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

doi: 10.4121/c7935d6a-d6ae-42e7-af7e-0ae8cddf70d7.v1
The doi above is for this specific version of this dataset, which is currently the latest. Newer versions may be published in the future. For a link that will always point to the latest version, please use
doi: 10.4121/c7935d6a-d6ae-42e7-af7e-0ae8cddf70d7
Datacite citation style:
van Workum, Dirk-Jan M.; Mehrem, Sarah L.; Snoek, Basten L.; Alderkamp, Marrit C.; Lapin, Dmitry et. al. (2024): Data underlying the publication: Lactuca super-pangenome reduces bias towards reference genes in lettuce research. Version 1. 4TU.ResearchData. dataset.
Other citation styles (APA, Harvard, MLA, Vancouver, Chicago, IEEE) available at Datacite

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.

  • 2024-06-06 first online, published, posted
FASTA, GFF3, .log, R, .out, .pdf, .tsv
  • TTW Perspective programme "LettuceKnow" (grant code P19-17) [more info...] The Dutch Research Council (NWO) and the breeding companies BASF, Bejo Zaden B.V., Limagrain, Enza Zaden Research & Development B.V., Rijk Zwaan Breeding B.V., Syngenta Seeds B.V., and Takii and Company Ltd.
Bioinformatics Group, Wageningen University & Research
Theoretical Biology & Bioinformatics, Utrecht University
Translational Plant Biology, Utrecht University
Biosystematics Group, Wageningen University & Research
Department of Genetics, University Medical Center Utrecht


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