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I have chosen a medicinal plant from fabacea family and done barcoding using psbA trnfH primers. but i got 2 different amplicons for that particular primers . Can anyone please suggest me, your valuable comments.
if it is two clearly visible fragments, than either the primer sequences are not specific enough for the taxon or the annealing temperature is too low (assuming the PCR mix is appropriate). You could try a gradient PCR to check if more stringent temperatures will push the amplification towards one of the two fragments or try different primer.