There is a task to identify rapidly current variants of potyviruses in potato and tomato plants. What would yo recommend - NGS or Sanger method to make it faster? If NGS, what method shell we use for cDNA library?
Hey there,
the question is, on what base do you differentiate them? Do they have special genes/proteins to differentiate on? Then a PCR might be enough. If it is a single SNP or difference in a single genes activate site (for example) a Sanger sequencing might do the trick. If it is a combination of SNPs you are looking for, probably a PanelSequencing especially designed for this task might be the thing you are looking for. Do you have genes either expressed or not, you should probably try RNA-Sequencing.
Hope this helps.
Regards,
André
Hi,
I think you might use different methods according to your final goal, as André Marquardt was saying. Also I would say that "faster" does not mean better but if you would like to use a faster method NGS is the case. Is more costly, possibly, but has higher quality data in my opinion.
Did you have a look at the following material?
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104580
https://mra.asm.org/content/8/2/e01607-18
Article Plant Virology and Next Generation Sequencing: Experiences w...
https://dl.sciencesocieties.org/publications/tpg/abstracts/8/1/plantgenome2014.09.0058
Article RNA viromes of the oriental hybrid lily cultivar “Sorbonne”
Chapter Genome Sequencing of Capsicum Species: Strategies, Assembly,...
Best regards
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