cff-version: 1.2.0
abstract: "<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>"
authors:
  - family-names: van Workum
    given-names: Dirk-Jan M.
    orcid: "https://orcid.org/0000-0001-6247-5499"
  - family-names: Mehrem
    given-names: Sarah L.
    orcid: "https://orcid.org/0009-0007-7711-0821"
  - family-names: Snoek
    given-names: Basten L.
    orcid: "https://orcid.org/0000-0001-5321-2996"
  - family-names: Alderkamp
    given-names: Marrit C.
  - family-names: Lapin
    given-names: Dmitry
    orcid: "https://orcid.org/0000-0001-9591-3950"
  - family-names: Mulder
    given-names: Flip F. M.
  - family-names: van den Ackerveken
    given-names: Guido
    orcid: "https://orcid.org/0000-0002-0183-8978"
  - family-names: de Ridder
    given-names: D. (Dick)
    orcid: "https://orcid.org/0000-0002-4944-4310"
  - family-names: Eric Schranz
    given-names: M.
    orcid: "https://orcid.org/0000-0001-6777-6565"
  - family-names: Smit
    given-names: Sandra
    orcid: "https://orcid.org/0000-0001-5239-5321"
title: "Data underlying the publication: Lactuca super-pangenome reduces bias towards reference genes in lettuce research"
keywords:
version: 1
identifiers:
  - type: doi
    value: 10.4121/c7935d6a-d6ae-42e7-af7e-0ae8cddf70d7.v1
license: CC BY 4.0
date-released: 2024-06-06