Renaissance in phytomedicines: promising implications of NGS technologies

Abstract

Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.

Forensic genetics and genomics: Much more than just a human affair

“…In this concern, in the last couple of decades, diverse molecular markers have been applied for the forensic identification of species and individuals (i.e., HRM coupled with specific barcodes or real-time PCR to analyze chloroplast DNA regions) [e.g., 153 , 154 ]. Importantly, second- and third-generation sequencing methodologies are providing affordable analysis of complex and degraded plant samples [ 155 , 156 ].…”

Field Guide to Plant Model Systems

“…However, the compounds often exist in minute quantities, in sometimes rare plants, making the identification of the genetic basis for biochemical pathways and their transfer to more tractable systems of both economic and environmental interest. Targeted genomic or transcriptomic sequencing of medicinal plant species (Hao et al, 2012; Sharma and Shrivastava, 2016) could lead to synthetic biology approaches to produce specific bioactive compounds in yeast or E. coli , as has been done with Artemisia annua , the source of artemisinin, a potent anti-malarial drug (Ro et al, 2006; Westfall et al, 2012), and the opium poppy Papaver somniferum , the source of medical opiates (Thodey et al, 2014). …”

Next generation sequencing-based exploration of genomes and transcriptomes of medicinal plants

“…Though genomic information is not available or little known for majority of medicinal plants, continuous efforts are made to accumulate more and more genomic resources for these non-model but important plant species. Studies carried out in recent years on different organeller genomes in medicinal plants are recently reviewed by Sharma and Shrivastava ( 2016 ). Some implications of NGS-based nuclear genomic studies on some traditionally used medicinal plants are summarized in Table 3 .…”

“…Thus, despite of many challenges in sequencing and assembling complex genomes, many whole genome sequencing project have been accomplished and many are underway, owing to revolutionary advances in sequencing technology and informatics tools. Nevertheless, immediate implications of NGS need to be important in the area of genome characterization, gene identification, comparative genomics, molecular markers mining, and more for development of value added phytomedicines (Sharma and Shrivastava 2016 ).…”

“…Studies have been conducted on medicinal plants at genome and transcriptome level allowing identification of key genes involved in the production of bioactive phytocompounds. The emergence of next generation sequencing (NGS) techniques led to the deep understanding of the biosynthesis pathways of biologically active phytocompounds after availability of enormous genomic/transcriptomics sequence data (Sharma and Shrivastava 2016 ). Comparative genomics, expression analysis, homology search, functional annotation, and phylogenetic analysis further facilitate the identification of genes involved in the production of secondary metabolites and biochemical pathways in medicinal plants.…”