The de novo reference genome and transcriptome assemblies of the wild tomato species Solanum chilense

Background Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced stress resistance in tomato breeding. In addition, S. chilense serves as a model system to study adaptation of plants to drought and to investigate the evolution of seed banks. However to date, the absence of a well annotated reference genome in this compulsory outcrossing very heterozygote species limited in-depth studies on the genes involved in the above-mentioned processes. Findings We generated ~134 Gb of DNA and 157 Gb of RNA sequence data, which yielded a draft genome with an estimated length of 914 Mb in total encoding2 5,885 high-confidence (hc) predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% (18,290) of the hc gene models are additionally supported by RNAseq data derived from leaf tissue samples. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% BUSCO genes, which is in range of high-quality genome for non-inbred plants. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assess its assembly quality. We reveal the existence of unique gene families of NLRs to S. chilense. Comparative genomics analyses of S. chilense, cultivated tomato S. lycopersicum and its wild relative S. pennellii genomes revealed similar levels of highly syntenic gene clusters between the three species. Conclusions We generated the first genome and transcriptome sequence assembly for the wild tomato species Solanum chilense and demonstrate its value in comparative genomics analyses. We make these genomes available for scientific community as an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, evolution of self-incompatibility, as well as for tomato breeding.