title: The internal transcribed spacer (ITS) region and trnH-psbA [corrected] are suitable candidate loci for DNA barcoding of tropical tree species of India.
abstract: 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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: Genetics and Molecular Biology Division, Council for Scientific and Industrial Research-National Botanical Research Institute, Lucknow, Uttar Pradesh, India.
authors: Abhinandan Mani
authors: AM
authors: Tripathi
authors: Antariksh
authors: A
authors: Tyagi
authors: Anoop
authors: A
authors: Kumar
authors: Akanksha
authors: A
authors: Singh
authors: Shivani
authors: S
authors: Singh
authors: Lal Babu
authors: LB
authors: Chaudhary
authors: Sribash
authors: S
authors: Roy
mesh_terms: D001483:Base Sequence; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D021903:DNA, Ribosomal Spacer / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics*; D014644:Genetic Variation; D005843:Geography; D007194:India; D008969:Molecular Sequence Data; D010802:Phylogeny; D012015:Reference Standards; D017215:Satellite Communications; D013045:Species Specificity; D014197:Trees / Q000145:classification* / Q000235:genetics*; D014329:Tropical Climate
chemical_list: D021903:DNA, Ribosomal Spacer