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Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/pld3.55openalex-snapshot

Virus‐induced gene silencing database for phenomics and functional genomics in Nicotiana benthamiana

inferredcites →https://doi.org/10.1002/pmic.201700071openalex-snapshot

Sma3s: A universal tool for easy functional annotation of proteomes and transcriptomes

inferredcites →https://doi.org/10.1007/s00438-015-0989-7openalex-snapshot

Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes

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The SGN VIGS Tool: User-Friendly Software to Design Virus-Induced Gene Silencing (VIGS) Constructs for Functional Genomics

inferredcites →https://doi.org/10.1016/j.molp.2017.01.003openalex-snapshot

CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants

inferredcites →https://doi.org/10.1016/j.pbi.2008.04.007openalex-snapshot

Enzyme–inhibitor interactions at the plant–pathogen interface

inferredcites →https://doi.org/10.1021/pr101065jopenalex-snapshot

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

inferredcites →https://doi.org/10.1038/nature10158openalex-snapshot

Genome sequence and analysis of the tuber crop potato

inferredcites →https://doi.org/10.1038/nature11119openalex-snapshot

The tomato genome sequence provides insights into fleshy fruit evolution

inferredcites →https://doi.org/10.1038/nbt.1511openalex-snapshot

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

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.2877openalex-snapshot

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

inferredcites →https://doi.org/10.1038/ng.3565openalex-snapshot

A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

inferredcites →https://doi.org/10.1038/nmeth.1701openalex-snapshot

SignalP 4.0: discriminating signal peptides from transmembrane regions

inferredcites →https://doi.org/10.1038/nplants.2015.165openalex-snapshot

The extremophile Nicotiana benthamiana has traded viral defence for early vigour

inferredcites →https://doi.org/10.1038/nplants.2016.74openalex-snapshot

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

inferredcites →https://doi.org/10.1038/nprot.2006.286openalex-snapshot

Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants

inferredcites →https://doi.org/10.1038/nprot.2007.261openalex-snapshot

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

inferredcites →https://doi.org/10.1038/nprot.2014.092openalex-snapshot

Tobacco rattle virus–based virus-induced gene silencing in Nicotiana benthamiana

inferredcites →https://doi.org/10.1038/nprot.2016.136openalex-snapshot

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

inferredcites →https://doi.org/10.1038/s41598-018-28769-0openalex-snapshot

The tomato subtilase family includes several cell death-related proteinases with caspase specificity

inferredcites →https://doi.org/10.1073/pnas.1400975111openalex-snapshot

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

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.1702041114openalex-snapshot

NLR network mediates immunity to diverse plant pathogens

inferredcites →https://doi.org/10.1074/mcp.m111.011015openalex-snapshot

Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

inferredcites →https://doi.org/10.1074/mcp.m113.031591openalex-snapshot

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

inferredcites →https://doi.org/10.1074/mcp.t500030-mcp200openalex-snapshot

Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap

inferredcites →https://doi.org/10.1093/aob/mcm326openalex-snapshot

The Ups and Downs of Genome Size Evolution in Polyploid Species of Nicotiana (Solanaceae)

inferredcites →https://doi.org/10.1093/bioinformatics/btr010openalex-snapshot

A novel hybrid gene prediction method employing protein multiple sequence alignments

inferredcites →https://doi.org/10.1093/bioinformatics/bts565openalex-snapshot

CD-HIT: accelerated for clustering the next-generation sequencing data

inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

inferredcites →https://doi.org/10.1093/dnares/dsu027openalex-snapshot

Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World

inferredcites →https://doi.org/10.1093/jxb/ery434openalex-snapshot

High-throughput sequencing data and the impact of plant gene annotation quality

inferredcites →https://doi.org/10.1093/molbev/msx319openalex-snapshot

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

inferredcites →https://doi.org/10.1093/molbev/msy096openalex-snapshot

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot

limma powers differential expression analyses for RNA-sequencing and microarray studies

inferredcites →https://doi.org/10.1093/nar/gkv1145openalex-snapshot

2016 update of the PRIDE database and its related tools

inferredcites →https://doi.org/10.1093/nar/gkv1344openalex-snapshot

The Pfam protein families database: towards a more sustainable future

inferredcites →https://doi.org/10.1093/nar/gkv279openalex-snapshot

The EMBL-EBI bioinformatics web and programmatic tools framework

inferredcites →https://doi.org/10.1093/nar/gkx1134openalex-snapshot

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

inferredcites →https://doi.org/10.1093/nar/gky995openalex-snapshot

The Pfam protein families database in 2019

inferredcites →https://doi.org/10.1094/mpmi-06-12-0148-taopenalex-snapshot

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

inferredcites →https://doi.org/10.1094/mpmi-10-16-0218-ropenalex-snapshot

Evolutionary History of Subtilases in Land Plants and Their Involvement in Symbiotic Interactions

inferredcites →https://doi.org/10.1094/mpmi-21-8-1015openalex-snapshot

Nicotiana benthamiana : Its History and Future as a Model for Plant–Pathogen Interactions

inferredcites →https://doi.org/10.1111/nph.12277openalex-snapshot

Apoplastic immunity and its suppression by filamentous plant pathogens

inferredcites →https://doi.org/10.1111/nph.14946openalex-snapshot

ApoplastP : prediction of effectors and plant proteins in the apoplast using machine learning

inferredcites →https://doi.org/10.1111/pbi.12852openalex-snapshot

The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire

inferredcites →https://doi.org/10.1111/pbi.13092openalex-snapshot

Activity‐based proteomics reveals nine target proteases for the recombinant protein‐stabilizing inhibitor Sl CYS 8 in Nicotiana benthamiana

inferredcites →https://doi.org/10.1111/tpj.13415openalex-snapshot

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome

inferredcites →https://doi.org/10.1146/annurev-arplant-050213-035850openalex-snapshot

Plant Molecular Pharming for the Treatment of Chronic and Infectious Diseases

inferredcites →https://doi.org/10.1186/1471-2105-7-62openalex-snapshot

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

inferredcites →https://doi.org/10.1186/1471-2105-9-278openalex-snapshot

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

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/10.1214/16-aoas920openalex-snapshot

Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression

inferredcites →https://doi.org/10.1371/journal.pone.0052717openalex-snapshot

Advanced Engineering of Lipid Metabolism in Nicotiana benthamiana Using a Draft Genome and the V2 Viral Silencing-Suppressor Protein

inferredcites →https://doi.org/10.1371/journal.pone.0091776openalex-snapshot

Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

inferredcites →https://doi.org/10.1385/1-59745-130-4:143openalex-snapshot

Nicotiana (Nicotiana tobaccum, Nicotiana benthamiana)

inferredcites →https://doi.org/10.32614/cran.package.imputelcmdopenalex-snapshot

imputeLCMD: A Collection of Methods for Left-Censored Missing Data Imputation

What points at this work

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

inferred← citeshttps://doi.org/10.1016/j.copbio.2019.10.006openalex-snapshot

Proteases of Nicotiana benthamiana: an emerging battle for molecular farming

inferred← citeshttps://doi.org/10.1016/j.virol.2020.04.002openalex-snapshot

Plant SNAREs SYP22 and SYP23 interact with Tobacco mosaic virus 126 kDa protein and SYP2s are required for normal local virus accumulation and spread

inferred← citeshttps://doi.org/10.1021/acs.jafc.4c09341openalex-snapshot

Nanomediated Stimulation: An Alternative to Brassinolide Hormone Replacement Therapy for Plant Resistance Activation

inferred← citeshttps://doi.org/10.1038/s41467-020-18069-5openalex-snapshot

Evolution of a guarded decoy protease and its receptor in solanaceous plants

inferred← citeshttps://doi.org/10.1101/2020.07.29.225110openalex-snapshot

Glycosylation of bioactive C 13 -apocarotenols in Nicotiana benthamiana and Mentha × piperita

inferred← citeshttps://doi.org/10.1104/pp.20.00953openalex-snapshot

Six Uridine-Diphosphate Glycosyltransferases Catalyze the Glycosylation of Bioactive C13-Apocarotenols

inferred← citeshttps://doi.org/10.1111/tpj.15082openalex-snapshot

Functional requirement of the Arabidopsis importin‐α nuclear transport receptor family in autoimmunity mediated by the NLR protein SNC1

inferred← citeshttps://doi.org/10.3390/ijms222212395openalex-snapshot

Distinct and Overlapping Functions of Miscanthus sinensis MYB Transcription Factors SCM1 and MYB103 in Lignin Biosynthesis

inferred← citeshttps://doi.org/10.70675/5bbbc886z8505z466dza2bbz1b4165376f95openalex-snapshot

Interplay between the phosphoinositides and the plant cytoskeleton during plant cytokinesis in Arabidopsis thaliana

inferred← citeshttps://doi.org/10.7554/elife.73837openalex-snapshot

The Arabidopsis SAC9 enzyme is enriched in a cortical population of early endosomes and restricts PI(4,5)P2 at the plasma membrane

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