Abstract
Despite the therapeutic importance of cannabinoids, the scarcity of gap-free Cannabis genomes has limited the dissection of the genetic and genomic basis of cannabinoid biosynthesis and genome evolution. Here, we generated two haplotype-phased, gap-free, gold-standard assemblies and used them to investigate post-polyploid genome remodelling and refine the evolutionary history of cannabinoid synthase genes. Analyses of these gap-free assemblies recovered a γ whole-genome triplication (WGT) signal shared with core eudicots and provided no evidence for additional lineage-specific whole-genome duplication (WGD) in Cannabis. The extant Cannabis genome reflects long-term retention and divergence of a subset of γ-derived duplicates, together with subsequent non-WGD-derived gene duplications and repeat-associated remodelling that contributed substantially to present-day genome diversification. Furthermore, phylogenomic, structural and syntenic evidence indicate that a precursor duplication predating the Cannabis-Humulus split gave rise to two lineages retained in Cannabis on chromosomes 7 and 2. In Cannabis, the chromosome 7 lineage subsequently expanded and diversified into the functional cannabinoid synthase genes, whereas Humulus retained only the lineage resembling the Cannabis chromosome 2 copy. This asymmetric retention and diversification provide new insights into the origin and specialization of cannabinoid biosynthesis in Cannabis. Together, these results provide a high-quality genomic framework for understanding the history of polyploidy, the evolution of the cannabinoid synthase gene and genome diversification in Cannabis.
Authors
Zhang J, Qin C, Li Z, Zhao L, Biswas A, Liu T, Luan M, Li L, Li D, Yan J