DNA barcoding, microarrays and next generation sequencing: recent tools for genetic diversity estimation and authentication of medicinal plants

Abstract

DNA barcoding, microarray technology and next generation sequencing have emerged as promising tools for the elucidation of plant genetic diversity and its conservation. They are proving to be immensely helpful in authenticating the useful medicinal plants for herbal drug preparations. These newer versions of molecular markers utilize short genetic markers in the genome to characterize the organism to a particular species. This has the potential not only to classify the known and yet unknown species but also has a promising future to link the medicinally important plants according to their properties. The newer trends being followed in DNA chips and barcoding pave the way for a future with many different possibilities. Several of these possibilities might be: characterization of unknown species in a considerably less time than usual, identification of newer medicinal properties possessed by the species and also updating the data of the already existing but unnoticed properties. This can assist us to cure many different diseases and will also generate novel opportunities in medicinal drug delivery and targeting.

DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market

“…In parallel with many algorithmic advances through de novo sequencing, targeted resequencing, RNA interface to metagenomics, the technique is now encompassing the Sanger sequencing platform in DNA barcoding (especially metabarcoding) with additional advantages of longer average sequence read lengths from Roche's 454 sequencing platform (Kircher and Kelso, 2010). The enormous number of reads generated by NGS enabled the sequencing of entire genomes at an unprecedented speed, which have proved to be very useful for phylogenetics at deeper level and genome evolution analysis, which in turn greatly helps in authenticating the useful medicinal plants for herbal drug preparations (Sarwat and Yamdagni, 2014). Amplicon sequencing using ion torrent or 454 technologies could potentially recover all of the filler plant species.…”

Renaissance in phytomedicines: promising implications of NGS technologies

“…Secondly, high scalability of the NGS platforms and capacity to process multiple samples/PCR amplicons in one run give rapidity and reliability to the DNA sequence-based identification methods. The platforms generating longer reads as Roche can give more output with enough throughputs (Sarwat and Yamdagni 2014). Coghlan et al (2012) identified various illegal as well as protected and toxic biological materials in various herbal products.…”

Authentication of medicinal plants by DNA markers

“…All of them retain their distinctive enzyme systems, sequencing chemistry, hardware and software engineering (Mardis 2008;Shendure and Ji 2008;Metzker 2010); also, the sequencing reads obtained with these technologies varies in total sequencing output. Among these Illumina/Solexa and Applied Biosystems/SOLiD platforms have the ability to generate tens of millions of short reads (25-35 bp) per run; whereas Roche/454, might generate a few hundred thousand to 1 million reads of 400-500 bp DNA fragments per run (Sarwat and Yamdagni 2015). However, it must be kept in mind that Roche/454 is more advantageous regarding the identification of species because this system is more rapid and produces longer read lengths (Metzker 2010).…”