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.

姜 ( Zingiber officinale))，姜科的模式种，是分布最广的药用植物和香料之一。在这里，我们报告了高质量、染色体​​规模的姜“竹根”参考基因组(Hi-C) 读取。姜基因组被分为两个单倍型，单倍型 1（1.53 Gb，重叠群 N50 为 4.68 M）和单倍型 0（1.51 Gb，重叠群 N50 为 5.28 M）。同源姜染色体保持良好的基因对共线性。在 17,226 对等位基因中，11.9% 的等位基因表现出差异表达。基于姜基因组测序、转录组分析和代谢组学分析的结果，PAL，C4H，4CL，CST，C3 ' ħ，C3OMT，CCOMT，CSE，PKS，AOR，DHN，和DHT。这些分析还确定了可能调节姜酚类似物合成的转录因子网络。总体而言，本研究为进一步研究生姜生物学和育种提供了极好的资源，为更好地了解生姜进化奠定了基础，并为物种特异性姜酚生物合成提供了完整的生物合成途径。