De novo chromosome-level assembly of the endangered Pilocarpus microphyllus highlights genomic resources for conservation and sustainable pilocarpine extraction

Pilocarpus microphyllus (jaborandi) is an endangered plant species with significant bioeconomic relevance, as it is the main known source of pilocarpine, an alkaloid widely used in the treatment of glaucoma and other diseases. Here, we present a functionally annotated, haplotype-phased, chromosome-level genome for P. microphyllus, combining PacBio HiFi and Hi-C sequencing. The final genome assembly spans 2.6 Gb anchored into 22 chromosomes across 95 scaffolds, with a scaffold N50 of 120.9 Mb and a BUSCO completeness score of 99.66%. We obtained 28,319 unique protein-coding loci, of which 28,090 were functionally annotated to the RefSeq database. Repetitive sequences constituted 88.98% of the total genome length. This near-T2T genome provides a robust molecular foundation for investigating the pilocarpine biosynthetic pathway and supports future population-level studies, thereby contributing to improved management and conservation strategies.