A genome assembly of ginger (Zingiber officinale Roscoe) provides insights into genome evolution and 6‐gingerol biosynthesis

SUMMARY Ginger is cultivated in tropical and subtropical regions and is one of the most crucial spices worldwide owing to its special taste and scent. Here, we present a high‐quality genome assembly for ‘Small Laiwu Ginger’, a famous cultivated ginger in northern China. The ginger genome was phased into two haplotypes, haplotype A (1.55Gb), and haplotype B (1.44Gb). Analysis of Ty1/Copia and Ty3/Gypsy LTR retrotransposon families revealed that both have undergone multiple retrotransposon bursts about 0–1 million years ago. In addition to a recent whole‐genome duplication event, there has been a lineage‐specific expansion of genes involved in stilbenoid, diarylheptanoid, and gingerol biosynthesis, thereby enhancing 6‐gingerol biosynthesis. Furthermore, we focused on the biosynthesis of 6‐gingerol, the most important gingerol, and screened key transcription factors ZoMYB106 and ZobHLH148 that regulate 6‐gingerol synthesis by transcriptomic and metabolomic analysis in the ginger rhizome at four growth stages. The results of yeast one‐hybrid, electrophoretic mobility shift, and dual‐luciferase reporter gene assays showed that both ZoMYB106 and ZobHLH148 bind to the promoters of the key rate‐limiting enzyme genes ZoCCOMT1 and ZoCCOMT2 in the 6‐gingerol synthesis pathway and promote their transcriptional activities. The reference genome, transcriptome, and metabolome data pave the way for further research on the molecular mechanism underlying the biosynthesis of 6‐gingerol. Furthermore, it provides precious new resources for the study on the biology and molecular breeding of ginger.