Chromosome-scale genome assemblies of wild tomato relatives Solanum habrochaites and Solanum galapagense reveal structural variants associated with stress tolerance and terpene biosynthesis

Dear Editor, Introducing beneficial genes/alleles from wild relatives into the cultivated tomato has been an important approach for tomato breeding.Solanum habrochaites and S.galapagense have been widely used as germplasm donors in modern breeding to improve biotic and abiotic stress tolerance of tomato.S.habrochaites grows in the Peruvian Andes at altitudes up to 3300 m and is notable for its tolerance of chilling and drought and resistance to many diseases and pests.S.galapagense is endemic to the Galápagos Islands,has extraordinary salt tolerance and insect resistance,and appears even more closely related to the cultivated tomato(Solanum lycopersicum)than Solanum pimpinellifolium,the wild progenitor of cultivated tomato[1].Due to their importance,draft genomes of these two species have been assembled using Illumina short-read sequencing[2]or PacBio long-read sequencing[3].However,high levels of fragmentation and/or the lack of chromosome-scale assemblies have limited their applications in tomato breeding and research.