ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2020
Integrating transcriptome and metabolome reveals molecular networks involved in genetic and environmental variation in tobacco.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum.Nature communications · 2025Article
- Continuous carbon source supply is essential for high rifamycin productivity ofActa biochimica et biophysica Sinica · 2025Article
- Transcriptomic and metabolomic analysis of carotenoid metabolism and accumulation of carotenoid-derived products in tobacco leaves before and after curing.Frontiers in plant science · 2025Article
- Integrated metabolomics and metagenomics reveal plant-microbe interactions driving aroma differentiation in flue-cured tobacco leaves.Frontiers in plant science · 2025Article
- Review
- Multi-Omics Analysis of a Chromosome Segment Substitution Line Reveals a New Regulation Network for Soybean Seed Storage Profile.International journal of molecular sciences · 2024Article
- Proteomic and metabolomic revealed the effect of shading treatment on cigar tobacco.Frontiers in plant science · 2024Article
- Clonostachys rosea 'omics profiling: identification of putative metabolite-gene associations mediating its in vitro antagonism against Fusarium graminearum.BMC genomics · 2023Article
- Grapevine scion gene expression is driven by rootstock and environment interaction.BMC plant biology · 2023Article
- Transcriptomics ofFrontiers in bioengineering and biotechnology · 2023Article
- Unravelling the molecular mechanism underlying drought stress response in chickpeaFrontiers in plant science · 2023Article
- Soil microbiota plays a key regulatory role in the outbreak of tobacco root rot.Frontiers in microbiology · 2023Article
- INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation.PLoS computational biology · 2022Article
- Systems biology for crop improvement.The plant genome · 2021Review
- Article
- CE-MS for metabolomics: Developments and applications in the period 2018-2020.Electrophoresis · 2021Review
- Mechanism of Intermittent Deep Tillage and Different Depths Improving Crop Growth From the Perspective of Rhizosphere Soil Nutrients, Root System Architectures, Bacterial Communities, and Functional Profiles.Frontiers in microbiology · 2021Article
- Metabolic Profiling of Resistant and Susceptible Tobaccos Response Incited byFrontiers in plant science · 2021Article
Corrections and comments
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Authors and funding
17 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Tobacco (Nicotiana tabacum) is one of the most widely cultivated commercial non-food crops with significant social and economic impacts. Here we profiled transcriptome and metabolome from 54 tobacco samples (2-3 replicates; n = 151 in total) collected from three varieties (i.e. genetic factor), three locations (i.e. environmental factor), and six developmental stages (i.e. developmental process). We identified 3,405 differentially expressed (DE) genes (DEGs) and 371 DE metabolites, respectively. We used quantitative real-time PCR to validate 20 DEGs, and confirmed 18/20 (90%) DEGs between three locations and 16/20 (80%) with the same trend across developmental stages. We then constructed nine co-expression gene modules and four co-expression metabolite modules , and defined seven de novo regulatory networks, including nicotine- and carotenoid-related regulatory networks. A novel two-way Pearson correlation approach was further proposed to integrate co-expression gene and metabolite modules to identify joint gene-metabolite relations. Finally, we further integrated DE and network results to prioritize genes by its functional importance and identified a top-ranked novel gene, LOC107773232, as a potential regulator involved in the carotenoid metabolism pathway. Thus, the results and systems-biology approaches provide a new avenue to understand the molecular mechanisms underlying complex genetic and environmental perturbations in tobacco.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.