bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.07.29.605693

Comparative metabolomics of wild and cultivated yew: insights into metabolic diversity and environmental adaptability

wang, d.·zhang, y.
View original source ↗Export metadata ↓

Abstract

Taxus cuspidata is a well-known gymnosperm with great ornamental and medicinal value. The study aims to reveal the metabolic differences between wild and cultivated species of T. cuspidata, and to analyze the genetic and ecological factors behind these differences. This study conducted a comparative metabolomics analysis of wild and cultivated T. cuspidata based on LC-MS/MS technology. The results showed: (1) A total of 7030 metabolites were identified, primarily including flavonoids, organic acids, phenolic acids, amino acids and their derivatives, lipids, and alkaloids, among others; (2) 2381 differential metabolites were confirmed: 949 higher in cultivated species and 1432 higher in wild species, which suggesting wild species have more advantageous metabolites. (3) Through KEGG annotation, 20 significant metabolic pathways were identified, with sugar metabolism, photosynthesis, and sulfur metabolism were significantly higher in wild species. In contrast, pathways related to most amino acids and their derivatives, flavonoids, terpenoids, polyphenols, alkaloids, and plant hormones were significantly higher in cultivated species. In conclusion, the wild species are inferior to cultivated species in terms of drought resistance, growth rate, and medicinal value for cancer treatment. However, the advantage of wild species lies in their significantly higher diversity of upregulated secondary metabolites due to their rich genetic resources, which exhibit greater metabolic diversity and environmental adaptability, which enhances their survival capability. Furthermore, the wild species exhibit significantly higher efficiency in photosynthesis and sugar metabolism compared to cultivated species, enabling them to better withstand low-temperature stress. This study has provided the direction for research into the mechanisms of stress resistance in T. cuspidata and has also established a theoretical basis for formulating scientifically and reasonable conservation strategies for wild species.

Explore related subjects

molecular biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

wang, d., zhang, y.. 2024-07-29. Comparative metabolomics of wild and cultivated yew: insights into metabolic diversity and environmental adaptability. https://doi.org/10.1101/2024.07.29.605693

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Dietary selenium deficiency drives sex-specific circadian disturbance through redox imbalance and causes early systolic dysfunction in mice

Background: Selenium is a vital trace element involved in antioxidant defence and cardiovascular health. Although selenium deficiency is implicated in cardiomyopathies, its early cardiac effects and underlying mechanisms remain poorly defined. Methods: C57BL6/Njr mice were fed either a selenium deficient or control diet for 12 weeks. Systemic selenium status, cardiac function by echocardiography, left ventricular (LV) transcriptomic profiles, redox balance, and circadian pathway markers were assessed, including sex-specific analyses. Results: Selenium deficiency reduced plasma selenium levels without inducing overt cardiac hypertrophy or fibrosis. Echocardiography showed preserved ejection fraction and fractional shortening but reduced global longitudinal strain, indicating early systolic dysfunction. Cardiac stress markers were increased predominantly in male mice. Left ventricular RNA sequencing revealed enrichment of pathways related to cardiac remodelling, redox regulation, mitochondrial function, and circadian rhythm. Additional protein and metabolic analyses supported sex-specific redox circadian alterations, with males showing a more pronounced stress response profile. Conclusions: Dietary selenium deficiency induces early myocardial dysfunction and molecular remodelling before overt cardiac failure. These changes are associated with redox and circadian pathway disruption and show sex specific features, suggesting that selenium contributes to cardiac homeostasis through sex dependent redox circadian regulation.

molecular biology↗
bioRxiv2026

Dysregulation of FMR1 Splicing in Human Fragile X Syndrome

Fragile X Syndrome (FXS) is a neuro-developmental disorder caused by a CGG expansion in FMR1, leading to transcriptional silencing and loss of the encoded protein FMRP. Surprisingly, ~70% of FXS individuals express FMR1, but the RNA is mis-spliced to isoform FMR1-217, composed of exon 1 spliced to a pseudo-exon in intron 1 and cannot produce FMRP. Splice-switching ASOs rescue proper FMR1 splicing and restore FMRP. FMR1-217 mis-splicing increases with CGG repeat length and is negatively correlated with patient IQ. FMR1-217 is associated with ribosome footprints, indicating it is translated into a polypeptide that may impair cognition. R-loops form at the FMR1 locus and extend into the pseudo-exon, but splice-switching ASOs reduce FMR1-217 and elevate FMRP independently of R-loop formation. DRB-based transcription analysis identified impaired Pol II elongation at the 5 prime region of FMR1 in FXS cells, indicated by accumulation of hypophosphorylated Pol II at the transcription start site. Consistent with this, camptothecin-induced Pol II stalling increased FMR1-217 pseudo-exon inclusion. The splicing factors PTBP1 and PTBP2 regulate FMR1-217 splicing in a differentiation stage-dependent manner. Together, these findings indicate that FMR1-217 mis-splicing in FXS is associated with CGG repeat expansion, R-loop formation, impaired co-transcriptional Pol II elongation and context-dependent regulation by PTBP1/PTBP2.

molecular biology↗
bioRxiv2026

Hidden Biodiversity in Wildlife Trade Networks: DNA Barcoding Reveals Fish and Crocodilian Species in Commercialized Swim Bladders

International wildlife trade represents one of the major drivers of biodiversity exploitation worldwide. However, the true taxonomic diversity embedded within commercial wildlife products often remains unknown because processing removes diagnostic morphological characteristics, preventing reliable species identification. Consequently, biodiversity assessments based solely on product labels may substantially underestimate the diversity of species involved in trade networks. To investigate hidden biodiversity within wildlife trade products, we applied DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene to 77 products commercialized as fish swim bladders and seized at Guarulhos International Airport, Brazil. Molecular analyses successfully identified all samples and revealed the presence of four species: Plagioscion auratus (n = 38), Cynoscion acoupa (n = 7), Melanosuchus niger (n = 17), and Caiman crocodilus (n = 15). Fish species accounted for 71.4% of all samples, whereas crocodilians represented 28.6%, demonstrating that products marketed under a single commercial category may conceal substantial taxonomic diversity. Notably, the occurrence of two Amazonian crocodilian species within a trade chain traditionally associated with fish products reveals a previously undocumented component of the international wildlife trade. Our findings demonstrate that DNA barcoding is an effective tool for uncovering hidden biodiversity within processed wildlife products and provide evidence that wildlife trade networks may involve a broader spectrum of species than suggested by commercial labels. These results highlight the importance of molecular surveillance for biodiversity monitoring, wildlife trade regulation, and conservation planning.

molecular biology↗