A reference genome of Solanum habrochaites

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Caromel, Bernard | Lagnel, Jacques | Iampietro, Carole | Coant, Marie-Claire Le | Sallaberry, Marine | Duboscq, Renaud | Bachellez, Alexandre | Massire, Anne | Bouchez, Olivier | Lluch, Jérôme | Lefebvre, Véronique

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International audience. Related species have been used in tomato breeding as sources of resistance to many diseases. Genetic maps based on progenies issued from interspecific crosses highlighted chromosomal rearrangements between the cultivated tomato (Solanum lycopersicum) and related species. Genome rearrangements limit therefore the use of the tomato reference genome sequence to study interesting loci in related species. High-quality genomes from tomato-related species are available for S. pimpinellifolium and S. pennellii. However, no high-quality genome is available to date for S. habrochaites, a species carrying resistance to several pests and pathogens. We thus constructed a reference genome of S. habrochaites, using a combination of PacBio Hifi sequencing and Hi-C technology for scaffolding. Following the PacBio Hifi sequencing, we assembled the genome with a total size of 1.03Gbp in 959 contigs, with N50 of 14 Mb, using Hifiasm software. Then, the contigs were scaffolded using Hi-C data to obtain chromosome-scale pseudo-molecules. Finally, the assembly was polished using Illumina short reads. We aim to use this novel reference genome of S. habrochaites to accurately identify resistance QTLs in regions rearranged between the genomes of S. habrochaites and of cultivated tomato.

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