A chromosome-level genome assembly ofSolanum chilense, a tomato wild relative associated with resistance to salinity and drought

Abstract

AbstractSolanum chilenseis a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. In this study we generated a high-quality, chromosome-level,de novoassembly for theS. chilenseaccession LA1972 using a hybrid assembly strategy with ∼180 Gbp of Illumina short reads and ∼50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium® reads. The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ∼219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for ade novotranscriptome assembly. This chromosome-level, high-quality reference genome forS. chilenseaccession LA1972 will support future breeding efforts for more sustainable tomato production. Gene sequences related to drought and salt resistance were compared betweenS. chilenseandS. lycopersicumto identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1andethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.