Yafu Zhou

Helleborus thibetanus, an endemic species in China, is a medicinal and ornamental plant. The seeds exhibit epicotyl morphophysiological dormancy. In this study, we performed transcriptome and metabolome analyses at four stages: freshly harvested mature seeds (S1), radicle-emerged seeds (S2), seeds with 2 cm root length (S3), and plumule-germinated seeds (S4). A total of 70,383 unigenes were obtained. Furthermore, 768 and 686 metabolites were identified by positive ion mode and negative ion mode, respectively. The expression levels of genes involved in terpenoid backbone biosynthesis and downstream gibberellin (GA) biosynthesis pathways were higher in the S2, S3, and S4 stages, which suggests that GA was associated with seed germination. The expression level of embryo development genes was higher in the S1 or S2 stages. The genes related to cell wall metabolism (EXP, XTH/XETs) were highly expressed in the S2, S3, and S4 stages, which promoted cell wall loosening and endosperm weakening, thereby facilitating seed germination. The genes involved in sucrose and starch metabolism were highly expressed during embryo development and germination (S2–S4), which indicates that they provided essential nutrients and energy for H. thibetanus seed germination. Our results provide a foundation for further research and facilitate the propagation of H. thibetanus seeds.

The tribe Meconematini (Meconematinae) is a species-rich lineage whose genus- and species-level classifications remain taxonomically controversial. In this study, we obtained 17 new mitochondrial genomes using high-throughput sequencing and conducted the first comparative genomic and phylogenomic analyses within this tribe. The mitogenomes of Meconematini exhibit conserved structural features typical of Meconematinae, including conserved gene order, pronounced AT bias, and negative GC-skew. Notably, a rare mitochondrial initiation codon (GTG) was identified in the ATP6 gene in Meconematini. Evolutionary analyses indicated that strong purifying selection has dominated the evolution of Meconematini mitogenomes. Phylogenetic reconstructions strongly supported the monophyly of the genera Microconema Liu and Decma Gorochov, as well as the subgenus Eoxizicus Gorochov. In contrast, the genera Phlugiolopsis Zeuner, Xizicus Gorochov, and Xiphidiopsis Redtenbacher were not recovered as monophyletic. Additionally, the phylogenetic results support the recognition of Eoxizicus and Euxiphidiopsis Gorochov as distinct genera. Importantly, mitogenomic divergence patterns were correlated with genitalia structural traits: genera within the proximal clade possess membranous male genitalia (hagloid type), whereas those in more basal clades exhibit partially or fully sclerotized genitalia (tettigonioid or grylloid type). These findings collectively enable the proposal of taxonomic revisions for the non-monophyletic genera and establish a mitogenomic baseline for reconciling morphological convergence with evolutionary relationships in Meconematini.

To investigate the characteristics of rhizosphere soil microbial communities associated with Schisandra sphenanthera across different altitudinal gradients and to reveal the driving factors of microbial community dynamics, this study collected rhizosphere soil samples at four elevations: 900 m (HB1), 1100 m (HB2), 1300 m (HB3), and 1500 m (HB4). High-throughput sequencing and molecular ecological network analysis were employed to analyze the microbial community composition and species interactions. A null model was applied to elucidate community assembly mechanisms. The results demonstrated that bacterial communities were dominated by Proteobacteria, Acidobacteriota, Actinobacteriota, and Chloroflexi. The relative abundance of Proteobacteria increased with elevation, while that of Acidobacteriota and Actinobacteriota declined. Fungal communities were primarily composed of Ascomycota and Basidiomycota, with both showing elevated relative abundances at higher altitudes. Diversity indices revealed that HB2 exhibited the highest bacterial Chao, Ace, and Shannon indices but the lowest Simpson index. For fungi, HB3 displayed the highest Chao and Ace indices, whereas HB4 showed the highest Shannon index and the lowest Simpson index. Ecological network analysis indicated stronger bacterial competition at lower elevations and enhanced cooperation at higher elevations, contrasting with fungal communities that exhibited increased competition at higher altitudes. Altitude and soil nutrients were negatively correlated with soil carbon content, while plant nutrients and fungal diversity positively correlated with soil carbon. Null model analysis suggested that deterministic processes dominated bacterial community assembly, whereas stochastic processes governed fungal assembly. These findings highlight significant altitudinal shifts in the microbial community structure and assembly mechanisms in S. sphenanthera rhizosphere soils, driven by the synergistic effects of soil nutrients, plant growth, and fungal diversity. This study provides critical insights into microbial ecology and carbon cycling in alpine ecosystems, offering a scientific basis for ecosystem management and conservation.

Introduction: Programmed cell death (PCD) is a fundamental biological process crucial for plant development. Despite recent advancements in our understanding of PCD’s molecular mechanisms, the intricate orchestration of this process within plant cells remains enigmatic. To address this knowledge gap, the present study focuses on Decaisnea insignis, a plant species renowned for its unique fruit anatomy, including laticiferous canals that secrete latex. While extensive anatomical studies have elucidated the structural features of these canals,molecular insights into their developmental regulation, particularly the involvement of PCD, are lacking.Methods: In this study, we sequenced the single-cell transcriptomes at two developmental stage of Decaisnea insignis fruit using the technology known as 10x Genomics (S1, S2). Using sequencing technology combining full- length RNA sequencing and single-nucleus RNA sequencing (snRNA-seq) in combination with ultrastructural analyses, our study revealed a cellular map of Decaisnea insignis fruit at the single-cell level and identified different cell types.Results: In particular, we identified a possible PCD-mediated cluster of Decaisnea insignis fruit lactiferous canals in epidermal cells and clarified the expression patterns of DiRD21A (a hydrolase) and DiLSD1 (a transcription factor), which may be closely related to the development of laticiferous canals in Decaisnea insignis fruits.Discussion: By integrating high-resolution gene expression profiling with visual insights into cellular transformations, we sought to more precisely characterize the regulatory role of PCD during the developmental formation of lactiferous canals in Decaisnea insignis fruit.

The title compound, C12H10N2O3, was obtained by the de­acetyl­ation reaction of 1-(6-amino-5-nitro­naphthalen-2-yl)ethanone in a concentrated sulfuric acid methanol solution. The mol­ecule comprises a naphthalene ring system bearing an acetyl group (C-3), an amino group (C-7), and a nitro group (C-8). In the crystal, the mol­ecules are assembled into a two-dimensional network by N⋯H/H⋯N and O⋯H/H⋯O hydrogen-bonding inter­actions. n–π and π–π stacking inter­actions are the dominant inter­actions in the three-dimensional crystal packing. Hirshfeld surface analysis indicates that the most important contributions are from O⋯H/H⋯O (34.9%), H⋯H (33.7%), and C⋯H/H⋯C (11.0%) contacts. The energies of the frontier mol­ecular orbitals were computed using density functional theory (DFT) calculations at the B3LYP-D3BJ/def2-TZVP level of theory and the LUMO–HOMO energy gap of the mol­ecule is 3.765 eV.

The title compound, C₁₄H₁₂N₂O₄, was obtained from 2-acetyl-6-aminonaphthalene through two-step reactions of acetylation and nitration. The molecule comprises the naphthalene ring system consisting of functional systems bearing a acetyl group (C-2), a nitro group (C-5), and an acetylamino group (C-6). In the crystal, the molecules are assembled into two-dimensional sheet-like structures by intermolecular N—H...O and C—H...O hydrogen-bonding interactions. Hirshfeld surface analysis illustrates that the most important contributions to the crystal packing are from O...H/H...O (43.7%), H...H (31.0%), and C...H/H...C (8.5%) contacts.

Corydalis yanhusuo is a medicinal herb in China that has been widely used to treat various kinds of pain. The tuber is the main organ of C. yanhusuo used for medicinal purposes, but changes in related genes during the development of the tuber have rarely been reported. To identify the differentially expressed genes during tuber development, C. yanhusuo full-length transcriptomic sequencing was performed using single-molecule real-time technology, and tubers at three development stages were selected for comparative transcriptome analysis. A total of 90,496 full-length non-chimeric transcripts were obtained, and 19,341 transcripts were annotated in at least one public database. A total of 9221 differentially expressed genes were identified during the swelling process of C. yanhusuo tuber. A Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis revealed that differentially expressed genes associated with a “starch and sucrose metabolism pathway”, “phenylpropanoid biosynthesis pathway”, “isoquinoline alkaloid biosynthesis pathway”, “zeatin biosynthesis pathway”, and “brassinosteroid biosynthesis pathway” were predominantly enriched. In addition, the genes involved in cell wall metabolism were potentially associated with tuber swelling. These processes regulated and were involved in C. yanhusuo tuber development. The results provide a foundation for further research on tuber formation in medicinal plants.

Natural rubber is one of the most important industrial raw materials, and its biosynthesis is still a fascinating process that is still largely unknown. In this research, we studied Decaisnea insignis, a unique rubber-producing plant that is different from other rubber-producing species due to the presence of lactiferous canals in its pericarp. The present study aims to provide novel insights into the mechanisms underlying rubber accumulation and PCD by subjecting the Decaisnea insignis laticiferous canals to light microscopy, TUNEL assay, and DAPI staining, as well as viability analysis, cellular ultrastructure analysis, and molecular analysis using light microscopy, scanning electron microscopy, immunofluorescence labeling, transmission electron microscopy, and transcriptome sequencing. At the cellular level, the origin of small rubber particles in the laticiferous canals had no morphological correlation with other organelles, and these particles were freely produced in the cytosol. The volume of the rubber particles increased at the sunken and expanding stage, which were identified as having the characteristics of programmed cell death (PCD); meanwhile, plenty of the rubber precursors or rubber particles were engulfed by the vacuoles, indicating a vacuole-mediated autophagy process. The accumulation of rubber particles occurred after the degeneration of protoplasts, suggesting a close association between rubber biosynthesis and PCD. The molecular analysis revealed the expression patterns of key genes involved in rubber biosynthesis. The upstream genes DiIPP, DiFPP, and DiGGPPS showed a decreasing trend during fruit ripening, while DiHRT, which is responsible for rubber particle extension, exhibited the highest expression level during the rubber particle formation. Moreover, the transcription factors related to PCD, DiLSD1, and DiLOL2 showed a negative correlation with the expression pattern of DiHRT, thus exhibiting strict rules of sequential expression during rubber biosynthesis. Additionally, the expression trends of DiXCP1 and DiCEP1, which act as proteases during PCD, were positively correlated with DiGGPPS expression. In conclusion, the findings suggest that the autophagic PCD may play a crucial role in rubber accumulation in D. insignis. Further research is still needed to fully understand the complex regulatory network underlying rubber biosynthesis in plants.

Plant glandular trichomes have received much attention due to their commercial and biological value. Recent studies have focused on the development of various glands in plants, suggesting that programmed cell death (PCD) may play an important role during the development of plant secretory structures. However, the development processes and cytological characteristics in different types of plant secretory structures differed significantly. This study aims to provide new data on the developmental PCD of the capitate glandular hairs in Dictamnus dasycarpus. Light, scanning, immunofluorescence labeling, and transmission electron microscopy were used to determine the different developmental processes of the capitate glandular hairs from a cytological perspective. Morphologically, the capitate glandular hair originates from one initial epidermal cell and differentiates into a multicellular trichome characterized by two basal cells, two lines of stalk cells, and a multicellular head. It is also histochemically detected by essential oils. TUNEL-positive reactions identified nuclei with diffused fluorescence or an irregular figure by DAPI, and Evans blue staining showed that the head and stalk cells lost their viability. Ultrastructural evidence revealed the developmental process by two possible modes of PCD. Non-autolytic PCD was characterized by buckling cell walls and degenerated nuclei, mitochondria, plastids, multivesicular body (MVB), and end-expanded endoplasmic reticulum in the condensed cytoplasm, which were mainly observed in the head cells. The MVB was detected in the degraded vacuole, a degraded nucleus with condensed chromatin and diffused membrane, and eventual loss of the vacuole membrane integrity exhibited typical evidence of vacuole-mediated autolytic PCD in the stalk cells. Furthermore, protoplasm degeneration coupled with dark oil droplets and numerous micro-dark osmiophilic substances was observed during late stages. The secretion mode of essential oils is also described in this paper.

Iris (Iridaceae) is one of the most widely admired ornamental plants. It has been used mainly in medicine due to the high concentration of chlorogenic acid (CGA), flavonoids, isoflavones, lignans, and other compounds in its rhizomes. In iris, the gene functions related to CGA and flavonoids biosynthesis are still unclear. In this study, we compared the I. germanica rhizome with a high accumulation level of CGA but a low accumulation level of flavonoids, and the I. pallida rhizome with a low accumulation level of CGA but a high accumulation level of flavonoids at the transcriptome and metabolome levels. A total of 761 metabolites were detected, including 202 flavonoids and 106 phenolic acids based on metabolome profiling. In total, 135 flavonoids were highly accumulated in I. pallida, including three flavanols, 51 flavonoids, 12 flavonoid carbonosides, 31 flavonols, and 21 isoflavones. Based on single-molecule long-read sequencing technology, 94,461 transcripts were identified in iris. Expression analysis indicated that the high accumulation level of C4H and 4CL in I. germanica were essential for CGA accumulation, while CHS, DFR, ANS, ANR, LAR, and 3GT were essential for flavonoids biosynthesis in I. pallida. Many transcription factors such as transcript_83288 (MYB), transcript_57970 (WRKY), and transcript_77465 (WRKY) act as regulators, playing important roles in these biological processes. Our findings provide new insights into the molecular mechanisms associated with the biosynthesis and regulation of flavonoids and CGA in the iris rhizome, and highlight the usefulness of an integrated approach for understanding this process.