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COI barcoding of oomycetes and the design of arrays for environmental samples

COI barcoding of oomycetes and the design of arrays for environmental samples. André Lévesque, Gregg Robideau and Wen Chen Biodiversity, AAFC and Biology Department, Carleton University. mycoparasites. pythiosis.

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COI barcoding of oomycetes and the design of arrays for environmental samples

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  1. COI barcoding of oomycetes and the design of arrays for environmental samples André Lévesque, Gregg Robideau and Wen ChenBiodiversity, AAFC andBiology Department, Carleton University

  2. mycoparasites pythiosis Lévesque, C.A., and de Cock, A.W.A.M. 2004. Molecular phylogeny and taxonomy of the genus Pythium. Mycol. Res. 108:1363-1383. Evolution of all the species of the genus Pythium (ITS and LSU) Arthur de Cock, CBS, Netherlands,collection of « ex-type » cultures mycoparasite Other species are in the saprophyte to facultative plant parasite spectrum

  3. Gregg Robideau M.Sc. Candidate(since Sept 2007) Dept. of Biology Carleton University • ~700 COI sequences of oomycetes obtained to date • Over 80 species of Pythium, 20 species of Phytophthora, and several other genera such as Achlya,Peronophythora, and Saprolegnia

  4. K D A C B A B C COI Pythium Phylogeny: Tree Top Half

  5. Pythium attrantheridium vs. P. intermedium • P. attrantheridium is a recently described species, closely related to P. intermedium • ITS sequence divergence between these two species is only 5% • COI sequence divergence is 2.5-4.4% ITS COI

  6. Identify Up and Down regulated genes. Some techniques:EST’s and arrays Quantify most important genes affected RT-qPCR Identify « Up and Down » regulated species. Some techniques:PCR/cloning/sequencingand arrays Quantify most important species affected (RT)-qPCR There is an analogy between barcoding marker gene(s) for all species and the sequencing all the genes of one species (genomics) There are also analogies with functional genomics:

  7. James T. Tambong, A.W.A.M. de Cock, N.A. Tinker, and C.A. Lévesque. 2006. Oligonucleotide array for identification and detection of Pythium species. Applied & Environmental Microbiology 72:2691-2706

  8. 13 Pythium species found by array hybridization Soil processing with Pythium ITS array

  9. Direct processing of environment samples -Comparing treatments Non-Compacted Compacted Non-Compacted Compacted 500 gallons tanks at the front and rear of tractor

  10. Spot intensities analyzed using Genepix Pro 3.0 software Chemiluminogrammes showing hybridization patterns in soil compaction experiments Non-compacted Soil Compacted Soil (4 years)

  11. Effect of soil compaction on populations of different Pythium species(hybridization signals of species-specific oligonucleotides spotted on DNA array)

  12. DNA arrays developed so far by our group • Pythium and Phytophthora – ITS • Fusarium – EF1 • Penicillium – Beta Tubulin • Apple, greenhouse and cranberry pathogens - ITS

  13. Design of COI array for Penicillium

  14. Signature Oligo (“Sigoli”) software developed for identifying unique sequence regions in large databases before using Array Designer Collaboration with Dr. Verónica Dahl, Department of computing sciences, Simon Fraser University Student: Manuel Zahariev

  15. Dr. Wen Chen

  16. Acknowledgements • NSERC and Genome Canada for financial support • Nicole Desaulniers and Rafik Assabgui for technical support

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