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 - <p>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.</p>
ER -