I have come across certain papers where ITS-2 is claimed as the standard DNA barcode gene. Apart from ITS-2 is there any other gene which can be used? If yes, why so? I am enclosing one such publication with my question to clarify my point.
It seems that the method done by Chem et al. (2010) in the given research article suggests that the ITS2 region of the plant genome has a high success rate of correct identification of a plant and differentiating closely related species. But given that the identification of a very specific locus of genes that will become the standard or "bench-mark" identifier of medicinal plants, as I would think, is still an emerging method. If we would think of the huge pool of genes that are not yet investigated it would be too hasty to fully suggest that the ITS2 region of the plant's DNA is the ultimate "bar code identifier" of a certain medicinal plant. It would be better to consider investigating other loci of genes that can even have a better accuracy of predicting the correct taxa/species of the medicinal plant. Also it would be wise to consider the other regions of the DNA so that various DNA sequences can be utilized as multiple evidences to prove the identity of the plant species. In the future, the improved method by Chen et al. may actually be a crucial step in the identification of medicinal plants but as in any science exhaustive reevaluation and re-investigation of the research results is a must in order to establish the validity and accuracy of the new method. Still, I reiterate the importance of multiple evidence/data for the unambiguous identification of a plant species.
There are some publications on DNA barcoding of orchids (check, e.g. Google Scholar). I suppose it is best to use the same markers otherwise one needs to build the barcode library anew.
The official CBOL DNA barcoding genes for plants are matK and rbcL (both plastid). These will probably not get you to the species level, so if you need exact species identification you may have to add in ITS (nrDNA) or psbA-trnH (plastid), and possibly others. You might also want to check out genes that have been used previously for phylogeny reconstruction in your taxon of interest.
Check out the CBOL website for more information http://www.barcodeoflife.org/
Use google scholar to find phylogenies of your taxon of interest.
Dear all
The problem with plants is that Kew and the Missouri are not agree to define a set of barcode genes.
The complete ITS region (ITS1, 5.8 RNA and ITS2) combine with matK is may be a reasonable equilibrium between easiness and information....but on orchids....take care they are very recent species the resolution will surely not be very good.
Cheers from Luc
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