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Background  DNA barcoding as a tool for species identification has been successful in animals and other organisms, including certain groups of plants. The exploration of this new tool for species identification, particularly in tree species, is very scanty from biodiversity-rich countries like India.  rbcL  and  matK  are standard barcode loci while ITS, and  trnH-psbA  are considered as supplementary loci for plants.    Methodology and Principal Findings  Plant barcode loci, namely,  rbcL ,  matK , ITS,  trnH-psbA,  and the recently proposed ITS2, were tested for their efficacy as barcode loci using 300 accessions of tropical tree species. We tested these loci for PCR, sequencing success, and species discrimination ability using three methods.  rbcL  was the best locus as far as PCR and sequencing success rate were concerned, but not for the species discrimination ability of tropical tree species. ITS and  trnH-psbA  were the second best loci in PCR and sequencing success, respectively. The species discrimination ability of ITS ranged from 24.4 percent to 74.3 percent and that of  trnH-psbA  was 25.6 percent to 67.7 percent, depending upon the data set and the method used.  matK  provided the least PCR success, followed by ITS2 (59. 0%). Species resolution by ITS2 and  rbcL  ranged from 9.0 percent to 48.7 percent and 13.2 percent to 43.6 percent, respectively. Further, we observed that the NCBI nucleotide database is poorly represented by the sequences of barcode loci studied here for tree species.    Conclusion  Although a conservative approach of a success rate of 60–70 percent by both ITS and  trnH-psbA  may not be considered as highly successful but would certainly help in large-scale biodiversity inventorization, particularly for tropical tree species, considering the standard success rate of plant DNA barcode program reported so far. The recommended  matK  and  rbcL  primers combination may not work in tropical tree species as barcode markers.

The Internal Transcribed Spacer (ITS) Region and trnhH-psbA Are Suitable Candidate Loci for DNA Barcoding of Tropical Tree Species of India