ArticleBMC genomics2013
Frequent loss of lineages and deficient duplications accounted for low copy number of disease resistance genes in Cucurbitaceae.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 69 citations in OpenAlex.
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
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- Local gene duplications drive extensive NLR copy number variation across multiple genotypes of Theobroma cacao.G3 (Bethesda, Md.) · 2025Article
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- Recent advances in the improvement of genetic resistance against disease in vegetable crops.Plant physiology · 2024Review
- Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome.Genome biology and evolution · 2024Article
- A highly diversified NLR cluster in melon contains homologs that confer powdery mildew and aphid resistance.Horticulture research · 2024Article
- Jurassic NLR: Conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1.The Plant cell · 2023Article
- Contribution of Duplicated Nucleotide-Binding Leucine-Rich Repeat (NLR) Genes to Wheat Disease Resistance.Plants (Basel, Switzerland) · 2023Review
- Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants.Plants (Basel, Switzerland) · 2023Review
- High-qualityFrontiers in plant science · 2023Article
- Unmasking the invaders: NLR-mal function in plant defense.Frontiers in plant science · 2023Review
- Article
- Genome-Wide Identification and Characterization of theInternational journal of molecular sciences · 2022Article
- Genome-Wide Analysis ofFrontiers in genetics · 2022Article
- Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in fourFrontiers in plant science · 2022Article
- Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered PlantPlants (Basel, Switzerland) · 2021Article
- Large-scale gene gains and losses molded the NLR defense arsenal during the Cucurbita evolution.Planta · 2021Article
- Plant NLR diversity: the known unknowns of pan-NLRomes.The Plant cell · 2021Review
- Distinct Evolutionary Patterns of NBS-Encoding Genes in Three Soapberry Family (Sapindaceae) Species.Frontiers in genetics · 2020Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe sequenced genomes of cucumber, melon and watermelon have relatively few R-genes, with 70, 75 and 55 copies only, respectively. The mechanism for low copy number of R-genes in Cucurbitaceae genomes remains unknown.
resultsManual annotation of R-genes in the sequenced genomes of Cucurbitaceae species showed that approximately half of them are pseudogenes. Comparative analysis of R-genes showed frequent loss of R-gene loci in different Cucurbitaceae species. Phylogenetic analysis, data mining and PCR cloning using degenerate primers indicated that Cucurbitaceae has limited number of R-gene lineages (subfamilies). Comparison between R-genes from Cucurbitaceae and those from poplar and soybean suggested frequent loss of R-gene lineages in Cucurbitaceae. Furthermore, the average number of R-genes per lineage in Cucurbitaceae species is approximately 1/3 that in soybean or poplar. Therefore, both loss of lineages and deficient duplications in extant lineages accounted for the low copy number of R-genes in Cucurbitaceae. No extensive chimeras of R-genes were found in any of the sequenced Cucurbitaceae genomes. Nevertheless, one lineage of R-genes from Trichosanthes kirilowii, a wild Cucurbitaceae species, exhibits chimeric structures caused by gene conversions, and may contain a large number of distinct R-genes in natural populations.
conclusionsCucurbitaceae species have limited number of R-gene lineages and each genome harbors relatively few R-genes. The scarcity of R-genes in Cucurbitaceae species was due to frequent loss of R-gene lineages and infrequent duplications in extant lineages. The evolutionary mechanisms for large variation of copy number of R-genes in different plant species were discussed.
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