1. 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

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

3. M.Sc. Candidate (since Sept 2007) Dept. of Biology Carleton University
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. COI Pythium Phylogeny: Tree Top HalfK D A C B A B C

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 %
ITS COI

6. There are also analogies with functional genomics:
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:
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/sequencing and arrays
Quantify most important species affected
(RT)-qPCR

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

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

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

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. Simon Fraser University Student: Manuel Zahariev
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