Crosstalk of Multi-Omics Platforms with Plants of Therapeutic Importance

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Abstract

From time immemorial, humans have exploited plants as a source of food and medicines. The World Health Organization (WHO) has recorded 21,000 plants with medicinal value out of 300,000 species available worldwide. The promising modern “multi-omics” platforms and tools have been proven as functional platforms able to endow us with comprehensive knowledge of the proteome, genome, transcriptome, and metabolome of medicinal plant systems so as to reveal the novel connected genetic (gene) pathways, proteins, regulator sequences and secondary metabolite (molecule) biosynthetic pathways of various drug and protein molecules from a variety of plants with therapeutic significance. This review paper endeavors to abridge the contemporary advancements in research areas of multi-omics and the information involved in decoding its prospective relevance to the utilization of plants with medicinal value in the present global scenario. The crosstalk of medicinal plants with genomics, transcriptomics, proteomics, and metabolomics approaches will be discussed.

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The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Alberto Casagrande (2007)

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.

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Natural Products as Sources of New Drugs from 1981 to 2014.

David J Newman, Gordon M Cragg (2016)

This contribution is a completely updated and expanded version of the four prior analogous reviews that were published in this journal in 1997, 2003, 2007, and 2012. In the case of all approved therapeutic agents, the time frame has been extended to cover the 34 years from January 1, 1981, to December 31, 2014, for all diseases worldwide, and from 1950 (earliest so far identified) to December 2014 for all approved antitumor drugs worldwide. As mentioned in the 2012 review, we have continued to utilize our secondary subdivision of a "natural product mimic", or "NM", to join the original primary divisions and the designation "natural product botanical", or "NB", to cover those botanical "defined mixtures" now recognized as drug entities by the U.S. FDA (and similar organizations). From the data presented in this review, the utilization of natural products and/or their novel structures, in order to discover and develop the final drug entity, is still alive and well. For example, in the area of cancer, over the time frame from around the 1940s to the end of 2014, of the 175 small molecules approved, 131, or 75%, are other than "S" (synthetic), with 85, or 49%, actually being either natural products or directly derived therefrom. In other areas, the influence of natural product structures is quite marked, with, as expected from prior information, the anti-infective area being dependent on natural products and their structures. We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore it is considered that this area of natural product research should be expanded significantly.

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One thousand plant transcriptomes and the phylogenomics of green plants

James Leebens-Mack, Michael S Barker, Eric J Carpenter … (2019)

Green plants (Viridiplantae) include around 450,000–500,000 species 1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.

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Author and article information

Contributors

Suleyman Allakhverdiev: Role: Academic Editor

Journal

Journal ID (nlm-ta): Cells

Journal ID (iso-abbrev): Cells

Journal ID (publisher-id): cells

Title: Cells

Publisher: MDPI

ISSN (Electronic): 2073-4409

Publication date (Electronic): 23 May 2021

Publication date Collection: June 2021

Volume: 10

Issue: 6

Electronic Location Identifier: 1296

Affiliations

[1 ]Government Department of School Education, Jammu 180001, Jammu and Kashmir, India; deepupandita@ 123456gmail.com

[2 ]Vatsalya Clinic, Krishna Nagar, New Delhi 110051, Delhi, India; dt.anunischal46@ 123456gmail.com

[3 ]Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani Anantnag 192101, Jammu and Kashmir, India; shabirhussainwani@ 123456gmail.com

[4 ]Physics Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh 84428, Saudi Arabia; haalyousef@ 123456pnu.edu.sa

[5 ]Applied Studies and Community Service College, King Saud University, Riyadh 11451, Saudi Arabia; aabdelbacki@ 123456ksu.edu.sa

[6 ]Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia; mlyafrasi@ 123456ksu.edu.sa (M.A.A.-Y.); falman@ 123456ksu.edu.sa (F.A.A.-M.); helansary@ 123456ksu.edu.sa (H.O.E.)

Author notes

[* ]Correspondence: shamohamed@ 123456pnu.edu.sa

Author information

Deepu Pandita https://orcid.org/0000-0002-8361-1872

Shabir Hussain Wani https://orcid.org/0000-0002-7456-4090

Hosam O. Elansary https://orcid.org/0000-0002-4476-2408

Article

Publisher ID: cells-10-01296

DOI: 10.3390/cells10061296

PMC ID: 8224614

PubMed ID: 34071113

SO-VID: dca2a563-5879-4699-b26b-b7d2d4316b7d

License:

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

History

Date received : 19 February 2021

Date accepted : 10 May 2021

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Crosstalk of Multi-Omics Platforms with Plants of Therapeutic Importance

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Most cited references 200

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.

Natural Products as Sources of New Drugs from 1981 to 2014.

One thousand plant transcriptomes and the phylogenomics of green plants

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