Abstract
DNA barcoding enables precise identification of species from analysis of unique DNA sequence of a target gene. The present study was undertaken to develop barcodes for different species of the genus Dalbergia, an economically important timber plant and is widely distributed in the tropics. Ten Dalbergia species selected from the Western Ghats of India were evaluated using three regions in the plastid genome (matK, rbcL, trnH-psbA), a nuclear transcribed spacer (nrITS) and their combinations, in order to discriminate them at species level. Five criteria: (i) inter and intraspecific distances, (ii) Neighbor Joining (NJ) trees, (iii) Best Match (BM) and Best Close Match (BCM), (iv) character based rank test and (v) Wilcoxon signed rank test were used for species discrimination. Among the evaluated loci, rbcL had the highest success rate for amplification and sequencing (97.6%), followed by matK (97.0%), trnH-psbA (94.7%) and nrITS (80.5%). The inter and intraspecific distances, along with Wilcoxon signed rank test, indicated a higher divergence for nrITS. The BM and BCM approaches revealed the highest rate of correct species identification (100%) with matK, matK+rbcL and matK+trnH-psb loci. These three loci, along with nrITS, were further supported by character based identification method. Considering the overall performance of these loci and their ranking with different approaches, we suggest matK and matK+rbcL as the most suitable barcodes to unambiguously differentiate Dalbergia species. These findings will potentially be helpful in delineating the various species of Dalbergia genus, as well as other related genera.
Highlights
In DNA barcoding, the sequence of a short stretch of DNA is used for accurate species identification [1], supplementing the classical taxonomic methods [2]
We have evaluated 37 primer pairs from plastid and nuclear genomes of which four loci were shortlisted and various statistical parameters were employed to demonstrate their potential as barcodes to unambiguously discriminate Dalbergia species
Nucleotide sequences of analyzed loci from all individuals were deposited in NCBI database (S1 Dataset; accession numbers—matK: KM276475-KM276412; rbcL: KM100059-KM099987; trnH-psbA: KM276322-KM276250 and nuclear internal transcribed spacer from ribosomal gene (nrITS): KM276165-KM276104)
Summary
In DNA barcoding, the sequence of a short stretch of DNA is used for accurate species identification [1], supplementing the classical taxonomic methods [2]. DNA barcoding has been successfully used for discriminating animal species, applying this approach for discriminating plant species is more difficult due to many challenges [3]. Plant mitochondrial genomes exhibit low rates of nucleotide substitution and high rates of chromosomal rearrangements [4], while extensive gene duplication occurs in the nuclear genome [5]. PLOS ONE | DOI:10.1371/journal.pone.0142965 November 16, 2015
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