  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 groups. We present a
reconstruction of three new reference genomes in support of our comparative
genome analyses. Sequence diversity in commercial breeding lines appears
extremely low, indicating the dramatic genetic erosion of crop tomatoes. This
is reflected by the SNP count in wild species which can exceed 10 million i.e.
20 fold higher than in crop accessions. Comparative sequence alignment reveals
group, species, and accession specific polymorphisms, which explain
characteristic fruit traits and growth habits in tomato accessions. Using gene
models from the annotated Heinz reference genome, we observe a bias in dN/dS
ratio in fruit and growth diversification genes compared to a random set of
genes, which probably is the result of a positive selection. We detected highly
divergent segments in wild S. lycopersicum species, and footprints of
introgressions in crop accessions originating from a common donor accession.
Phylogenetic relationships of fruit diversification and growth specific genes
from crop accessions show incomplete resolution and are dependent on the
introgression donor. In contrast, whole genome SNP information has sufficient
power to resolve the phylogenetic placement of 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. Our study
illustrates the need for multiple reference genomes in support of tomato
comparative genomics and Solanum genome evolution studies.
