Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

Tomato breeding in the genomics era: insights from a SNP array

(2013) Marcela Víquez-Zamora et al.   BMC GENOMICS

Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

(2013) Mathilde Causse et al.   BMC GENOMICS

Genome-Wide Association Studies Using Single Nucleotide Polymorphism Markers Developed by Re-Sequencing of the Genomes of Cultivated Tomato

(2013) K. Shirasawa et al.   DNA RESEARCH

SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

(2013) Cristina Esteras et al.   THEORETICAL AND APPLIED GENETICS

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA–Dependent RNA Polymerases

(2013) Maarten G. Verlaan et al.   PLoS Genetics

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

(2012) Joanne A Labate et al.   BMC PLANT BIOLOGY

Next-generation sequencing for understanding and accelerating crop domestication

(2012) R. J. Henry   Briefings in Functional Genomics

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

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

(2012) Aureliano Bombarely et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato

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

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

Variation Revealed by SNP Genotyping and Morphology Provides Insight into the Origin of the Tomato

(2012) Jose Blanca et al.   PLoS One

A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.)

(2012) Matthew W. Blair et al.   THEORETICAL AND APPLIED GENETICS

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

(2010) S-C Sim et al.   HEREDITY

Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato

(2010) Matthew D. Robbins et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE