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The genome and metabolome of the tobacco tree, Nicotiana glauca : a potential renewable feedstock for the bioeconomy

https://doi.org/10.1101/351429
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Outgoing claims: the papers this work cites, builds on, or argues with.

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UV‐B Induced Secondary Plant Metabolites
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A Conservative Amino Acid Substitution Alters the Regiospecificity of CYP94A2, a Fatty Acid Hydroxylase from the Plant Vicia sativa
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Nuclear DNA changes, genome differentiation and evolution inNicotiana (Solanaceae)
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Who Belongs in the Family?
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Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
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Plant genome sequencing — applications for crop improvement
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Plant volatile terpenoid metabolism: Biosynthetic genes, transcriptional regulation and subcellular compartmentation
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Scopoletin, an active principle of tree tobacco (Nicotiana glauca) inhibits human tumor vascularization in xenograft models and modulates ERK1, VEGF-A, and FGF-2 in computer model
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The impact of third generation genomic technologies on plant genome assembly
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Web-based resources for mass-spectrometry-based metabolomics: A user’s guide
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Molecular genetics of alkaloid biosynthesis in Nicotiana tabacum
inferredcites →https://doi.org/10.1016/j.phytol.2012.04.004openalex-snapshot
The identification and rapid extraction of hydrocarbons from Nicotiana glauca: A potential advanced renewable biofuel source
inferredcites →https://doi.org/10.1016/s0031-9422(00)80751-7openalex-snapshot
The alkaloid contents of sixty Nicotiana species
inferredcites →https://doi.org/10.1016/s0041-0101(02)00241-6openalex-snapshot
Calcinosis—calcinogenic plants
inferredcites →https://doi.org/10.1016/s0168-9452(00)00254-5openalex-snapshot
Nicotiana glauca: another plant species containing vitamin D3 metabolites
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The tomato genome sequence provides insights into fleshy fruit evolution
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Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae
inferredcites →https://doi.org/10.1038/ncomms4833openalex-snapshot
The tobacco genome sequence and its comparison with those of tomato and potato
inferredcites →https://doi.org/10.1038/ng.3046openalex-snapshot
The genome of the stress-tolerant wild tomato species Solanum pennellii
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Salmon provides fast and bias-aware quantification of transcript expression
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Gas chromatography mass spectrometry–based metabolite profiling in plants
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The Arabidopsis MALE STERILITY 2 protein shares similarity with reductases in elongation/condensation complexes
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Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids
inferredcites →https://doi.org/10.1073/pnas.1700073114openalex-snapshot
Wild tobacco genomes reveal the evolution of nicotine biosynthesis
inferredcites →https://doi.org/10.1073/pnas.97.13.7043openalex-snapshot
Hybridization as a stimulus for the evolution of invasiveness in plants?
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Nuclear DNA amounts in angiosperms: targets, trends and tomorrow
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Plant genome and transcriptome annotations: from misconceptions to simple solutions
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edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
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Trimmomatic: a flexible trimmer for Illumina sequence data
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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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Intragenic Recombination Events and Evidence for Hybrid Speciation in Nicotiana (Solanaceae)
inferredcites →https://doi.org/10.1093/molbev/mst030openalex-snapshot
FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection
inferredcites →https://doi.org/10.1093/molbev/msv035openalex-snapshot
Gene-Wide Identification of Episodic Selection
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Phylogeny.fr: robust phylogenetic analysis for the non-specialist
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PGSB PlantsDB: updates to the database framework for comparative plant genome research
inferredcites →https://doi.org/10.1093/pcp/pcm018openalex-snapshot
Molecular Cloning of N-methylputrescine Oxidase from Tobacco
inferredcites →https://doi.org/10.1093/pcp/pct179openalex-snapshot
Molecular Evolution of N-Methylputrescine Oxidase in Tobacco
inferredcites →https://doi.org/10.1101/gr.3804205openalex-snapshot
Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
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CER4 Encodes an Alcohol-Forming Fatty Acyl-Coenzyme A Reductase Involved in Cuticular Wax Production in Arabidopsis
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CYP86B1 Is Required for Very Long Chainω-Hydroxyacid andα,ω-Dicarboxylic Acid Synthesis in Root and Seed Suberin Polyester
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Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis
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The Formation and Function of Plant Cuticles
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FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants
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Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis1
inferredcites →https://doi.org/10.1104/pp.17.00070openalex-snapshot
Genomic Insights into the Evolution of the Nicotine Biosynthesis Pathway in Tobacco
inferredcites →https://doi.org/10.1105/tpc.111.083121openalex-snapshot
A Member of the PLEIOTROPIC DRUG RESISTANCE Family of ATP Binding Cassette Transporters Is Required for the Formation of a Functional Cuticle in Arabidopsis
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Identification of Novel Plant Peroxisomal Targeting Signals by a Combination of Machine Learning Methods and in Vivo Subcellular Targeting Analyses
inferredcites →https://doi.org/10.1105/tpc.111.086272openalex-snapshot
Recommendations for Reporting Metabolite Data
inferredcites →https://doi.org/10.1105/tpc.113.122242openalex-snapshot
Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks
inferredcites →https://doi.org/10.1105/tpc.16.00768openalex-snapshot
Protein Degradation Rate in Arabidopsis thaliana Leaf Growth and Development
inferredcites →https://doi.org/10.1105/tpc.17.00521openalex-snapshot
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
inferredcites →https://doi.org/10.1111/j.1742-4658.2010.07948.xopenalex-snapshot
Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological roles
inferredcites →https://doi.org/10.1111/pce.12231openalex-snapshot
M ercator: a fast and simple web server for genome scale functional annotation of plant sequence data
inferredcites →https://doi.org/10.1126/science.1102331openalex-snapshot
Plant Cuticular Lipid Export Requires an ABC Transporter
inferredcites →https://doi.org/10.1126/science.1177970openalex-snapshot
Beneficial Biofuels—The Food, Energy, and Environment Trilemma
inferredcites →https://doi.org/10.1186/2047-217x-1-18openalex-snapshot
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
inferredcites →https://doi.org/10.1186/gb-2013-14-6-r60openalex-snapshot
Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis
inferredcites →https://doi.org/10.1186/s12864-017-3791-6openalex-snapshot
A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency
inferredcites →https://doi.org/10.1186/s13104-018-3127-xopenalex-snapshot
Nicotiana glauca whole-genome investigation for cT-DNA study
inferredcites →https://doi.org/10.1186/s40709-016-0048-5openalex-snapshot
Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species
inferredcites →https://doi.org/10.1371/journal.pgen.1002764openalex-snapshot
Detecting Individual Sites Subject to Episodic Diversifying Selection
inferredcites →https://doi.org/10.1590/s1677-04202012000300008openalex-snapshot
Ecophysiological responses to drought and salinity in the cosmopolitan invader Nicotiana glauca
inferredcites →https://doi.org/10.2478/cttr-2013-0610openalex-snapshot
Alkaloid Composition of the Nicotiana Species
inferredcites →https://doi.org/10.3389/fpls.2012.00194openalex-snapshot
PredPlantPTS1: A Web Server for the Prediction of Plant Peroxisomal Proteins
inferredcites →https://doi.org/10.3389/fpls.2013.00136openalex-snapshot
Vitamin D in plants: a review of occurrence, analysis, and biosynthesis
inferredcites →https://doi.org/10.3390/ijms18010053openalex-snapshot
Transcriptional Regulation and Transport of Terpenoid Indole Alkaloid in Catharanthus roseus: Exploration of New Research Directions
inferredcites →https://doi.org/10.3791/51393openalex-snapshot
Transcript and Metabolite Profiling for the Evaluation of Tobacco Tree and Poplar as Feedstock for the Bio-based Industry
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Genetic dissection of seed characteristics in field pennycress via genome‐wide association mapping studies
inferred← citeshttps://doi.org/10.1007/978-3-030-29493-9_15openalex-snapshot
Production of Valuable Compounds in Tobacco
inferred← citeshttps://doi.org/10.1007/978-981-16-6974-3_8openalex-snapshot
Whole-Genome Sequencing of Plants: Past, Present, and Future
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Engineering the production of crocins and picrocrocin in heterologous plant systems
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De Novo Domestication: An Alternative Route toward New Crops for the Future
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Rice metabolic regulatory network spanning the entire life cycle
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A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology
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Cuticular Wax Composition is Essential for Plant Recovery Following Drought with Little Effect under Optimal Conditions
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Fatty Alcohols, a Minor Component of the Tree Tobacco Surface Wax, Reduce Insect Herbivory
inferred← citeshttps://doi.org/10.1101/2022.09.12.507566openalex-snapshot
Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights allopolyploidy-mediated innovations in N -acylnornicotine metabolism
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A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology
inferred← citeshttps://doi.org/10.1111/nph.18615openalex-snapshot
Tree tobacco ( Nicotiana glauca ) cuticular wax composition is essential for leaf retention during drought, facilitating a speedy recovery following rewatering
inferred← citeshttps://doi.org/10.1126/sciadv.ade8984openalex-snapshot
Evolutionary metabolomics of specialized metabolism diversification in the genus Nicotiana highlights N- acylnornicotine innovations
inferred← citeshttps://doi.org/10.3390/metabo12070575openalex-snapshot
The Biosynthesis of Non-Endogenous Apocarotenoids in Transgenic Nicotiana glauca
inferred← citeshttps://doi.org/10.70675/63486756z3916z4dd6z9701z5a91575bbd5eopenalex-snapshot
Metabolomics-centered exploration of plant specialized metabolism innovations : a case-study on the chemodiversity, biosynthesis and anti-herbivory functions of N-acylnornicotines in the genus Nicotiana
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