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Old 05-18-2017, 12:02 PM   #3
ATϟGC
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Location: Canada

Join Date: Jun 2013
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As you have mentioned, plant DNA barcoding to the species level is rather imperfect to put it mildly. Incomplete lineage sorting and hybridization have led to the sharing of chloroplast haplotypes in many taxa. Even if you have complete chloroplast genomes species-level identification with DNA is not possible in many groups due to rampant haplotype sharing.

If you do not have very many sequences to identify and/or if the taxonomic range is small, it is probably preferable to use a cladistic approach to construct a phylogeny with closely related sequences. You could use sequences from your own custom reference library (e.g. species in your study area) or use sequences from a BLAST search. If you have a large number of sequences from a broad range of taxa you might want to use a more high-throughput method like the RDP-naive Bayesian classifier (Wang et al 2007) trained with your own custom database or some other sequence clustering method.
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