Research Article Evaluation of the capacity of the DNA barcode ITS2 for identifying and discriminating dryland plants

Abstract

Many of the plants that grow in arid and semi-arid regions under harsh conditions (drought, salinity and misuse) are of medical importance. Desert plants also provide other benefits; so conservation efforts should be strengthened in these areas. In this study, three DNA barcodes-chloroplast maturase-K (matK), ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and secondary internal transcribed spacer (ITS2)-were tested in order to determine the ability of these markers to distinguish between various species. A total of 93 fresh and dry samples belonging to 30 plant families were examined. These are native to the arid lands around Makkah in the Kingdom of Saudi Arabia. Various tools and tests were used to evaluate the efficiency of the barcode markers; these included the basic local alignment search tool (BLAST), as well as the use of inter-and intraspecific distances, barcode gap, prediction of the secondary structure of the ITS2 and phylogenetic methods. The results confirmed the efficiency and superiority of the ITS2 loci over two chloroplast genes: matK and rbcL. ITS2 had a 97% success rate with amplification and a 95% success rate with sequencing, showing 100% identification at the family level, 77% identification at the genus level and 70% species resolution. A clear barcode gap was observed between inter-and intraspecific distances. Identification was achieved even in cases of degraded samples or old herbarium ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 18 (1): gmr18133 W.S. Al-Juhani 2 specimens. This study contributes to DNA barcode data by adding 224 DNA sequences of desert plants to the National Center for Biotechnology Information NCBI database. The results of this study are important and useful for application in each of the following fields: validation of medicinal plant identity, conservation, and taxonomic and evolutionary studies.

Barcoding High Resolution Melting (Bar‐HRM) enables the discrimination between toxic plants and edible vegetables prior to consumption and after digestion

“…HRM coupled with the ITS2 barcode has been shown to accurately detect plant species in complex food products (Bosmali et al., 2021; Grazina et al., 2020; Mishra et al., 2016). In this study, we used the ITS2 marker, given that it was previously shown to be effective in toxic and medicinal plant species delimitations, as well as for the authentication of processed herbal material (Anthoons et al., 2020; Chen et al., 2010; Liu et al., 2019; Nithaniyal et al., 2021), there is richness of sequences in repositories like GenBank, is suitable for amplification in degraded DNA (Al‐Juhani, 2019; Han et al., 2013), and has been also proposed by iBOL as an effective DNA barcode for many plant species (Yao et al., 2010). We screened a selection of eight pairs of edible and toxic plant species that are often misidentified in the field or commonly adulterated.…”

Plant DNA barcode library for native flowering plants in the arid region of northwestern China

“…Of the ~376,366 vascular plant species present worldwide (Qian et al, 2022), 80% still lack DNA barcodes. Studies in arid regions are sparse, and only a few DNA barcoding studies have been conducted; these include East Africa (Freeman et al, 2022; Gill et al, 2019), Central Asia (e.g., Allium L., Artemisia , Reaumuria L.) (Abugalieva et al, 2017; Turuspekov et al, 2018; Zhang et al, 2014) and southwest Asia (Saudi Arab) (Al‐Juhani, 2019; Bafeel et al, 2012). The arid region covers nearly 25% of the territory in China.…”