DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples

Abstract

It is commonly difficult to extract and amplify DNA from herbarium samples as they are old and preserved using different compounds. In addition, such samples are subjected to the accumulation of intrinsically produced plant substances over long periods (up to hundreds of years). DNA extraction from desert flora may pause added difficulties as many contain high levels of secondary metabolites. Herbarium samples from the Biology Department (UAE University) plant collection and fresh plant samples, collected from around Al-Ain (UAE), were used in this study. The three barcode loci for the coding genes matK, rbcL and rpoC1-were amplified. Our results showed that T. terresteris, H. robustum,T. pentandrus and Z. qatarense were amplified using all three primers for both fresh and herbaium samples. Both fresh and herbarium samples of C. comosum, however, were not amplified at all, using the three primers. Herbarium samples from A. javanica, C. imbricatum, T. aucherana and Z. simplex were not amplified with any of the three primers. For fresh samples 90, 90 and 80% of the samples were amplified using matK, rbcL and rpoC1, respectively. In short, fresh samples were significantly better amplified than those from herbarium sources, using the three primers. Both fresh and herbarium samples from one species (C. comosum), however, were not successfully amplified. It is also concluded that the rbcL regions showed real potentials to distinguish the UAE species under investigation into the appropriate family and genus.

Herbarium genomics: skimming and plastomics from archival specimens

“…To date, few plant and fungal herbarium DNA barcoding projects have been undertaken however (e.g. Osmundson et al 2013;Costion et al 2016;Do and Drábková 2016;Enan et al 2017) indicating that either PCR challenges or massive parallel sequencing approaches (as in Bakker et al 2016) still need further development. Bebber et al (2010) estimated that around 70,000 new species are already in herbarium collections, "waiting to be described" further underlining the notion that it is time to exploit and mine our herbarium collections genomically, especially with regards to plastomes (but see Gutaker and Burbano 2017), as these probably represent the most feasible and standardizable targets.…”

The effects of sample age and taxonomic origin on the success rate of DNA barcoding when using herbarium material

“…and herbarium samples quite good results (e.g., the present study; Kuzmina et al 2017), some investigations have reported low success rates for herbarium samples. For instance, in a small-scale investigation, Enan et al (2017) have reported that the success rates for matK and rbcL barcodes were 90% and 90% for fresh samples, but 40% and 50% for herbarium samples, respectively.…”

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

“…Recently, a few studies have been reported from the UAE and Iraq. The UAE was involved in authenticating date palm cultivars and a few medicinal plants (Enan and Ahamed, 2014; Enan and Ahamed, 2016; Enan et al, 2017). The authors analyzed matK and rpoC1 barcodes in 11 different date cultivars, with matK deemed to be more useful (Enan and Ahamed, 2014).…”

“…Recently, some attention has been devoted to genetic diversity analysis, species delimitation and barcoding desert plants in the UAE (Gairola et al, 2018). Enan et al (2017) highlighted that DNA barcoding has demonstrated promising outcomes from both fresh and herbarium samples of desert plants in the UAE. The authors concluded that the rbcL regions demonstrated a realistic potential to distinguish the UAE species under investigation into the appropriate family and genus.…”

“…However, the molecular identification and phylogenetic analysis of the UAE’s flora is yet to be investigated. The combination of rbcL and matK has been successful in barcoding some of the desert plants in the UAE (Enan et al, 2017). Recently, a project to barcode the entirety of UAE flora has been initiated at the Sharjah Research Academy (SRA).…”