ArticleHorticulture research2021
Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway.
Article in Horticulture research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Haplotype-resolved regulation of secondary metabolism in cannabis.Horticulture research · 2026Article
- Spatial Profiling of Gingerol and Shogaol Analogues in IntactMolecules (Basel, Switzerland) · 2026Article
- Integrated LC-MS and GC-MS based widely targeted metabolomics for characterizing quality traits in a high-yield chinese turmeric cultivar.Food chemistry: X · 2026Article
- A comparative analysis of root system characteristics, endogenous hormones, and transcriptome responses in tissue cultured ginger.BMC plant biology · 2026Article
- A chromosome-level genome assembly of Alpinia officinarum Hance sheds new light on its evolution and flavonoid biosynthesis.Molecular horticulture · 2025Article
- Ginger genome reveals the SMPED1 gene causing sex-phase synchrony and outcrossing in a flowering plant.Nature plants · 2025Article
- Genome-Wide Analysis and Expression Profiles of Auxin Response Factors in Ginger (International journal of molecular sciences · 2025Article
- The BBX family and their response to abiotic stress in ginger (Zingiber officinale Roscoe).BMC genomics · 2025Article
- Genome-Wide Identification and Expression Analysis of the HSP90 Gene Family in Relation to Developmental and Abiotic Stress in Ginger (Plants (Basel, Switzerland) · 2025Article
- Transcriptomic and metabolomic study of the biosynthetic pathways of bioactive components in Amomum tsaoko fruits.BMC plant biology · 2025Article
- Genome-wide characterization and expression analysis of the bHLH gene family in response to abiotic stresses in Zingiber officinale Roscoe.BMC genomics · 2025Article
- Haplotype-resolved genome assembly of Ficus carica L. reveals allele-specific expression in the fruit.The Plant journal : for cell and molecular biology · 2025Article
- The giant genome of lily provides insights into the hybridization of cultivated lilies.Nature communications · 2025Article
- Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits.Plant communications · 2024Article
- Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot.Microbiome · 2024Article
- Article
- Molecular and genetic regulation of petal number variation.Journal of experimental botany · 2024Review
- The MYB family and their response to abiotic stress in ginger (Zingiber officinale Roscoe).BMC genomics · 2024Article
- Whole-genome sequencing in medicinal plants: current progress and prospect.Science China. Life sciences · 2024Review
- Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe.BMC genomics · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
34 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ginger (Zingiber officinale), the type species of Zingiberaceae, is one of the most widespread medicinal plants and spices. Here, we report a high-quality, chromosome-scale reference genome of ginger 'Zhugen', a traditionally cultivated ginger in Southwest China used as a fresh vegetable, assembled from PacBio long reads, Illumina short reads, and high-throughput chromosome conformation capture (Hi-C) reads. The ginger genome was phased into two haplotypes, haplotype 1 (1.53 Gb with a contig N50 of 4.68 M) and haplotype 0 (1.51 Gb with a contig N50 of 5.28 M). Homologous ginger chromosomes maintained excellent gene pair collinearity. In 17,226 pairs of allelic genes, 11.9% exhibited differential expression between alleles. Based on the results of ginger genome sequencing, transcriptome analysis, and metabolomic analysis, we proposed a backbone biosynthetic pathway of gingerol analogs, which consists of 12 enzymatic gene families, PAL, C4H, 4CL, CST, C3'H, C3OMT, CCOMT, CSE, PKS, AOR, DHN, and DHT. These analyses also identified the likely transcription factor networks that regulate the synthesis of gingerol analogs. Overall, this study serves as an excellent resource for further research on ginger biology and breeding, lays a foundation for a better understanding of ginger evolution, and presents an intact biosynthetic pathway for species-specific gingerol biosynthesis.
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