Single Primer Enrichment Technology (SPET) for High-Throughput Genotyping in Tomato and Eggplant Germplasm

Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize

(2019) Davide Scaglione et al.   ANNALS OF BOTANY

A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution

(2019) Lorenzo Barchi et al.   Scientific Reports

Genetic diversity in a collection of Italian long storage tomato landraces as revealed by SNP markers array

(2018) Valentina Tranchida-Lombardo et al.   PLANT BIOSYSTEMS

The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance

(2018) Rozaimi Razali et al.   Frontiers in Plant Science

Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants

(2017) Pietro Gramazio et al.   EUPHYTICA

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

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

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application

(2017) Armin Scheben et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands

(2017) Yveline Pailles et al.   Frontiers in Plant Science

Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

(2017) Alberto Acquadro et al.   PLoS One

Crop wild relatives of the brinjal eggplant (Solanum melongena ): Poorly represented in genebanks and many species at risk of extinction

(2016) Mindy M. Syfert et al.   AMERICAN JOURNAL OF BOTANY

The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato

(2016) Francisco J. Herraiz et al.   BMC GENOMICS

JAK-STAT and G-protein-coupled receptor signaling pathways are frequently altered in epitheliotropic intestinal T-cell lymphoma

(2016) M-L Nairismägi et al.   LEUKEMIA

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Development of backcross generations and new interspecific hybrid combinations for introgression breeding in eggplant ( Solanum melongena )

(2016) Brice Kouassi et al.   SCIENTIA HORTICULTURAE

Using genomic repeats for phylogenomics: a case study in wild tomatoes (SolanumsectionLycopersicon: Solanaceae)

(2015) Steven Dodsworth et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

(2015) José Blanca et al.   BMC GENOMICS

High-throughput genotyping for species identification and diversity assessment in germplasm collections

(2015) Annaliese S. Mason et al.   Molecular Ecology Resources

MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes

(2015) Mun Hua Tan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

(2015) Jonathan A. Scolnick et al.   PLoS One

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

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

(2014) et al.   PLANT JOURNAL

Conventional and phenomics characterization provides insight into the diversity and relationships of hypervariable scarlet (Solanum aethiopicum L.) and gboma (S. macrocarpon L.) eggplant complexes

(2014) Mariola Plazas et al.   Frontiers in Plant Science

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

(2013) Tiina Särkinen et al.   BMC EVOLUTIONARY BIOLOGY

African spinySolanum(subgenusLeptostemonum, Solanaceae): a thorny phylogenetic tangle

(2013) Maria. S. Vorontsova et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Genetics and Consequences of Crop Domestication

(2013) Sherry A. Flint-Garcia   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement

(2013) Kassa Semagn et al.   MOLECULAR BREEDING

The Population Structure and Diversity of Eggplant from Asia and the Mediterranean Basin

(2013) Fabio Cericola et al.   PLoS One

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication

(2012) Rachel S. Meyer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

(2012) Sung-Chur Sim et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Development and characterization of genomic simple sequence repeat markers in eggplant and their application to the study of diversity and relationships in a collection of different cultivar types and origins

(2011) Santiago Vilanova et al.   MOLECULAR BREEDING

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

SNPs Occur in Regions with Less Genomic Sequence Conservation

(2011) John C. Castle   PLoS One

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits

(2010) L. Kamenetzky et al.   PLANT PHYSIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history?

(2009) Flor Rodriguez et al.   BMC EVOLUTIONARY BIOLOGY

DID EGG-LAYING BOAS BREAK DOLLO'S LAW? PHYLOGENETIC EVIDENCE FOR REVERSAL TO OVIPARITY IN SAND BOAS (ERYX: BOIDAE)

(2009) Vincent J. Lynch et al.   EVOLUTION

Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles

(2009) Robert C. Thomson et al.   SYSTEMATIC BIOLOGY

ISSR variations in eggplant (Solanum melongena L.) and related Solanum species

(2008) Shiro Isshiki et al.   SCIENTIA HORTICULTURAE