A haplotype-resolved triploid genome assembly of Zingiber striolatum sheds light on genome expansion and trait evolution in Zingiberaceae
4 affiliations
- 1College of Ecology, Zunyi Normal University, Zunyi 563006, China.
- 2State 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.
- 3Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China.
- 4China Strait Horticulture Technology Innovation Hub, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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.
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BibTeX
@article{chen2026haplotyperesolved,
title = {{A haplotype-resolved triploid genome assembly of Zingiber striolatum sheds light on genome expansion and trait evolution in Zingiberaceae}},
author = {Zhi-Feng Chen and Wei-Hong Sun and Li-Yao Su and Guo-Fei Tan and Yu Lu and Lian Luo and Wen-Hui Li and Chun-Xiao Li and Zi-Wei Tan and Zhuang Zhao and Chang-Ling Sui and Zhong-Jian Liu and Ai-Sheng Xiong},
journal = {Horticulture research},
year = {2026},
month = jun,
doi = {10.1093/hr/uhag214},
url = {https://europepmc.org/article/PMC/PMC13719175},
note = {CC BY},
}
RIS
TY - JOUR
TI - A haplotype-resolved triploid genome assembly of Zingiber striolatum sheds light on genome expansion and trait evolution in Zingiberaceae
AU - Zhi-Feng Chen
AU - Wei-Hong Sun
AU - Li-Yao Su
AU - Guo-Fei Tan
AU - Yu Lu
AU - Lian Luo
AU - Wen-Hui Li
AU - Chun-Xiao Li
AU - Zi-Wei Tan
AU - Zhuang Zhao
AU - Chang-Ling Sui
AU - Zhong-Jian Liu
AU - Ai-Sheng Xiong
PY - 2026
DA - 2026/06/03
JO - Horticulture research
DO - 10.1093/hr/uhag214
UR - https://europepmc.org/article/PMC/PMC13719175
AB - 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.
SN - 2662-6810
SN - 2052-7276
ER -