Whole genome sequencing of Curcuma xanthorrhiza Roxb. reveals ploidy-driven speciation and divergent specialized metabolite biosynthesis in the genus Curcuma.
Abstract
Curcuma xanthorrhiza Roxb., commonly known as javanese turmeric (temulawak), is a rhizomatous herb with significant ethnobotanical and nutraceutical importance, valued for producing curcuminoids and xanthorrhizol. Despite its considerable medicinal and economic value, the genomic basis underlying these important traits has remained largely uncharacterized. This study presents its first whole-genome assembly, generated through a hybrid sequencing strategy utilizing 21.82 Gb of PacBio HiFi and 21.46 Gb of Illumina short-read data. Independent k-mer profiling and assembly-based analyses converged on a triploid genome architecture, resulting in a 579.07 Mb contig-level assembly (N50 = 1.48 Mb) with high completeness (BUSCO: 94.5-97.7%), 42,169 annotated protein-coding genes and a PSAURON score of 98.4. Comparative phylogenomic analysis across the Zingiberaceae revealed that while C. xanthorrhiza diverged from its sister taxon Curcuma caesia Roxb. recently (~ 1.76 Mya), it exhibits profound macrosynteny disruption, a net gene-family contraction, and the most compact gene complement among the sampled species. Genome-wide mining of biosynthetic gene clusters identified 26 candidates, including a paralogous pair of curcuminoid loci, though further validation by RNA-seq co-expression is needed. Additionally, genome-wide homology-search identified AC50XY_029945 as the strongest candidate (S)-β-bisabolene synthase for xanthorrhizol biosynthesis, proposed as a trans-acting, dispersed pathway architecture involving 51 candidate CYP71 cytochrome P450s, an SDR oxidoreductase, and co-located WRKY/ERF/MYB transcription factors. These results establish the first nuclear genomic resource for C. xanthorrhiza, highlighting the role of ploidy-driven genome instability in driving rapid-speciation and secondary metabolite diversification in the genus Curcuma.
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