TY - DATA T1 - Data underlying the publication: Lactuca super-pangenome reduces bias towards reference genes in lettuce research PY - 2024/06/06 AU - Dirk-Jan M. van Workum AU - Sarah L. Mehrem AU - Basten L. Snoek AU - Marrit C. Alderkamp AU - Dmitry Lapin AU - Flip F. M. Mulder AU - Guido van den Ackerveken AU - D. (Dick) de Ridder AU - M. Eric Schranz AU - Sandra Smit UR - DO - 10.4121/c7935d6a-d6ae-42e7-af7e-0ae8cddf70d7.v1 KW - lettuce KW - Lactuca sativa KW - pangenomics KW - super-pangenome KW - PAV-GWAS N2 -

Supplementary data belonging to "Lactuca super-pangenome reduces bias towards reference genes in lettuce research". In order to get an overview of the gene content of the genus Lactuca, we used WGS data of 474 accessions beloning to L. sativa, L. serriola, L. saligna and L. virosa 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 Lactuca 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 L. sativa 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.

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