ArticleGigaScience2019
A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
- Genetic variation in a plant-parasitic nematode is associated with host gene expression changes conserved across evolutionarily distant host plants.G3 (Bethesda, Md.) · 2026Article
- Development of long InDel markers through whole genome resequencing for variety purity detection in cucumber.Scientific reports · 2026Article
- Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon.Nature genetics · 2026Article
- Comprehensive analysis of the GeBP gene family in cucumber highlights functional divergence in fruit development and stress tolerance.BMC plant biology · 2026Article
- A PLETHORA3/7 transcription factor shapes cucumber shoot architecture.The New phytologist · 2026Article
- Multiomics analysis ofHorticulture research · 2026Article
- Graph-based pangenome reveals structural variation dynamics during cucumber breeding.Nature genetics · 2026Article
- A comprehensive analysis of two Chinese cucumber genomes and a mutant population as resources for precision breeding.Horticulture research · 2026Article
- Comparative analysis of the Aquaporin gene family in Cucurbitaceae: insights into evolutionary patterns and functional diversity.BMC plant biology · 2026Article
- Haplotype applications in genomic selection.Genome biology · 2026Review
- Genome-wide identification of HXK gene families in cucumber and watermelon: CsHXK1 and ClHXK6 play key roles in responding to multiple stresses.BMC plant biology · 2026Article
- Molecular Pathways Associated with Cold Tolerance in Grafted Cucumber (Plants (Basel, Switzerland) · 2025Article
- A near-complete genome assembly of cucumber line 6457 and identification of candidate gene controlling pedicel length.Horticulture research · 2025Article
- The cucumber (Cucumis sativus L.) mitochondrial genome: intraspecific structural variation, repetitive architecture, and comparative evolutionary dynamics.BMC plant biology · 2025Article
- Co-domestication of cold tolerance and female flower is determined by CsEIN2 in cucumber.Plant biotechnology journal · 2025Article
- Multiomics analysis of gibberellin involved in far-red light-regulated internode elongation in cucumber seedlings.Plant cell reports · 2025Article
- Better together: Subgenomes for allotetraploid potato wild relative Solanum acaule Bitt. reveal origins in Petota Clade 3 and 4.The plant genome · 2025Article
- Interspecies predictions of growth traits from quantitative transcriptome data acquired during fruit development.Journal of experimental botany · 2025Article
- The silicon efflux transporter BEC1 is essential for bloom formation and stress tolerance in cucumber.Journal of integrative plant biology · 2025Article
- Cucumber green mottle mosaic virus encodes additional small proteins with specific subcellular localizations and virulence function.Science China. Life sciences · 2025Article
57 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAccurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential.
findingsWe assembled single-molecule real-time (SMRT) long reads to generate an improved cucumber reference genome. This version contains 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, and provides 29.0 Mb more sequence data than previous versions. Using 10X Genomics and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (∼211.0 Mb) were directly linked into 7 pseudo-chromosome sequences. The newly assembled regions show much higher guanine-cytosine or adenine-thymine content than found previously, which is likely to have been inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons and 1,078 novel genes including 239 tandemly duplicated genes. For example, we found 4 tandemly duplicated tyrosylprotein sulfotransferases, in contrast to the single copy of the gene found previously and in most other plants.
conclusionThis high-quality genome presents novel features of the cucumber genome and will serve as a valuable resource for genetic research in cucumber and plant comparative genomics.
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