Genome assembly and analysis of Lactuca virosa : implications for lettuce breeding

作者：Wei Xiong, Dirk‐Jan M. van Workum, Lidija Berke, Linda V. Bakker, Elio Schijlen, Frank F M Becker, Henri van de Geest, Sander Peters, Richard W. Michelmore, R. van Treuren, Marieke Jeuken, Sandra Smit, M. Eric Schranz · 发表于：G3 Genes Genomes Genetics · 年份：2023 · DOI：10.1093/g3journal/jkad204 · 被引用次数：14 · 研究领域：Plant Molecular Biology Research、Chromosomal and Genetic Variations、Plant tissue culture and regeneration

Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x = 2n = 18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the 3 Lactuca species as core, accessory, and unique. In addition, we identified 3 interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using 3-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicated the evolutionary patterns and mechanism...