Which DNA barcode is best for identifying native plants? I'm currently using ITS and trnL, but I'm not getting enough resolution at the species level. For one plant, DNA amplified with both ITS and trnL gave completely different results when I ran BLASTn against the RefSeq plant genome database. Any advice would be appreciated.
There are plenty of options: ITS, rbcL, matK and trnL. Optimally you would want to include multiple barcodes due to this very issue. The continual development of reference databases is also an important consideration as they get more accurate over time. One option is to filter the reference database to include only native species.
Thanks Carl. I've used ITS and trnL and not getting good resolutions. Creating reference database is a good option I'll look at.
You could consider that ITS usually is great for species-level resolution but trnL is better for higher taxonomic levels. For native plants, usually combining 3 loci is often required to have an accurate id. trnH-psbA would be a good complement to use alongside ITS.
Thank you Behnam great advice. I used ITS but still getting multiple hits. Maybe trnL and ITS are not ideal barcode for Eucalyptus ID. I'll try trnH-psbA and see if it works.
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