataloging Computationally Putative Resistance Genes in Putative Resistance Genes in
Grape and Their Grape and Their Corresponding Pathogenicity Corresponding Pathogenicity
Genes”Genes”Bioinformatics ProjectBioinformatics Project
Dr. Yaqoub AshhabDr. Yaqoub Ashhab
Amer Wazwaz & Murad Shneawer Amer Wazwaz & Murad Shneawer
26/5/201126/5/2011
OutlineOutline
IntroductionIntroduction
ObjectivesObjectives Pathogenicity GenesPathogenicity Genes
Resistance GenesResistance Genes
Project’s ProcedureProject’s Procedure
Real ExamplesReal Examples
IntroductionIntroduction
Gene-for-gene theory
Multipotent genes
Patho-systems resemblance projection
Systemic Acquired Resistance SAR Phytolexins
Regulator of Pathogenicity Factor rpf gene
Project’s Procedure
Searching main pathogenicity genes in Arabidopsisthaliana main pathogens Pathogen Model
Searching main resistance genes in Arabidopsis thaliana Host Model
Cataloging them according to importance
BLAST these genes’ with raw genomes’ data
Real Examples (1)Real Examples (1)
rpfF
Xylella fastidiosa subsp Temecula1
Gene ID: 1144610
Xylella fastidiosa subsp. fastidiosa
complete genome
ACCESSION CP002165
Xylella fastidiosa
Real Examples (2)Real Examples (2)
virB2
Agrobacterium tumefaciens
Gene ID: 1224319
Agrobacterium vitis
complete sequence NC_011988.1 :
Accession
Agrobacterium vitis
Agrobacterium vitis
2 .Resistance Genes
Computationally verifying resistance genes in Vitis vinifera based on
Arabidopsis Thaliana .
NCBI and tair Databases .
WHY Arabidopsis Thaliana as a model plant small genome only 157 Mbp .small genome only 157 Mbp .
Useful genetic mapping and Useful genetic mapping and SequencingSequencing
Rapid and Small life cycle .Rapid and Small life cycle .
well suited for light microscopy analysiswell suited for light microscopy analysis
Search for Resistance Genes in Arabidopsis Thaliana
1. PR5 (Gene ID: 843842) CDS
PR5 v.s Vitis vinifera
82% identity in Vitis vinifera
Vitis vinifera PR5 v.s CDS identity 82%
2 .NPR1 (Gene ID: 842733) CDS
Blast NPR1 v.s Vitis vinifera
NPR1 V.S 72 % Vitis vinifera
3 .Blast RPS4 Gene ID ( 834561) CDS V.S Vitis vinifera
83%Vitis vinifera RPS4 V.S
