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Jianbin Yan

Publications and source records attributed to Jianbin Yan.

5 recordsLinked to original sources
PubMed2026

Haplotype-resolved genome of Forsythia suspensa reveals the reticulate evolution in Oleaceae and a novel gene cluster regulating stamen development.

The olive family (Oleaceae) comprises numerous species of economic, horticultural, and medicinal importance. Despite its significance, the evolutionary history of this complex family remains enigmatic. Here, we generated a high-quality haplotype-resolved genome of Forsythia suspensa, a distylous species that occupies a key phylogenetic position in Oleaceae. The 2 haplotypes exhibit significant allelic divergence with potential allele-specific regulation. We reconstructed the polyploidization history of Oleaceae by confirming and precisely dating a shared whole-genome triplication and an independent whole-genome duplication event. We revealed a complex reticulate evolution that gave rise to the tribe Oleeae: an initial hybridization between Forsythieae (♂) and Jasmineae (♀), a subsequent backcrossing event, and a final whole-genome duplication. We identified a novel tandemly duplicated pectin methylesterase inhibitor gene cluster that regulates filament length and pollen size via restricting cell elongation in the long-styled morph. Dosage augmentation via stepwise cluster formation (0.99 to 3.83 Mya) may contribute to maintaining stamen traits of the long-styled morph. These FsPMEIs are co-expressed with many cell wall-related genes, suggesting a functional link in cell wall modification. Our study reveals the reticulate evolution in Oleaceae and a novel gene cluster controlling stamen development in F. suspensa and provides valuable haplotype-resolved genomic resources for heterostylous species, offering novel framework and molecular pathways to understand plant adaptive evolution.

Forsythia↗
PubMed2026

Biosynthesis and heterologous production of the α-agarofuran scaffold of Celangulin V from Celastrus angulatus.

Celangulin V is a widely used biopesticide derived from Celastrus angulatus, and features antifeedant and insecticidal properties as a dihydro-β-agarofuran (DHβAF) sesquiterpenoid. Its biosynthesis remains largely unexplored. Here, we assemble a chromosome-level and haplotype-resolved reference genome of C. angulatus, with each haplotype assembled into 23 pseudochromosomes and achieving scaffold N50 of 14.31 and 14.01 Mb, respectively. This high-quality genome reveals that a recent β whole-genome triplication (β-WGT) event occurred ~34.3 million years ago, and that the expansion of sesquiterpene synthases and cytochrome P450s from the CYP71BE family results from whole-genome duplication (WGD) event and tandem duplication, respectively. We identify CaTPS16 as a γ-eudesmol synthase, and show that CYP71BE416 further catalyzes the γ-eudesmol to tetrahydrofuran ring α-agarofuran for Celangulin V biosynthesis. We further achieve the de novo synthesis of α-agarofuran in Saccharomyces cerevisiae through combined coexpression of these genes. This study has significantly increases the available genomic resources of the Celastraceae family, improves our understanding of the biosynthetic origins and evolution of the tetrahydrofuran ring in DHβAF sesquiterpenoids, and enables its heterologous bioproduction in microbial chassis.

Celastrus↗
PubMed2026

DeepMASS v.2: An enhanced deep learning platform for large-scale discovery and structural annotation of unknown plant metabolites.

Determining the structures of unknown metabolites remains a fundamental bottleneck in plant metabolomics, as the vast chemical diversity of plant secondary metabolites far exceeds the coverage of existing spectral libraries. Here, we present DeepMASS v.2, a substantially enhanced platform for annotating unknown metabolites from liquid chromatography-tandem mass spectrometry data, designed to address this challenge at scale. DeepMASS v.2 leverages a semantic spectral representation model trained on millions of spectra from GNPS, NIST, and in-house resources. By integrating Spec2Vec-based embeddings with HNSW (hierarchical navigable small world) graph retrieval and a unified chemical space defined by molecular fingerprints, DeepMASS v.2 identifies structurally related neighbors of unknown spectra and ranks candidate structures according to their proximity to the predicted structural neighborhoods within chemical space. Benchmarking against Critical Assessment of Small Molecule Identification datasets and a curated natural product collection demonstrated that DeepMASS v.2 outperforms state-of-the-art in silico annotation tools, including SIRIUS, CFM-ID, MetFrag, and MS-Finder. Importantly, DeepMASS v.2 maintains strong performance for metabolites absent from spectral libraries, highlighting its capacity to annotate genuinely unknown compounds. Application of DeepMASS v.2 to large-scale plant metabolomics datasets demonstrated its ability to expand accessible metabolome coverage. Implemented as an intuitive web platform, DeepMASS v.2 provides the community with a scalable, interpretable, and high-throughput solution for structural annotation, enabling more comprehensive characterization of plant chemical diversity and accelerating natural product discovery in molecular plant science. The DeepMASS v.2 web server is publicly available at http://deepmass.cn.

Metabolomics↗
PubMed2026

Complete biosynthesis of the anticancer cephalotaxinone and homoerythratine.

Cephalotaxine-type and homoerythrina-type alkaloids are structurally unique and biologically important natural products isolated from endangered species that belong to the genus Cephalotaxus. Among them, homoharringtonine (HHT [1]) is a marketed drug used to treat leukemia. However, the scalable production of HHT is significantly hindered by limited natural resources. Despite intensive investigation over half a century, the complete biosynthetic pathways of these alkaloids remain unknown. Here, we applied a comprehensive multi-omics analysis and used a set of chemically synthesized standard compounds to identify the missing enzymes required for the biosynthesis of cephalotaxinone and homoerythratine. We also uncovered a rare case of divergent oxidation catalyzed by two highly homologous cytochrome P450 enzymes, CfCYP2 and CfCYP3, in the biosynthesis of two structurally distinct alkaloids. We further identified the key residues that significantly affect the divergent oxidation outcomes and ultimately reconstituted the complete biosynthetic pathways for producing these two alkaloids in N. benthamiana.

Cephalotaxus↗
PubMed2025

Multi-Omics Analyses Reveal the Red and Far-Red Light Combination Enhancing Heterologous Protein and Metabolite Production in Nicotiana benthamiana.

Transient expression of exogenous protein in Nicotiana benthamiana leaves via agroinfiltration offers a rapid and efficient platform for functional gene discovery and heterologous production of valuable eukaryotic proteins and metabolites. Though light quality is an important factor for plant photomorphogenesis, its impact on the efficiency of transient expression remains unexplored. In this study, we examined the influence of five representative light qualities with varying wavelength mix on the N. benthamiana growth and recombinant green fluorescent protein (GFP) production. Plants with red and far-red light treatment (LED-red) showed the highest GFP expression, 57.4% higher than white light. Further study showed that a higher dosage of post-infiltration Agrobacterium and the resulting increase in the number of transcripts contribute to the expression rate enhancement. Moreover, as for exogenous metabolites, a 76.5% increase of accumulated taxadiene was also observed in LED-red group. Integrated transcriptomic, proteomic and metabolomic revealed that LED-red plants reduced the resistance pathways before infiltration, inducing a higher dosage of post-agroinfiltration Agrobacterium. Our results suggest that N. benthamiana grown under LED-red creates a more favorable environment for Agrobacterium growth, enhancing heterologous protein and metabolite production. This study highlights the potential utilization of light quality as an implementable tool in plant synthetic biology.

Nicotiana↗