Supporting data for "Phased High-Quality Genome of the Gymnosperm Himalayan Yew Assists in Paclitaxel Pathway Exploration"

<i>Taxus wallichiana</i> is an important species for paclitaxel production. Previous genome versions for <i>Taxus spp.</i> have been limited by extensive gaps, hindering the complete annotation and mining of paclitaxel (known as taxol commercially) synthesis pathway-related genes. <br>Here, we present the first phased high-quality reference genome of <i>Taxus wallichiana</i>, which significantly improves assembly quality and corrects large-scale assembly errors present in previous versions. The two haplotypes are 9.87 Gb and 9.98 Gb in length, respectively, and all 24 chromosomes were assembled with telomeres at both ends. Based on this high-quality genome (TWv1), we inferred that the candidate sex chromosome of <i>Taxus wallichiana</i> is chr12, and its sex determination system may follow a ZW model. Particularly, we identified and experimentally validated a batch of 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODDs), which may be key C4-C20 epoxidases in the paclitaxel synthesis pathway.<br>This study not only provides a valuable data resource for gene mining in the biosynthetic pathways of secondary metabolites such as paclitaxel but also offers the highest-quality reference genome of gymnosperms to date for the identification of sex chromosomes, facilitating comparative genomic studies among gymnosperms.