ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2024
Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- De novo haplotype-resolved genome assembly of the endemic kiwifruit Actinidia hubeiensis.Scientific data · 2026Article
- Chromosome-level haplotype-resolved genome assembly of kiwifruit (Actinidia eriantha).Scientific data · 2026Article
- Kiwifruit genomics and applications: recent advances, current challenges, and future prospects.Horticulture research · 2026Article
- Allelic structural variation at the NLR25-1 locus enhances defense against Pseudomonas syringae in kiwifruit.Genome biology · 2026Article
- Pangenome Analysis Reveals Structural Variations Associated With Citric Acid Accumulation in Prunus mume.Plant biotechnology journal · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Pangenome analyses of tea plants reveal structural variations driving gene expression alterations and agronomic trait diversification.Nature communications · 2025Article
- KPGD: A kiwifruit pangenome database for comprehensive mining of genetic diversity in the genus Actinidia.Plant communications · 2025Article
- A chromosome-level genome assembly of Guimi No. 2 (Actinidia chinensis).Scientific data · 2025Article
- Construction of the super pan-genome for the genusHorticulture research · 2025Article
- Chromosome-level genome assembly assisting for dissecting mechanism of anthocyanin regulation in kiwifruit (Actinidia arguta).Molecular horticulture · 2025Article
- Expression Analysis of Chlorophyll-Degradation-Related Genes inPlants (Basel, Switzerland) · 2025Article
- Genome-wide identification and expression analysis of proline synthesis and catabolism genes in kiwifruit: exploring the role ofFrontiers in plant science · 2025Article
- Genomes of diverse Actinidia species provide insights into cis-regulatory motifs and genes associated with critical traits.BMC biology · 2024Article
- Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
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Authors and funding
17 authors.
Funding
Abstract
Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.
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