Plant breeders face many challenges in their line of work. Among those is the constant need to innovate. New customer preferences, higher nutritional value, the need for resistant crops and increased stress tolerance (biological or environmental) are some of the reasons for the need to develop innovative crops with new traits. The knowledge of the natural variation and the exploitation of the genetic diversity of available plants (crops or wild) is the most powerful tool at the disposition of breeders. Tomato is a commercially important crop and it is a model species for fleshy fruit plants and the important nightshade clade. In this thesis I have created a large dataset of 82 resequenced varieties (52 crop accessions and 30 wild accessions from 13 species), 3 new de novo wild tomato genomes and 3 new programs for assisting in new genomic initiatives. From introgression analysis, species identification and assembly closure, the body of work presented in this thesis should serve the genomics research community, and especially those involved in plant breeding, to improve their workflow and reduce analysis time.