I would like to make a molecular survey of chytrids or oomycetes possibly infecting my diatom cultures. Does anyone know about as specific as possible primers to do that (for each group separately, of course)?
Dear Maria Valeria,
I would strongly recommend to use one of the most commonly used marker genes cox2 or ITS (cox1 might also be helpful) so you will be able to identify your organisms to species level. Unfortunately, the cox2 primers developed by Hudspeth et al. 2000 have the problem to also amplify diatoms so it might be useful to check the primers with sequence information from Genebank first and change the sequence to exclude diatoms. Or you try ITS (Dc6 - Cooke et al. 2000, LR0 - reverse complement to LR0R (Moncalvo et al., 1995)). But I never checked ITS for specificity within the Stramenopiles so diatoms might also be amplified.
Good luck
Thank you all of you for your kind suggestions and particularly thanks to Sebastian. I will check if a cox sequence is already available for my diatom species in GB (and otherwise I have to generate it) and check the primers. I will also check the ITS primers you suggest. Thank you again!
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