Data underlying the publication: Lactuca super-pangenome reduces bias towards reference genes in lettuce research

Supplementary data belonging to "<em>Lactuca</em> super-pangenome reduces bias towards reference genes in lettuce research". In order to get an overview of the gene content of the genus <em>Lactuca</em>, we used WGS data of 474 accessions beloning to <em>L. sativa</em>, <em>L. serriola</em>, <em>L. saligna</em> and <em>L. virosa</em> for the construction of a linear pangenome per species. This linear pangenome was built using the assemble-and-iteratively-add approach. Once constructed, presence-absence variation (PAV) and copy-number variation (CNV) were calculated from the WGS data on the linear pangenomes. The PAV data was integrated across species into a <em>Lactuca</em> wide table that contains the variation for each of the 474 accessions for all genes in the super-pangenome. This super-pangenome resource was then used for functional characterisation of the core and variable genes, and a phylogeny of all accessions. Finally, we used the <em>L. sativa</em> PAV data to show its complementary and benefits in GWAS over SNPs. All data underlying these analyses is bundled together in one tarball including README.