{
  "abstract": "The genus Zingiber represents an economically important group within Zingiberaceae, distinguished by its aromatic and bioactive rhizomes. Zingiber striolatum Diels is an endemic Chinese medicinal and edible plant highly valued for its flower buds, which are rich in natural red pigments (yanghe red pigment, YRP). Here, we present the first haplotype-resolved, chromosome-scale assembly of 'Ziyanghe,' a purplish-red-bud cultivar widely grown in Guizhou Province. The triploid genome was resolved into three haplotypes: subA (2.80 Gb), subB1 (2.66 Gb), and subB2 (2.64 Gb), with the latter two exhibiting strong collinearity. Comparative analysis across five Zingiberaceae genomes revealed a family-specific whole-genome duplication ~ 52.5 million years ago (Mya) and lineage-specific bursts of long terminal repeat retrotransposons occurring between 0.15 and 0.66 Mya. These events likely contributed to substantial genome expansion in Z. striolatum. Evolutionary analysis of gene families suggested parallel subgenome adaptation to montane shade environments and rhizome-specific volatile biosynthesis. Metabolomic profiling identified cyanidin-3-O-glucoside, peonidin-3-O-glucoside, delphinidin-3-O-glucoside, and delphinidin-3-O-rutinoside as the major YRP components, with quercetin-3-O-glucoside functioning as a co-pigment. Integrated multi-omics analysis provides a preliminary molecular framework for YRP biosynthesis. This high-quality genomic resource significantly enhances phylogenomic understanding of Zingiberaceae and provides a foundation for the genetic improvement and metabolic engineering of anthocyanin biosynthesis in this species.",
  "abstract_shown": true,
  "affiliations": [
    "College of Ecology, Zunyi Normal University, Zunyi 563006, China.",
    "State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.",
    "Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China.",
    "China Strait Horticulture Technology Innovation Hub, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 13,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Zhi-Feng Chen"
    },
    {
      "affs": [
        0
      ],
      "name": "Wei-Hong Sun"
    },
    {
      "affs": [
        1
      ],
      "name": "Li-Yao Su"
    },
    {
      "affs": [
        2
      ],
      "name": "Guo-Fei Tan"
    },
    {
      "affs": [
        0
      ],
      "name": "Yu Lu"
    },
    {
      "affs": [
        0
      ],
      "name": "Lian Luo"
    },
    {
      "affs": [
        3
      ],
      "name": "Wen-Hui Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Chun-Xiao Li"
    },
    {
      "affs": [
        0
      ],
      "name": "Zi-Wei Tan"
    },
    {
      "affs": [
        0
      ],
      "name": "Zhuang Zhao"
    },
    {
      "affs": [
        0
      ],
      "name": "Chang-Ling Sui"
    },
    {
      "affs": [
        3
      ],
      "name": "Zhong-Jian Liu",
      "orcid": "0000-0003-4390-3878"
    },
    {
      "affs": [
        1
      ],
      "name": "Ai-Sheng Xiong",
      "orcid": "0000-0002-7900-5001"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/dpkzr2hew3t2p.bib",
  "cited_by": 0,
  "doi": "10.1093/hr/uhag214",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13719175/?tool=EBI",
  "id": "dpkzr2hew3t2p",
  "issns": [
    "2662-6810",
    "2052-7276"
  ],
  "landing_url": "https://europepmc.org/article/PMC/PMC13719175",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI01140"
    ],
    [
      "heading",
      "AcademicSubjects/SCI01210"
    ],
    [
      "heading",
      "Article"
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    [
      "openalex",
      "1110|Chromosomal and Genetic Variations"
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  "openalex": "W7163557776",
  "pdf_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13719175/pdf/?tool=EBI",
  "pmcid": "PMC13719175",
  "pmid": "42960366",
  "published": "2026-06-03",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/dpkzr2hew3t2p.ris",
  "sources": [
    {
      "first_seen": "2026-10-31T00:20:39Z",
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      "native_id": "PMC13719175",
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      "url": "https://doi.org/10.1093/hr/uhag214"
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  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1110|Chromosomal and Genetic Variations",
      "subfield": "plant-biology"
    }
  ],
  "title": "A haplotype-resolved triploid genome assembly of Zingiber striolatum sheds light on genome expansion and trait evolution in Zingiberaceae",
  "title_text": "A haplotype-resolved triploid genome assembly of Zingiber striolatum sheds light on genome expansion and trait evolution in Zingiberaceae",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:23:03Z",
  "url": "https://research.draconitic.com/paper/dpkzr2hew3t2p",
  "venue": "Horticulture research",
  "versions": []
}