Multi‐Omics Reveal Haplotype‐Specific BGC Divergence and Organ‐Specific Iridoid Glycoside Accumulation in Endemic Species Rehmannia chingii

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Iridoid glycosides (IGs) are key bioactive metabolites within the genus Rehmannia. However, the molecular mechanisms underlying geographical and organ-specific divergence in IG accumulation, and the biosynthetic gene clusters (BGCs) between chromosomal haplotypes, remain poorly understood in Rehmannia chingii, an endemic species in eastern China. Here, we performed a series of analyses using a high-quality, haplotype-resolved genome assembly of R. chingii from the Tianmu Mountain. Combined with the known widely targeted metabolomic profiles, seven differentially accumulated IGs were identified. Due to the higher data completeness of the second haplotype (Haplotype II: 1.1696 Gb), it was selected as the reference genome for transcriptomic analysis to ensure a reliable quantification of the expression levels of core synthase genes. Building upon these multi-omics findings, a putative IG biosynthetic gene cluster on Chr 11 in Haplotype II was further identified, which includes TPS-g, G10H, CYP76, CYP704B, and ADH genes. In contrast, the corresponding region on Chr 11 in Haplotype I (1.1573 Gb) was inferred to constitute a putative fatty acid-terpene biosynthetic gene cluster, primarily due to the presence of a BAHD acyltransferase gene at the distal end of the cluster. Collectively, this study provides comprehensive genomic and metabolic resources for investigating IG biosynthesis in R. chingii from two distinct geographical populations. Our results highlight haplotype-specific divergence in BGC architecture on Chr 11 and provide insights into the regulatory mechanisms underlying organ- and geographic population-specific metabolic variation. These findings also establish a foundation for the conservation and rational utilization of R. chingii germplasm resources.

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