I am having plan to do gene expression analysis on plant under abiotic stress threat. However, there is no data about its genome or gene sequence of that, even in NCBI. How can I design primer to amplify my candidate genes if I dont even know its gene sequence? Can I use ETS sequence from closest phylogeny organism?
Yes that's how I would start. First use NCBI Taxonomy browser with your species name and targeted gene to find which closely related species have available sequences for that gene. Once done align all the sequences (10-15 should do). Then try to design degenerate primers, it usually works, but go well below the calculated Tm when you perform the PCR.
Yes that's how I would start. First use NCBI Taxonomy browser with your species name and targeted gene to find which closely related species have available sequences for that gene. Once done align all the sequences (10-15 should do). Then try to design degenerate primers, it usually works, but go well below the calculated Tm when you perform the PCR.
Beside what Hogo mentioned, there are a few methodologies for finding out which genes may be up or down regulated upon stresses, such as differential displays and microarrays. Such experiments have been done long time ago toward many important host-stress interactions.
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