Archipelago architecture and evolution of paclitaxel biosynthesis revealed by the Pseudotaxus chienii haplotype-resolved genome

Abstract Pseudotaxus chienii , the only species in the genus Pseudotaxus , is closely related to Taxus genus. Whether P. chienii can produce paclitaxel has long remained controversial. Here, we present a chromosome-level, haplotype-resolved genome of P. chienii , with each haplotype ( ~ 15.4 Gb) exhibiting high continuity and completeness. We identify a structurally conserved yet physically dispersed genomic region, termed the Taxane Biosynthetic Archipelago (TBA), containing three biosynthetic gene clusters and collinear core genes essential for taxane biosynthesis. Integrative transcriptomic, metabolite, and heterologous enzymatic analyses reveal that while P. chienii retains a largely conserved genomic architecture associated with paclitaxel biosynthesis, its terminal pathway shows severe functional degradation and may have largely lost the functional capacity for paclitaxel production. Concurrently, it exhibits significant accumulation of taxinine J. This study provides an evolutionary framework for interpreting the long-standing debate on paclitaxel production beyond Taxus , and understanding the evolutionary decay of complex specialized pathways.