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The genome of Pseudotaxus chienii, a relict conifer endemic to China, provides insights into the origin and evolution of taxane biosynthesis

ABSTRACT: The genome of Pseudotaxus chienii, a relict conifer endemic to China, provides insights into the origin and evolution of taxane biosynthesis

PROVIDER: PRJNA1216184 | ENA |

REPOSITORIES: ENA

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The genome of Pseudotaxus chienii, a relict conifer endemic to China, provides insights into the origin and evolution of taxane biosynthesis

Project description:As a sister genus to Taxus, Pseudotaxus holds significant importance for studying the origin and evolution of the taxane biosynthesis pathway. However, the reference genome of P. chienii, the sole species of Pseudotaxus, is not yet available. We have completed a chromosome-level genome assembly of P. chienii, with a total length of 15.6 Gb. P. chienii possesses only a partial pathway for Taxol biosynthesis, which terminates before the enzyme taxane 2α-O-benzoyl transferase (TBT), a crucial enzyme responsible for the production of 10-deacetylbaccatin III. With the emergence of the Taxus genus, the limitation posed by TBT is overcome, allowing for the extension of the existing taxane biosynthesis pathway into a complete Taxol biosynthesis pathway. Protein structure analysis revealed that the structure of metal ion catalysis sites in taxadiene synthase (TS) is conserved across the Pseudotaxus and Taxus genera, providing potential sites for enhancing TS activity through enzyme engineering. This comparative genomic analysis contributes to our understanding of the origin and evolution of taxane biosynthesis within the Taxaceae family.

2025-01-27 | GSE288094 | GEO

Pseudotaxus chienii

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Pseudotaxus chienii

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Lindera chienii

Project description:Lindera chienii overview

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Project description:Lindera chienii Raw sequence reads

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Project description:Characterization of transcriptomes of Pseudotaxus chienii

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EST-SSR-based landscape genetics of <i>Pseudotaxus chienii</i>, a tertiary relict conifer endemic to China.

Project description:Pseudotaxus chienii, belonging to the monotypic genus Pseudotaxus (Taxaceae), is a relict conifer endemic to China. Its populations are usually small and patchily distributed, having a low capacity of natural regeneration. To gain a clearer understanding of how landscape variables affect the local adaptation of P. chienii, we applied EST-SSR markers in conjunction with landscape genetics methods: (a) to examine the population genetic pattern and spatial genetic structure; (b) to perform genome scan and selection scan to identify outlier loci and the associated landscape variables; and (c) to model the ecological niche under climate change. As a result, P. chienii was found to have a moderate level of genetic variation and a high level of genetic differentiation. Its populations displayed a significant positive relationship between the genetic and geographical distance (i.e., "isolation by distance" pattern) and a strong fine-scale spatial genetic structure within 2 km. A putatively adaptive locus EMS6 (functionally annotated to cellulose synthase A catalytic subunit 7) was identified, which was found significantly associated with soil Cu, K, and Pb content and the combined effects of temperature and precipitation. Moreover, P. chienii was predicted to experience significant range contractions in future climate change scenarios. Our results highlight the potential of specific soil metal content and climate variables as the driving force of adaptive genetic differentiation in P. chienii. The data would also be useful to develop a conservation action plan for P. chienii.

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Salix chienii

Project description:Salix chienii Cheng complete chloroplast genome sequencing and assembly

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Specific kinesin expression profiles associated with taxane resistance in breast cancer

Project description:Purpose: Breast cancer is a genetically heterogenous disease with subtypes differing in prognosis and chemosensitivity. The basal-like breast cancer (BLBC) molecular subtype is associated with poorer outcomes, but is more responsive to taxane-based chemotherapy. We evaluated the role of kinesins, motor proteins interacting with microtubules, in influencing taxane resistance. Experimental Design: Kinesin (KIF) expression was studied in one local dataset comprising all taxane resistant breast cancers in relation to taxane resistance. Data in the NCI-60 cell line dataset (GSE5846) nd the MDACC dataset (GSE20194) is separately detailed. Results: In the local dataset, the kinesin KIF26B is overexpressed in taxane-resistant residual breast cancers post-chemotherapy. Conclusions: We show that kinesin overexpression correlates with taxane resistance in BLBC cell lines and tissue. Our results suggest a potential approach to overcoming taxane resistance through concurrent or sequential use of kinesin inhibitors, highlighting the ATP-binding domain as a drug development target.

2012-12-01 | GSE22796 | GEO

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