KV 1509-025 Genome reconstruction and structural detection for Solanum lycopersicum (BO-26.03-007-003)

Despite the powerful Next Generation Sequencing technology and genome assembly algorithms, disclosure of genome structures, which is needed to assess colinearity, has not reached a level that allows selection of compatible donor species and recipient crops for sequence based ‘precision breeding’, nor does it allow assessment of the genome structure diversity as a basis for understanding the tomato pan-genome, phylogenetic relationships of crop accessions and related wild species, and chromosome evolution. This limitation is mainly due to highly fragmented assemblies from short NGS reads, consisting of sequence contigs lacking scaffold order, position, and orientation information. Disclosure of genome structure is of eminent practical importance for efficient hybridization breeding, as genome structure of the parental species is a crucial factor directly influencing crossing success. Furthermore, insight in genome structures is needed to understand chromosome rearrangement dynamics, explain genome evolution, and necessary for the analysis of the topological context of target genes. This project aims at improving contiguity and completing fragmented NGS assemblies that have been generated in the 150 tomato genome project tomato crop accessions and related wild species. The improved contiguity will allow a more comprehensive view of genome structures and insight into structural variations supporting the selection of compatible breeding parents in relation to target traits.