ArticleInternational journal of molecular sciences2023
Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber.
Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 27 citations in OpenAlex.
- Comparative complete chloroplast genome analysis ofFrontiers in plant science · 2026Article
- Characterization of the chloroplast genome of a relict tree, Pterocarya fraxinifolia (Juglandaceae), and its comparative analysis.Scientific reports · 2025Article
- Wheat chloroplast pangenome reveals frequent intramolecular recombination in the inverted repeat regions.BMC plant biology · 2025Article
- The cucumber (Cucumis sativus L.) mitochondrial genome: intraspecific structural variation, repetitive architecture, and comparative evolutionary dynamics.BMC plant biology · 2025Article
- Comparative analysis of Chloroplast genomes in 48 samples from 5 species and 2 varieties of Agropyron Gaertn. (Poaceae, Triticeae).BMC genomics · 2025Article
- Plastid Phylogenomics ofInternational journal of molecular sciences · 2025Article
- Pan-Plastome Analysis Reveals the Genetic Diversity and Genetic Divergence ofInternational journal of molecular sciences · 2025Article
- Comparative pan-genome analysis of Huperzia and Phlegmariurus and transcriptomics reveals thermal adaptation in Huperzia.Functional & integrative genomics · 2025Article
- Comparative Genomics and Phylogenetics of Chloroplasts Reveal Lower Rates of Genetic Variation in Mango (Ecology and evolution · 2025Article
- Current and future pangenomic research in cucurbit crops.Breeding science · 2025Article
- Mitochondrial Genome Insights into Evolution and Gene Regulation inInternational journal of molecular sciences · 2025Article
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- Comparative Chloroplast Genomes Analysis Provided Adaptive Evolution Insights inInternational journal of molecular sciences · 2024Article
- Decoding the Chloroplast Genome ofInternational journal of molecular sciences · 2024Article
- Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation inInternational journal of molecular sciences · 2024Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616-157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339-86,883 bp), a small single copy (SSC, 18,069-18,363 bp), and two inverted repeats (IRs, 25,166-25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that
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