TY - DATA
T1 - Supplementary data for the publication: Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding
PY - 2023/09/04
AU - Wei Xiong
UR - https://data.4tu.nl/articles/dataset/_/21900588
DO - 10.4121/21900588.v1
KW - lettuce breeding
KW - Lactuca virosa
KW - genome assembly
KW - immune genes
KW - Transposable Elements
KW - comparative genomics
KW - plant genome evolution
N2 - <p class="ql-align-justify">This dataset supports the <em>Lactuca virosa</em> genome assembly manuscript published on <strong>G3:Genes|Genomes|Genetics</strong> journal, entitled: Genome assembly and analysis of <em>Lactuca virosa</em>: implications for lettuce breeding. <em style="color: black;">Lactuca virosa</em><span style="color: black;"> (bitter lettuce) belongs to the Asteraceae, the largest flowing plant family, and is a wild relative of the economic crop lettuce (</span><em style="color: black;">Lactuca sativa</em><span style="color: black;"> L.) found across Eurasia. Despite the hybrid barrier, </span><em style="color: black;">L. virosa</em><span style="color: black;"> can still be crossed with lettuce via the bridge of </span><em style="color: black;">L. serriola</em><span style="color: black;"> or embryo rescue techniques. </span><em style="color: black;">L. virosa</em><span style="color: black;"> is resistant to various pests and pathogens and therefore an essential donor of genetic variation for lettuce breeding, especially resistance to the currant-lettuce aphid (</span><em style="color: black;">Nasonovia ribisnigri</em><span style="color: black;">). Moreover, </span><em style="color: black;">L. virosa</em><span style="color: black;"> contributes to agronomic traits like a robust root system and mitigated defoliation in modern crisphead cultivars via introgression breeding. To date, the genetic variation of the mentioned traits and the pedigree history of hybridization remains primarily unknown for </span><em style="color: black;">L. virosa</em><span style="color: black;">. </span>In contrast to other species within the lettuce gene pool, <em>L. virosa</em> has a significantly larger genome size, potentially hampering chromosome pairing. <span style="color: black;">This combination of breeding and fundamental interests has attracted collaborators with diverse expertise from different fields to participate in this project</span>. To <span style="color: black;">obtain a high-quality genome sequence for </span><em style="color: black;">L. virosa</em><span style="color: black;">,</span> we employed<span style="color: black;"> a mixed dataset of long-read (Pacbio 20x) and short-read (Illumina 70x) sequencing and scaffolding approaches of Bionano and Hi-C technologies. The resulting assembly has 5,855 super-scaffolds with an N50 of 316.9 Mb. The final assembly contains 3.45 Gb (96% complete BUSCOs) and 39,887 predicted gene models (90% complete BUSCOs). This reference genome sequence of </span><em style="color: black;">L. virosa</em><span style="color: black;"> obtained in this study provides knowledge about genomic and genetic variation within this species. It facilitates various genomic comparisons to two other available </span><em style="color: black;">Lactuca</em><span style="color: black;"> genome assemblies (</span><em style="color: black;">L. sativa</em><span style="color: black;"> and </span><em style="color: black;">L. saligna</em><span style="color: black;">), forming a complete spectrum of the lettuce germplasm for lettuce breeding. This dataset contains five files, containing the detailed outputs of the genome assembling, genome annotation, homology grouping and whole-genome screening.</span></p>
ER -