Genomic structural variants (SVs), including insertions/deletions (indels), inversions, and duplications, are the causative genetic variants for many domestication traits of crops 7. Recently, a chromosome-scale assembly of an SP accession, BGV006775, was generated using Nanopore long reads, providing a valuable resource for the Solanaceae community 6. Although these assemblies provided some essential genomic information for SP, they are highly fragmented and incomplete, limiting their applications as robust references in tomato breeding and research. 5), have been generated using Illumina short-read sequencing technology. Due to the importance of SP, draft genome assemblies of two accessions, LA1589 (ref. The fact that SP can freely hybridize with SLL has enabled the incorporation of SP alleles into modern tomato cultivars to improve disease resistance, abiotic stress tolerance, and other fruit quality traits 3. cerasiforme (SLC), which was later improved into the big-fruited tomato S. It was domesticated in South America to give rise to S. pimpinellifolium (SP) carrying red, small, and round fruits is the wild progenitor of the cultivated tomato. Tomato ( Solanum lycopersicum) is the world’s leading vegetable crop with a total production of 182 million tons and a worth over US $60 billion in 2018 ( ). The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato.
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