Bhagwat Rasika M, Dholakia Bhushan B, Kadoo Narendra Y, Balasundaran M, Gupta Vidya S
Plant Molecular Biology Group, Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India.
Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India.
PLoS One. 2015 Nov 16;10(11):e0142965. doi: 10.1371/journal.pone.0142965. eCollection 2015.
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.
DNA条形码技术能够通过分析目标基因的独特DNA序列来精确鉴定物种。本研究旨在为黄檀属的不同物种开发条形码，黄檀属是一种具有重要经济价值的木材植物，广泛分布于热带地区。从印度西高止山脉选取了10种黄檀属物种，利用质体基因组中的三个区域（matK、rbcL、trnH-psbA）、一个核转录间隔区（nrITS）及其组合进行评估，以便在物种水平上对它们进行区分。使用五个标准：（i）种间和种内距离，（ii）邻接法（NJ）树，（iii）最佳匹配（BM）和最佳近匹配（BCM），（iv）基于特征的秩检验，以及（v）威尔科克森符号秩检验来进行物种区分。在所评估的基因座中，rbcL的扩增和测序成功率最高（97.6%），其次是matK（97.0%）、trnH-psbA（94.7%）和nrITS（80.5%）。种间和种内距离以及威尔科克森符号秩检验表明，nrITS的差异更大。BM和BCM方法显示，matK、matK+rbcL和matK+trnH-psb基因座的正确物种识别率最高（100%）。基于特征的识别方法进一步支持了这三个基因座以及nrITS。考虑到这些基因座的整体性能及其在不同方法中的排名，我们建议将matK和matK+rbcL作为明确区分黄檀属物种的最合适条形码。这些发现可能有助于划分黄檀属的各种物种以及其他相关属。
