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Background: Earlier, we successfully worked on two plant DNA barcode projects, one genera specific and the other one involving tree species from a province. In recent efforts, we are leading a consortium of six institutes of the Council of Scientific and Industrial Research to barcode plant species across India, where each institute is focusing on a respective phytogeographic location. As a part of this project, CSIR-NBRI is involved in DNA barcoding of a wild life sanctuary, Govind Wildlife Sanctuary, in the west Himalayan state of Uttarakhand. Results: We have collected 238 angiosperms, 270 bryophytes, 255 pteridophytes, 265 lichens, and 154 algae species from the sanctuary, spanning a wide climatic range, mainly due to a steep altitudinal gradient (1300-6315 m.a.s.l.). So far we have analyzed 178 accessions of angiosperm plants from this hot spot using the four standard plant barcode loci. MatK was not used further after initial failure in PCR amplifications. PCR success ranged from 88% to 95%, trnH-psbA being the lowest and rbcL being the highest. ITS exhibited the lowest rate of sequencing success, while trnH-psbA exhibited the highest. ITS and trnH-psbA exhibited 90% success in species identification. Among the non-flowering plants, 75 accessions of lichen have been analyzed using ITS. PCR and sequencing success was 75% and 80%, respectively. Contamination with other fungi was a major problem faced during sequencing of lichen samples. Barcoding of other lower group of plant species from this region will be carried out in the near future. Under the consortium, our main aim is to develop a plant barcode data base of high-value medicinal plants. Significance: Barcoding the flora, including a lower group of plant species of a particular hot spot, spanning a wide range of climatic zones, will certainly impact on conservation, policy making, and environmental protection by different government agencies. The study will also help test the efficacy in resolving species identification in a specific geographic region., Ref.: Genome, 58(5): 163-303 (2015) dx.doi.org/10.1139/gen-2015-0087. On page 273, the abstract entitled 'Plant barcoding of a wildlife sanctuary across a wide climatic zone, Uttaranchal, India' was printed without author corrections. [...]

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. [ABSTRACT FROM AUTHOR]

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.