Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life

Abstract

Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

Comparing Medicinal Uses of Cochlospermaceae throughout Its Geographic Range with Insights from Molecular Phylogenetics

“…Here we have combined both the phylogenetic and ethnobotanical approaches by choosing a geographically-widespread plant family, reconstructing a molecular phylogeny for the family, mapping ethnobotanical data onto the resulting phylogeny, and evaluating correlations between the evolutionary relatedness of the species and their ethnobotanical uses by different cultural groups who live in different geographic regions. Studies such as this that utilize phylogenetic patterns of medicinal properties within plant lineages are few [10,[21][22][23][24][25][26][27][28][29]. Saslis-Lagoudakis et al [10] concluded that phylogenetic cross-cultural comparisons can focus screening efforts on the closest relatives of medicinal plants already in use as traditional medicines.…”

An Encyclopedia of Herb-Disease, a Quick Shortcut for Herbal Research: A Comprehension Based on Iranian Herbal Studies

“…It has been reported that chemometric analyses such as reversed-phase high-performance liquid chromatography and biochemical markers can be used for analyzing and classifying intra-specific genetic relationship of plant populations [20,21]. Nowadays, scientists are encouraged to bioinformatics technics and the omics-based approaches in traditional medicine and ethnomedicine studies [22][23][24][25] which can be of help to manage the herbal research as large-scale datarich studies.…”

Integrated omics analysis of specialized metabolism in medicinal plants

“…Whole‐genome sequences of medicinal plants are a vital resource for understanding total biosynthetic potential. It also promote the development of natural medicines and the selection of cultivars with good agricultural traits and high levels of desired metabolites of medicinal and pharmaceutical importance (Hao and Xiao, ; Unamba et al ., ). Dependence on medicinal plants for the extraction of important bioactive metabolites has proved to be an unsustainable approach (Chang and Keasling, ; Facchini et al ., ); therefore, knowledge of biosynthetic pathway elements provides an opportunity to develope alternate sources for these compunds.…”

“…So far, whole‐genome sequences of 183 land plants have been released in the NCBI Genome database, 58 being completed and submitted in 2016 alone (a total of 68 genome sequences were released in 2016) (Table ) with 23 plant species being used primarily for medicinal purposes or described in different traditional medicinal practices. Genomic sequences provide essential information on plant origin, evolution, inheritable traits, developmental and physiological schematics, epigenomic regulation and metabolic potential, which serve as the basis for deciphering genome diversity and chemo‐diversity at the molecular level (Dhanapal and Govindaraj, ; Hao and Xiao, ; Unamba et al ., ). Genomic sequences assist in the development of accessible and robust functional genomic resources, such as full‐length complementary DNA clone sets, tagged mutant lines and a rapid and facile transformation method.…”

“…RNA-seq has proved to be a powerful tool with a diverse range of applications, not just limited to the accurate quantification of differential transcript expression, including for low-abundance transcripts, but also for the detection of exon/exon boundaries, alternative splicing, transcribed regions and simple sequence repeats, all in a single run (Martin et al, 2013). RNA-seq reads can be assembled de novo without mapping to the reference genomic sequences, which makes it an invaluable asset for the identification of genes and their expression analysis in non-model medicinal plants (De Luca et al, 2012a;Hao and Xiao, 2015;Rai and Saito, 2016). Over the last few years, RNA-seq-based transcriptome profiling and de novo transcriptome assembly, co-expression and comparative transcriptome analysis of various plant species, including medicinal plants, have attracted a lot of interest and have become an attractive alternative for generating genetic resources for plants of biological importance (Martin et al, 2013;Xiao et al, 2013;Han et al, 2015;Unamba et al, 2015;Wang et al, 2016b).…”