Transcriptome and comparative chloroplast genome analysis of Taxus yunnanensis individuals with high and low paclitaxel yield

Paclitaxel has been isolated from the bark of Taxus brevifolia since 1967 and has been used as an anti-cancer drug for the treatment of various cancers such as breast cancer, lung cancer, and ovarian cancer (Weaver, 2014). However, owing to the destructive harvesting at production sites, the complex purification process, and low yield, the supply of paclitaxel remains far from meeting market demand (Mutanda et al., 2021). To increase the yield of paclitaxel, a paclitaxel total synthesis method has been reported (Nicolaou et al., 1994). However, its complex synthesis process leads to a decrease in yield, an increase in cost, and the production of various toxic products, making this method difficult to commercialize (Ahmed Khalil et al., 2022). After elucidating the total synthesis method of paclitaxel, a semi-synthesis method was also published, starting from a high-content paclitaxel intermediate, such as 10-deacetyl baccatin III (10-DAB), to chemically synthesize paclitaxel (Baloglu and Kingston, 1999). Later, Chen et al. (Chen et al., 2003) isolated endophytic fungi that can produce paclitaxel from the branches and bark of T. yunnanensis, but of the two viable commercial production schemes, semi-synthesis (Kingston et al., 1994) and biosynthesis (Kolewe et al., 2008), semi-synthesis production still relies on plant materials (Li et al., 2015). Existing research shows that the difference in expression of key genes is responsible for the difference in content of paclitaxel and paclitaxel intermediates among different species (Yu et al., 2021), so identifying high-paclitaxel-yield individuals is an important direction for optimizing production.