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If I want to determine if a single strain or a mix of strains of myrtle rust is responsible for the incursion of this fungal disease to Australia, should I use Next-Gen seq or RNA-seq or even RT-PCR?
This disease is hypothesised to be just one strain when first arrived in NSW and later spread into four states and has a wide host range on native plants in the Myrtaceae, and so the population of the fungus across Australia should be identical having propagated from that original strain.
As for controls, should I use the strains from NSW as a standard? what other key control will be important? Do I need to do a normalisation strategy using housekeeping genes?
RNA-seq is a sub-type of "Next gen" seq.
This sounds a lot like a homework assignment...