Hi everybody,
I used universal primers to find the origin of plant or plants made material by insect and now I have a mixed PCR product of several plants. Is there a method to recognize all plant species?
Thanks in advance
Whatever happened to species-specific primers? See the attached for details. You could also do a DNA barcoding since you already used universal primers. DNA barcoding is a useful technique for the molecular identification of organisms. This technique uses PCR to amplify a fragment of the cytochrome oxidase I (COI) gene, which is then sequenced and compared to a database of known organisms. For plants, other genes such as rbcL and matK are commonly used for their barcoding identification. Plants represent a more complex barcoding problem than other eukaryotes (such as animals) because plant mitochondrial genomes have a low nucleotide substitution rate. It has been found that genes other than cytochrome oxidase I (COI) should be used for plant identification because there are not enough changes in the COI between 15 different plant groups. Various combinations of plant specific markers (rpoC1+rpoB+matK or rpoC1+matK+trnH-psbA; rbcL+trnH-psbA; atpF-H+psbKI+matK) can be used for plant barcoding.
Next-Gen sequencing is probably the cheapest option and the most likely to be publishable. Otherwise, you need to clone and sequence a LOT of PCR products to be confident you have found the majority of the sequences using DNA barcoding.
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