Hello,
I am working with a susceptible and a resistant line against a specific fungus. After inoculation, there is no fungal development in the resistant line, allowing me to extract RNA from the lesion site without issue. However, in the susceptible line, the fungus proliferates, and when I extract total RNA from the lesion, a substantial portion originates from the fungus, which I am not interested in sequencing. Is there a way to remove or reduce the fungal RNA, or should I simply increase the sequencing depth to obtain comparable results between the resistant and susceptible lines?
Thank you
This is a common challenge when studying host-pathogen interactions. Once fungal colonization occurs in the susceptible line, it's difficult to extract pure plant RNA from infected tissues. Unfortunately, there is no simple way to physically remove fungal RNA post-extraction.
If tissue dissection is not feasible, you might consider using plant-specific rRNA depletion kits rather than poly-A selection, which can reduce non-target RNA background. Alternatively, increasing sequencing depth and bioinformatically filtering out fungal reads by aligning to a reference genome is a practical and widely used solution.
For reagents, plant-specific rRNA depletion and RNA enrichment tools are available from providers like Thermo Fisher, Sigma-Aldrich, and BOC Sciences, all of which offer customizable options that can be adapted to mixed RNA samples from infected tissues.
Hope this helps.
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