Integrated omics analysis of specialized metabolism in medicinal plants

The Plant Journal, Journal Year: 2017, Volume and Issue: 90(4), P. 764 - 787

Published: Jan. 21, 2017

Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to explore the biosynthetic pathways these metabolites, mainly due scarcity genomics resources. However, recent advances high-throughput large-scale analytical methods have enabled discover for plant-based medicinal metabolites. The reduced cost generating omics datasets and development computational tools analysis integration led elucidation several bioactive origin. These discoveries inspired synthetic biology approaches develop microbial systems produce originating from plants, an alternative sustainable medicinally chemicals. Since demand compounds increasing world's population, understanding complete biosynthesis becomes identify or reliable sources future. Here, we review contributions major our We briefly discuss different integrating extract biologically relevant knowledge application construction reconstruction metabolic models.

Language: Английский

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Next-Generation Breeding Strategies for Climate-Ready Crops

Frontiers in Plant Science, Journal Year: 2021, Volume and Issue: 12

Published: July 21, 2021

Climate change is a threat to global food security due the reduction of crop productivity around globe. Food matter concern for stakeholders and policymakers as population predicted bypass 10 billion in coming years. Crop improvement via modern breeding techniques along with efficient agronomic practices innovations microbiome applications, exploiting natural variations underutilized crops an excellent way forward fulfill future requirements. In this review, we describe next-generation tools that can be used increase production by developing climate-resilient superior genotypes cope challenges security. Recent genomic-assisted (GAB) strategies allow construction highly annotated pan-genomes give snapshot full landscape genetic diversity (GD) recapture lost gene repertoire species. Pan-genomes provide new platforms exploit these unique genes or variation optimizing programs. The advent clustered regularly interspaced short palindromic repeat/CRISPR-associated (CRISPR/Cas) systems, such prime editing, base de nova domestication, has institutionalized idea genome editing revamped improvement. Also, availability versatile Cas orthologs, including Cas9, Cas12, Cas13, Cas14, improved efficiency. Now, CRISPR/Cas systems have numerous applications research successfully edit major develop resistance against abiotic biotic stress. By adopting high-throughput phenotyping approaches big data analytics like artificial intelligence (AI) machine learning (ML), agriculture heading toward automation digitalization. integration speed genomic phenomic rapid identifications ultimately accelerate addition, multidisciplinary open exciting avenues climate-ready

Language: Английский

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Deciphering genetic factors that determine melon fruit‐quality traits using RNA‐Seq‐based high‐resolution QTL and eQTL mapping

The Plant Journal, Journal Year: 2018, Volume and Issue: 94(1), P. 169 - 191

Published: Jan. 31, 2018

Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic transcriptomic data from a recombinant inbred line (RIL) population. RNA sequencing (RNA-Seq) of 96 RILs yielded highly saturated collection > 58 000 single-nucleotide polymorphisms, identifying 6636 recombination events that separated the genome into 3663 genomic bins. Bin-based QTL 79 129 fruit-quality traits taste, aroma color resulted in 241 QTL. Thiol acyltransferase (CmThAT1) gene identified within interval its product, S-methyl-thioacetate, key component aroma. Metabolic activity CmThAT1-encoded protein validated bacteria vitro. flesh intensity candidate white-flesh (CmPPR1), one two major determining melon. CmPPR1 encodes member pentatricopeptide family, involved processing plastids, where carotenoid chlorophyll pigments accumulate. Network 12 eQTL mapped for 8000 differentially expressed genes supported role expression level plastid targeted genes. We highlight potential RNA-Seq-based small moderate size, advanced RIL populations precise marker-assisted breeding discovery. provide following resources: population genotyped with unique set SNP markers, confined segments harbor governing eQTLs.

Language: Английский

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Species-independent analytical tools for next-generation agriculture

Nature Plants, Journal Year: 2020, Volume and Issue: 6(12), P. 1408 - 1417

Published: Nov. 30, 2020

Innovative approaches are urgently required to alleviate the growing pressure on agriculture meet rising demand for food. A key challenge plant biology is bridge notable knowledge gap between our detailed understanding of model plants grown under laboratory conditions and agriculturally important crops cultivated in fields or production facilities. This Perspective highlights recent development new analytical tools that rapid non-destructive provide tissue-, cell- organelle-specific information living real time, with potential extend across multiple species field applications. We evaluate utility engineered nanosensors portable Raman spectroscopy detect biotic abiotic stresses, monitor hormonal signalling as well characterize soil, phytobiome crop health a non- minimally invasive manner. propose leveraging these aforementioned fundamental synthesis integration expertise from biology, engineering data science. Lastly, we assess economic discuss implementation strategies will ensure acceptance successful modern future farming practices traditional urban agriculture.

Language: Английский

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Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze)

Scientific Reports, Journal Year: 2016, Volume and Issue: 6(1)

Published: July 28, 2016

Abstract To unravel the molecular mechanism of defense against blister blight (BB) disease caused by an obligate biotrophic fungus, Exobasidium vexans , transcriptome BB interaction with resistance and susceptible tea genotypes was analysed through RNA-seq using Illumina GAIIx at four different stages during ~20-day cycle. Approximately 69 million high quality reads were assembled de novo yielding 37,790 unique transcripts more than 55% being functionally annotated. Differentially expressed, 149 related transcripts/genes, namely enzymes, genes, multidrug resistant transporters, transcription factors, retrotransposons, metacaspases chaperons observed in RG, suggesting their role defending BB. Being present major hub, putative master regulators among these candidates identified from predetermined protein-protein network Arabidopsis thaliana . Further, confirmation abundant expression well-known RPM1, RPS2 RPP13 quantitative Real Time PCR indicates salicylic acid jasmonic acid, possibly induce synthesis antimicrobial compounds, required to overcome virulence E. Compendiously, current study provides a comprehensive gene insights into serve as resource for unravelling possible regulatory immunity various biotic stresses other crops.

Language: Английский

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Novelin silicotools for designing peptide-based subunit vaccines and immunotherapeutics

Briefings in Bioinformatics, Journal Year: 2016, Volume and Issue: unknown, P. bbw025 - bbw025

Published: March 25, 2016

The conventional approach for designing vaccine against a particular disease involves stimulation of the immune system using whole pathogen responsible disease. In post-genomic era, major challenge is to identify antigenic regions or epitopes that can stimulate different arms system. past two decades, numerous methods and databases have been developed immunotherapy various pathogen-causing diseases. This review describes computational resources important subunit vaccines epitope-based immunotherapy. First, immunological are described maintain epitopes, antigens targets. followed by in silico tools used predicting linear conformational B-cell required activating humoral immunity. Finally, information on T-cell epitope prediction provided includes indirect like Major Histocompatibility Complex transporter-associated protein binders. Different studies validating predicted also examined critically. enlists novel available cell-mediated potential. These could be as they may activate adaptive Authors emphasized need develop adjuvants innate simultaneously. addition, attention has given predict general therapeutic properties peptides half-life, cytotoxicity toxicity.

Language: Английский

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Plant GATA Factors: Their Biology, Phylogeny, and Phylogenomics

Annual Review of Plant Biology, Journal Year: 2022, Volume and Issue: 73(1), P. 123 - 148

Published: Feb. 7, 2022

GATA factors are evolutionarily conserved transcription that found in animals, fungi, and plants. Compared to of the size plant family is increased. In angiosperms, four main classes seven structural subfamilies can be defined. recent years, knowledge about biological role regulation GATAs has substantially improved. Individual members have been implicated photomorphogenic growth, chlorophyll biosynthesis, chloroplast development, photosynthesis, stomata formation, as well root, leaf, flower development. this review, we summarize current factors. Using phylogenomic analysis, trace evolutionary origin green lineage examine their relationship animal fungal GATAs. Finally, speculate a possible conservation GATA-regulated functions across animal, fungal, kingdoms.

Language: Английский

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Plant synthetic biology for producing potent phyto-antimicrobials to combat antimicrobial resistance

Biotechnology Advances, Journal Year: 2021, Volume and Issue: 48, P. 107729 - 107729

Published: March 9, 2021

Language: Английский

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Recent advances in triterpenoid pathway elucidation and engineering

Biotechnology Advances, Journal Year: 2023, Volume and Issue: 68, P. 108214 - 108214

Published: July 20, 2023

Language: Английский

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Integrative Approaches to Abiotic Stress Management in Crops: Combining Bioinformatics Educational Tools and Artificial Intelligence Applications

Sustainability, Journal Year: 2024, Volume and Issue: 16(17), P. 7651 - 7651

Published: Sept. 3, 2024

Abiotic stresses, including drought, salinity, extreme temperatures and nutrient deficiencies, pose significant challenges to crop production global food security. To combat these challenges, the integration of bioinformatics educational tools AI applications provide a synergistic approach identify analyze stress-responsive genes, regulatory networks molecular markers associated with stress tolerance. Bioinformatics offer robust framework for data collection, storage initial analysis, while enhance pattern recognition, predictive modeling real-time processing capabilities. This review uniquely integrates applications, highlighting their combined role in managing abiotic plants crops. The novelty is demonstrated by multiomics algorithms, providing deeper insights into response pathways, biomarker discovery recognition. Key include resistance gene network inference, omics plant monitoring through fusion remote sensing AI-assisted phenomics. Challenges such as handling big data, model interpretability, overfitting experimental validation remain there, but future prospects involve developing user-friendly platforms, establishing common standards, interdisciplinary collaboration harnessing mitigation strategies Educational initiatives, collaborations trainings are essential equip next generation researchers required skills utilize advanced effectively. convergence holds vast accelerating development stress-resilient crops, optimizing agricultural practices ensuring security under increasing environmental pressures. Moreover, this integrated crucial advancing sustainable agriculture amidst growing challenges.

Language: Английский

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