TY - DATA T1 - Supplementary data for the publication: Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding PY - 2023/09/04 AU - Wei Xiong UR - https://data.4tu.nl/articles/dataset/_/21900588 DO - 10.4121/21900588.v1 KW - lettuce breeding KW - Lactuca virosa KW - genome assembly KW - immune genes KW - Transposable Elements KW - comparative genomics KW - plant genome evolution N2 -

This dataset supports the Lactuca virosa genome assembly manuscript published on G3:Genes|Genomes|Genetics journal, entitled: Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding. Lactuca virosa (bitter lettuce) belongs to the Asteraceae, the largest flowing plant family, and is a wild relative of the economic crop lettuce (Lactuca sativa L.) found across Eurasia. Despite the hybrid barrier, L. virosa can still be crossed with lettuce via the bridge of L. serriola or embryo rescue techniques. L. virosa is resistant to various pests and pathogens and therefore an essential donor of genetic variation for lettuce breeding, especially resistance to the currant-lettuce aphid (Nasonovia ribisnigri). Moreover, L. virosa contributes to agronomic traits like a robust root system and mitigated defoliation in modern crisphead cultivars via introgression breeding. To date, the genetic variation of the mentioned traits and the pedigree history of hybridization remains primarily unknown for L. virosa. In contrast to other species within the lettuce gene pool, L. virosa has a significantly larger genome size, potentially hampering chromosome pairing. This combination of breeding and fundamental interests has attracted collaborators with diverse expertise from different fields to participate in this project. To obtain a high-quality genome sequence for L. virosa, we employed a mixed dataset of long-read (Pacbio 20x) and short-read (Illumina 70x) sequencing and scaffolding approaches of Bionano and Hi-C technologies. The resulting assembly has 5,855 super-scaffolds with an N50 of 316.9 Mb. The final assembly contains 3.45 Gb (96% complete BUSCOs) and 39,887 predicted gene models (90% complete BUSCOs). This reference genome sequence of L. virosa obtained in this study provides knowledge about genomic and genetic variation within this species. It facilitates various genomic comparisons to two other available Lactuca genome assemblies (L. sativa and L. saligna), forming a complete spectrum of the lettuce germplasm for lettuce breeding. This dataset contains five files, containing the detailed outputs of the genome assembling, genome annotation, homology grouping and whole-genome screening.

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