Testing four proposed barcoding markers for the identification of species within Ligustrum L. (Oleaceae)

Abstract

DNA barcoding is a biological technique that uses short and standardized genes or DNA regions to facilitate species identification. DNA barcoding has been used successfully in several animal and plant groups. Ligustrum (Oleaceae) species occur widely throughout the world and are used as medicinal plants in China. Therefore, the accurate identification of species in this genus is necessary. Four potential DNA barcodes, namely the nuclear ribosomal internal transcribed spacer (ITS) and three chloroplast (cp) DNA regions (rbcL, matK, and trnH-psbA), were used to differentiate species within Ligustrum. BLAST, character-based method, tree-based methods and TAXONDNA analysis were used to investigate the molecular identification capabilities of the chosen markers for discriminating 92 samples representing 20 species of this genus. The results showed that the ITS sequences have the most variable information, followed by trnH-psbA, matK, and rbcL. All sequences of the four regions correctly identified the species at the genus level using BLAST alignment. At the species level, the discriminating power of rbcL, matK, trnH-psbA, and ITS based on neighbor-joining (NJ) trees was 36.8%, 38.9%, 77.8%, and 80%, respectively. Using character-based and maximum parsimony (MP) tree methods together, the discriminating ability of trnH-psbA increased to 88.9%. All species could be differentiated using ITS when combining the NJ tree method with character-based or MP tree methods. Overall, the results indicate that DNA barcoding is an effective molecular identification method for Ligustrum species. We propose the nuclear ribosomal ITS as a plant barcode for plant identification and trnH-psbA as a candidate barcode sequence.

Plant DNA barcoding in China

“…Dong et al (2011) used rbcL, matK and ITS to evaluate the five species of Pterygiella (Orabanchaceae) and found that only ITS could successfully identify all species of this genus. Similar conclusions were drawn when genetic gaps among species of Hedyotis (Rubiaceae) (Guo et al, 2011), Ligustrum (Oleaceae) (Gu et al, 2011), Primula (Primulaceae) (Yan et al, 2011) and Tetrastigma (Vitaceae) (Fu et al, 2011) were evaluated by the proposed plastid DNA markers and ITS. At the family level, Du et al (2011), Xiang et al (2011) and Shi et al (2011 studied the application of the proposed DNA barcodes for the species identification of Potamogetonaceae, Juglandaceae and Zingiberaceae.…”

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

“…Each region has its own strengths and weaknesses to be considered before establishing the universal barcode loci for plants. While rbcL remained as the most effective loci in terms of sequence quality and recovery, but not in species discrimination ability [6], [13], [25], matK was found to be effective in species discrimination in some cases [7], [13], [21], [29], [33], but not in others [25], [35], [36]. Moreover, in most cases, sequence recovery and the quality of matK was not as effective as that with rbcL [7], [25], [37].…”

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

“…In the Oleaceae, only the nuclear ribosomal internal transcribed spacer (nITS) and the cpDNA trnH-psbA intergenic region harboured enough nucleotide polymorphisms to delineate and identify satisfactorily species in the genus Ligustrum , while rbcL and matK had poor discrimination [82]. Other case studies involving perennial genera generally resulted in mixed or negative results.…”