A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity

De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance

(2021) Corentin Molitor et al.   BIOINFORMATICS

A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

(2021) Guangwei Li et al.   NATURE GENETICS

Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales

(2021) Sarita Muñoz-Gómez et al.   Frontiers in Plant Science

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

(2021) Saleh Alseekh et al.   NATURE METHODS

A Review of the Most Common and Economically Important Diseases That Undermine the Cultivation of Tomato Crop in the Mediterranean Basin

(2021) Stefano Panno et al.   Agronomy-Basel

What's behind purple tomatoes? Insight into the mechanisms of anthocyanin synthesis in tomato fruits

(2020) Sara Colanero et al.   PLANT PHYSIOLOGY

Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex

(2020) Takayuki Tohge et al.   Molecular Plant

Ptr1 evolved convergently with RPS2 and Mr5 to mediate recognition of AvrRpt2 in diverse solanaceous species

(2020) Carolina Mazo‐Molina et al.   PLANT JOURNAL

The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire

(2020) Burkhard Steuernagel et al.   PLANT PHYSIOLOGY

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

Molecular Characterization of Differences between the Tomato Immune Receptors Flagellin Sensing 3 and Flagellin Sensing 2

(2020) Robyn Roberts et al.   PLANT PHYSIOLOGY

De novo genome assembly of two tomato ancestors, solanum pimpinellifolium and S. lycopersicum var. cerasiforme, by long-read sequencing

(2020) Hitomi Takei et al.   DNA RESEARCH

Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

(2020) Xin Wang et al.   Nature Communications

Nutritional Composition and Bioactive Compounds in Tomatoes and Their Impact on Human Health and Disease: A Review

(2020) Md Yousuf Ali et al.   Foods

MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis

(2019) Rainer Schwacke et al.   Molecular Plant

The Ptr1 locus of Solanum lycopersicoides confers resistance to race 1 strains of Pseudomonas syringae pv. tomato and to Ralstonia pseudosolanacearum by recognizing the type III effectors AvrRpt2/RipBN

(2019) Carolina Mazo-Molina et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Anthocyanin Fruit encodes an R2R3‐MYB transcription factor, SlAN2‐like, activating the transcription of SlMYBATV to fine‐tune anthocyanin content in tomato fruit

(2019) Shuangshuang Yan et al.   NEW PHYTOLOGIST

TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model

(2019) Gökhan Karakülah et al.   PeerJ

The genetics of fruit flavour preferences

(2018) Harry J. Klee et al.   NATURE REVIEWS GENETICS

A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population

(2018) Yaacov Micha Brog et al.   PLANT JOURNAL

Leveraging multiple transcriptome assembly methods for improved gene structure annotation

(2018) Luca Venturini et al.   GigaScience

Computational aspects underlying genome to phenome analysis in plants

(2018) Anthony M. Bolger et al.   PLANT JOURNAL

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

(2018) Shan Wu et al.   Nature Communications

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis

(2018) Daniel Mapleson et al.   GigaScience

Population Genomics in Wild Tomatoes—The Interplay of Divergence and Admixture

(2017) Ian Beddows et al.   Genome Biology and Evolution

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Green-fruited Solanum habrochaites lacks fruit-specific carotenogenesis due to metabolic and structural blocks

(2017) Himabindu Vasuki Kilambi et al.   JOURNAL OF EXPERIMENTAL BOTANY

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Arabidopsis thaliana RECEPTOR DEAD KINASE1 Functions as a Positive Regulator in Plant Responses to ABA

(2017) Dhinesh Kumar et al.   Molecular Plant

The Tomato Kinase Pti1 Contributes to Production of Reactive Oxygen Species in Response to Two Flagellin-Derived Peptides and Promotes Resistance to Pseudomonas syringae Infection

(2017) Simon Schwizer et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

AtPDS overexpression in tomato: exposing unique patterns of carotenoid self-regulation and an alternative strategy for the enhancement of fruit carotenoid content

(2017) Ryan P. McQuinn et al.   PLANT BIOTECHNOLOGY JOURNAL

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

VirusDetect: An automated pipeline for efficient virus discovery using deep sequencing of small RNAs

(2017) Yi Zheng et al.   VIROLOGY

Overexpression of annexin gene AnnSp2, enhances drought and salt tolerance through modulation of ABA synthesis and scavenging ROS in tomato

(2017) Raina Ijaz et al.   Scientific Reports

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Distinct Mechanisms of the ORANGE Protein in Controlling Carotenoid Flux

(2016) Noam Chayut et al.   PLANT PHYSIOLOGY

Genomic variation in tomato, from wild ancestors to contemporary breeding accessions

(2015) José Blanca et al.   BMC GENOMICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

(2015) Susan R. Strickler et al.   PeerJ

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Resistance to Botrytis cinerea in Solanum lycopersicoides involves widespread transcriptional reprogramming

(2014) Jonathon E Smith et al.   BMC GENOMICS

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Exploring genetic variation in the tomato (SolanumsectionLycopersicon) clade by whole-genome sequencing

(2014) et al.   PLANT JOURNAL

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Pto Kinase Binds Two Domains of AvrPtoB and Its Proximity to the Effector E3 Ligase Determines if It Evades Degradation and Activates Plant Immunity

(2014) Johannes Mathieu et al.   PLoS Pathogens

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines

(2013) D. H. Chitwood et al.   PLANT CELL

Dissection of Tomato Lycopene Biosynthesis through Virus-Induced Gene Silencing

(2013) E. Fantini et al.   PLANT PHYSIOLOGY

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Chromosome evolution in Solanum traced by cross-species BAC-FISH

(2012) Dóra Szinay et al.   NEW PHYTOLOGIST

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

How Can Research on Plants Contribute to Promoting Human Health?

(2011) Cathie Martin et al.   PLANT CELL

A tomato LysM receptor-like kinase promotes immunity and its kinase activity is inhibited by AvrPtoB

(2011) Lirong Zeng et al.   PLANT JOURNAL

Combined transcriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation

(2011) Je Min Lee et al.   PLANT JOURNAL

Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens

(2010) Elena Albrecht et al.   ANNALS OF BOTANY

R/qtl: high-throughput multiple QTL mapping: Fig. 1.

(2010) Danny Arends et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Seedling salt tolerance in tomato

(2010) Junming Li et al.   EUPHYTICA

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

Interspecific reproductive barriers in the tomato clade: opportunities to decipher mechanisms of reproductive isolation

(2010) Patricia A. Bedinger et al.   SEXUAL PLANT REPRODUCTION

13C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research

(2009) Patrick Giavalisco et al.   ANALYTICAL CHEMISTRY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Multiple Repeats of a Promoter Segment Causes Transcription Factor Autoregulation in Red Apples

(2009) R. V. Espley et al.   PLANT CELL

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Comparative genetic linkage map of Solanum sect. Juglandifolia: evidence of chromosomal rearrangements and overall synteny with the tomatoes and related nightshades

(2008) Elena Albrecht et al.   THEORETICAL AND APPLIED GENETICS