The Taxus genome provides insights into paclitaxel biosynthesis

Abstract

The ancient gymnosperm genus Taxus is the exclusive source of the anticancer drug paclitaxel, yet no reference genome sequences are available for comprehensively elucidating the paclitaxel biosynthesis pathway. We have completed a chromosome-level genome of Taxus chinensis var. mairei with a total length of 10.23 gigabases. Taxus shared an ancestral whole-genome duplication with the coniferophyte lineage and underwent distinct transposon evolution. We discovered a unique physical and functional grouping of CYP725As (cytochrome P450) in the Taxus genome for paclitaxel biosynthesis. We also identified a gene cluster for taxadiene biosynthesis, which was formed mainly by gene duplications. This study will facilitate the elucidation of paclitaxel biosynthesis and unleash the biotechnological potential of Taxus.

Physiological, Proteomic Analysis, and Calcium-Related Gene Expression Reveal Taxus wallichiana var. mairei Adaptability to Acid Rain Stress Under Various Calcium Levels

“…Taxus wallichiana var. mairei is a well-known gymnosperm with great ornamental and medicinal value ( Gao et al, 2007 ; Cheng et al, 2021 ; Xiong et al, 2021 ). As an AR-resistant tree species, T. wallichiana var.…”

“…A recent study has presented a reference genome of T. wallichiana var. mairei , which will provide genetic resources and serve as a platform for identification and decoding of the AR resistance pathway in various Ca conditions in the future ( Cheng et al, 2021 ; Xiong et al, 2021 ). In this study, we conduct proteomic study to clarify the molecular mechanisms of various Ca levels in T. wallichiana var.…”

Repetitive Elements, Sequence Turnover and Cyto-Nuclear Gene Transfer in Gymnosperm Mitogenomes

“…Second, to confirm that the transcriptome-recovered mitochondrial genes (mitogenes) were in nuclear genomes, we used TBLASTN to search for matches of these genes in reference genomes of Cupressophytes and Gnetophytes, including Sequoiadendron giganteum ( Scott et al, 2020 ), Sequoia sempervirens ( Neale et al, 2021 ), Taxus chinensis ( Xiong et al, 2021 ), Taxus wallichiana ( Cheng et al, 2021 ), Gnetum montanum ( Wan et al, 2018 ), and Welwitschia mirabilis ( Wan et al, 2021 ) ( Supplementary Table S3 ).…”

From Genome Sequencing to CRISPR-Based Genome Editing for Climate-Resilient Forest Trees

“…To avoid the high heterozygosity in somatic cells of long-lived trees, one approach that was used for conifer genomes (e.g., Norway spruce (Picea abies L., 20 Gbp) [31] and loblolly pine (Pinus taeda L., 22 Gbp) [32]) was taking advantage of conifer seeds with a large haploid (1N) megagametophyte for providing DNA material. Alternatively, DNA from Taxus chinensis endosperm calli [33] containing haploid chromosomes (~10 Gbp in size) was used for whole-genome sequencing through Illumina (Illumina Inc., San Diego, US), Pacbio single-molecule real-time sequencing (Pacific Biosciences of California, Inc., Menlo Park, US), and Hi-C libraries. For the case of the 640-Mbp genome sequencing of flooded gum (Eucalyptus grandis, [34]), a genotype that was derived from one generation of selfing was used to mitigate the challenge of assembling a highly heterozygous eucalypt genome.…”