““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