Bioinformatics-assisted, integrated omics studies on medicinal plants

Abstract

The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein–protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.

Authentication of Zingiber Species Based on Analysis of Metabolite Profiles

“…Currently, identifying species in TCMs is changing more easily and scientifically. In recent years, the chloroplast (cp) genomes have shown great potential for species identification, especially between closely related herbal species ( Daniell et al, 2016 ; Rendón-Anaya et al, 2017 ; Ma et al, 2019 ; Teske et al, 2020 ). Therefore, the development of the cp genome resources of the Z. corallinum and Z. montanum is not only conducive to the accurate identification of closely related species, but can also greatly promote the improvement of chloroplast genetic engineering ( Kelly et al, 2011 ).…”

“…Multivariate statistical analysis like principal component analysis (PCA), partial least squares discrimination analysis (PLS-DA), and orthogonal PLS-DA (OPLS-DA) have received more and more attention in the field of analyzing massive data ( Black et al, 2016 ; Palmioli et al, 2020 ). Metabolomics methods based on multivariate statistical analysis have proven to be a powerful tool for phytochemical classification by finding differences in metabolites ( Claassen et al, 2019 ; Ma et al, 2019 ; Zhang et al, 2020 ).…”

Crosstalk of Multi-Omics Platforms with Plants of Therapeutic Importance

“…Another paper focused on studies of medicinal plants with bioinformatics-assisted tools. Their focus was a case study of multi-omics data-based workflow for the Dendrobium medicinal plant, and it incorporated very few details on the genomics, transcriptomics, proteomics and metabolomics of other important medicinal plants [ 46 ]. The potential applications of metabolomics as well as analytical techniques, statistical approaches and bioinformatics tools help us to understand the system-wide effects of Thai traditional medicine [ 47 ].…”

MPDB 2.0: a large scale and integrated medicinal plant database of Bangladesh

“…Since ancient times nature has always provided its favoured children (humans) with both remedies for fighting diseases and nutrition products to maintain good health via plants full of potent medicinal properties and nutritive values, [ 1 ] and our forefathers have utilized this boon from mother nature to the fullest, a sign of which can be still found in the local folk medicinal therapies [ 2 – 4 ]. While our predecessors hardly understood the underlying mechanisms and chemical mediators responsible for the efficacy of these plants, recent advancement in technology (which includes techniques, instrumentation, and automation in isolation and structural characterization) allows us to learn the underlying mechanisms of these herbal treatments in depth [ 5 , 6 ] and discover the full potential for the usage of these plants full of potent medicinal properties and nutritive values [ 7 , 8 ].…”