84 tomato accessions - Genetic variation in the tomato clade was explored by sequencing a selection of 84 tomato accessions and related wild species representative for the Lycopersicon, Arcanum, Eriopersicon and Neolycopersicon group. In addition, we present a reconstruction of three new reference genomes in support of our comparative genome analyses. This comparative analysis elucidates species specific chromosome structural differences. Furthermore, sequence diversity in commercial breeding lines appears extremely low, indicating the dramatic genetic erosion of crop tomatoes. For wild species the SNP frequency increases 20 folds to more than 10 million SNPs. Our study unequivocally illustrates the need for multiple reference genomes in support of tomato comparative genomics and Solanum genome evolution studies. Comparative sequence alignment reveals group, species, and accession specific polymorphisms within domestication syndrome genes, which are explanatory for characteristic fruit traits and growth habit in tomato accessions. Using gene models from the annotated Heinz reference genome, we observe a bias in dN/dS ratio in domestication syndrome genes compared to a random set of genes which probably is the result of a positive selection. Based on whole genome SNP information, we unambiguously resolved the phylogenetic placement for each accession in the four main groups in the Lycopersicon clade using Maximum Likelihood analyses. Phylogenetic relationships appear correlated with habitat and mating type and point to the occurrence of geographical races within these groups and thus are of practical importance for introgressive hybridization breeding.