UC Davis

Pangenome analysis becomes increasingly necessary as multiple genomes are sequenced from the same species. Lettuce (Lactuca sativa L.) is a commercially important crop with an annual farm-gate value of more than $3.1 billion in the United States. Whole genome re-sequencing efforts are underway to identify variations among different lettuce cultivars and wild germplasm. This dissertation reports on the generation and annotation of a new high-quality, telomere-to-telomere v11 reference genome assembly of L. sativa cv. Salinas based on Pacific BioSciences High-Fidelity reads, as a foundation for pangenome analyses. Chromosome-scale, high-quality assemblies were also generated for four domesticated genotypes of L. sativa (cv. La Brillante, cv. Ninja, PI251246, VIAE) and two wild accessions of L. serriola (US96UC23, Armenian 999). Several contemporary, publicly available, graph-based pangenome tools were evaluated for their ability to explore the large genome (~2.7 Gb) and high repeat content of Lactuca spp. Based on these assemblies, a pangenome of ~3 Gb encoding a total of 212,497 genes was generated. These genes were classified into 36,959 orthologous gene families, of which 23,751 were core families and 9,864 were dispensable families. Structural variants were assessed relative to the reference genome. Results from this pangenome analysis will allow the mapping of introgressed segments and a better understanding of structural and functional differences specific to a genotype. This dissertation provides a workflow for expanded pangenome analyses as more genome assemblies of Lactuca spp. become available in the near future. The pangenome resources will provide a foundation for syntenic inferences across multiple genotypes and species in the lettuce genepool and facilitate map-based cloning of agriculturally important genes.