“ Cataloging Computationally Putative Resistance Genes in Grape and Their Corresponding Pathogenicity Genes” Bioinformatic...
Outline <ul><li>Introduction </li></ul><ul><li>Objectives  </li></ul><ul><li>Pathogenicity Genes </li></ul><ul><li>Resista...
Introduction <ul><li>Gene-for-gene theory </li></ul><ul><li>Multipotent genes </li></ul><ul><li>Patho-systems resemblance ...
Project’s Procedure <ul><li>Searching main pathogenicity genes in  Arabidopsis </li></ul><ul><li>thaliana  main pathogens ...
Real Examples (1) rpfF   Xylella fastidiosa  subsp  Temecula1 Gene ID :  1144610   Xylella fastidiosa  subsp .  fastidiosa...
Xylella fastidiosa
Real Examples (2) virB2   Agrobacterium tumefaciens Gene ID :  1224319   Agrobacterium vitis complete sequence  NC_011988....
Agrobacterium vitis
Agrobacterium vitis
<ul><li>Computationally verifying resistance genes in Vitis vinifera based on Arabidopsis Thaliana . </li></ul><ul><li>NCB...
<ul><li>small genome only 157 Mbp . </li></ul><ul><li>Useful genetic mapping and Sequencing </li></ul><ul><li>Rapid and Sm...
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
 
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Cataloging computationally putative resistance genes in grape and

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Cataloging computationally putative resistance genes in grape and

  1. 1. “ Cataloging Computationally Putative Resistance Genes in Grape and Their Corresponding Pathogenicity Genes” Bioinformatics Project Dr. Yaqoub Ashhab Amer Wazwaz & Murad Shneawer 26/5/2011
  2. 2. Outline <ul><li>Introduction </li></ul><ul><li>Objectives </li></ul><ul><li>Pathogenicity Genes </li></ul><ul><li>Resistance Genes </li></ul><ul><li>Project’s Procedure </li></ul><ul><li>Real Examples </li></ul>
  3. 3. Introduction <ul><li>Gene-for-gene theory </li></ul><ul><li>Multipotent genes </li></ul><ul><li>Patho-systems resemblance projection </li></ul><ul><li>S ystemic A cquired R esistance SAR </li></ul><ul><li>Phytolexins </li></ul><ul><li>Regulator of Pathogenicity Factor rpf gene </li></ul>
  4. 4. Project’s Procedure <ul><li>Searching main pathogenicity genes in Arabidopsis </li></ul><ul><li>thaliana main pathogens Pathogen Model </li></ul><ul><li>Searching main resistance genes in Arabidopsis thaliana Host Model </li></ul><ul><li>Cataloging them according to importance </li></ul><ul><li>BLAST these genes’ with raw genomes’ data </li></ul>
  5. 5. Real Examples (1) rpfF Xylella fastidiosa subsp Temecula1 Gene ID : 1144610 Xylella fastidiosa subsp . fastidiosa complete genome ACCESSION CP002165
  6. 6. Xylella fastidiosa
  7. 7. Real Examples (2) virB2 Agrobacterium tumefaciens Gene ID : 1224319 Agrobacterium vitis complete sequence NC_011988.1 : Accession
  8. 8. Agrobacterium vitis
  9. 9. Agrobacterium vitis
  10. 10. <ul><li>Computationally verifying resistance genes in Vitis vinifera based on Arabidopsis Thaliana . </li></ul><ul><li>NCBI and tair Databases . </li></ul>2. Resistance Genes
  11. 11. <ul><li>small genome only 157 Mbp . </li></ul><ul><li>Useful genetic mapping and Sequencing </li></ul><ul><li>Rapid and Small life cycle . </li></ul><ul><li>well suited for light microscopy analysis </li></ul>WHY Arabidopsis Thaliana as a model plant
  12. 12. Search for Resistance Genes in Arabidopsis Thaliana
  13. 13. 1. PR5 ( Gene ID: 843842) CDS
  14. 14. PR5 v.s Vitis vinifera
  15. 16. 82% identity in Vitis vinifera
  16. 17. Vitis vinifera PR5 v.s CDS identity 82%
  17. 19. 2. NPR1 ( Gene ID: 842733) CDS
  18. 20. Blast NPR1 v.s Vitis vinifera
  19. 21. NPR1 V.S 72 % Vitis vinifera
  20. 22. 3. Blast RPS4 Gene ID ( 834561) CDS V.S Vitis vinifera
  21. 23. 83%Vitis vinifera RPS4 V.S

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