Expansins, a group of cell wall-loosening proteins, are involved in cell-wall loosening and cell enlargement in a pH-dependent manner. According to previous study, they were involved in plant growth and abiotic stress responses. However, information on the biological function of the expansin gene in moso bamboo is still limited. In this study, we identified a total of 82 expansin genes in moso bamboo, clustered into four subfamilies (α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA) and expansin-like B (EXPB)). Subsequently, the molecular structure, chromosomal location and phylogenetic relationship of the expansin genes of Phyllostachys edulis (PeEXs) were further characterized. A total of 14 pairs of tandem duplication genes and 31 pairs of segmented duplication genes were also identified, which may promote the expansion of the expansin gene family. Promoter analysis found many cis-acting elements related to growth and development and stress response, especially abscisic acid response element (ABRE). Expression pattern revealed that most PeEXs have tissue expression specificity. Meanwhile, the expression of some selected PeEXs was significantly upregulated mostly under abscisic acid (ABA) and polyethylene glycol (PEG) treatment, which implied that these genes actively respond to expression under abiotic stress. This study provided new insights into the structure, evolution and function prediction of the expansin gene family in moso bamboo.

Chionanthus retusus, an arbor tree of the Oleaceae family, is an ecologically and economically valuable ornamental plant for its remarkable adaptability in landscaping. During C. retusus breeding, we observed diverse floral shapes; however, no available genome for C. retusus has hindered the widespread identification of genes related to flower morphology. Thus, a de novo telomere-to-telomere (T2T) gap-free genome was generated. The assembly, incorporating high-coverage and long-read sequencing data, successfully yielded two complete haplotypes (687 and 683 Mb). The genome encompasses 42 864 predicted protein-coding genes, with all 46 telomeres and 23 centromeres in one haplotype. Whole genome duplication analysis revealed that C. retusus underwent one fewer event of whole-genome duplication after differentiation compared to other species in the Oleaceae family. Furthermore, flower vein diversity was the main reason for the differences in floral shapes. Auxin-related genes were responsible for petal shape formation on genome-based transcriptome analysis. Specifically, the removal and retention of the first intron in CrAUX/IAA20 resulted in the production of two transcripts, and the differences in the expression levels of CrAUX/IAA20 resulted in the variations of flower veins. Compared to transcripts lacking the first intron, transcripts with intron retention caused more severe decreases in the number and length of flower veins in transgenic Arabidopsis thaliana. Our findings will deepen our understanding of flower morphology development and provide important theoretical support for the cultivation of Oleaceae.

Efficiently extracting information from biological big data can be a huge challenge for people (especially those who lack programming skills). We developed S equence P rocessing and D ata E xtraction (SPDE) as an integrated tool for sequence processing and data extraction for gene family and omics analyses. Currently, SPDE has seven modules comprising 100 basic functions that range from single gene processing (e.g., translation, reverse complement, and primer design) to genome information extraction. All SPDE functions can be used without the need for programming or command lines. The SPDE interface has enough prompt information to help users run SPDE without barriers. In addition to its own functions, SPDE also incorporates the publicly available analyses tools (such as, NCBI-blast, HMMER, Primer3 and SAMtools), thereby making SPDE a comprehensive bioinformatics platform for big biological data analysis. Availability: SPDE was built using Python and can be run on 32-bit, 64-bit Windows and macOS systems. It is an open-source software that can be downloaded from https://github.com/simon19891216/SPDEv1.2.git . Contact: xudongzhuanyong@163.com

The biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are essential for sesquiterpenes and triterpenes, respectively, is primarily governed by the mevalonate pathway, wherein farnesyl pyrophosphate synthase (FPS) plays a pivotal role. This study identified eight members of the FPS gene family in Euphorbia hirta, designated EhFPS1–EhFPS8, through bioinformatics analysis, revealing their distribution across several chromosomes and a notable tandem gene cluster. The genes exhibited strong hydrophilic properties and key functional motifs crucial for enzyme activity. An in-depth analysis of the EhFPS genes highlighted their significant involvement in isoprenoid metabolism and lipid biosynthesis, with expression patterns influenced by hormones such as jasmonic acid and salicylic acid. Tissue-specific analysis demonstrated that certain FPS genes, particularly EhFPS1, EhFPS2, and EhFPS7, showed elevated expression levels in latex, suggesting their critical roles in terpenoid biosynthesis. Furthermore, subcellular localization studies have indicated that these proteins are primarily found in the cytoplasm, reinforcing their function in metabolic processes. These findings provide a foundational understanding of the FPS genes in E. hirta, including their gene structures, conserved domains, and evolutionary relationships. This study elucidates the potential roles of these genes in response to environmental factors, hormone signaling, and stress adaptation, thereby paving the way for future functional analyses aimed at exploring the regulation of terpenoid biosynthesis and enhancing stress tolerance in this species.

With the rapid accumulation of diverse omics datasets, achieving efficient management and integrative analysis of plant multi-omics data remains a major challenge. Conventional solutions rely on constructing web-based databases, which often demand substantial programming expertise and long-term financial support. To address these limitations, we developed the Plant Multi-omics Database Construction System (PlantMDCS)-a locally deployable, user-friendly, and collaborative platform that unifies database construction and downstream multi-omics analysis within a graphical environment. PlantMDCS adopts a decoupled front-end/back-end architecture. The back end serves as the core engine for data management and computation, and is responsible for the storage, preprocessing, integration, and hierarchical association of multi-omics data. Once initialized, the front end supports the complete research workflow, including data import, querying, integrative analysis and visualization. All operations can be performed without programming, while local resource usage is dominated by disk storage required for user-provided datasets rather than sustained computational overhead. Benchmarking across plant species ranging from Arabidopsis to hexaploid wheat demonstrated that database construction can be completed within minutes, independent of genome size or data complexity. PlantMDCS is designed for local deployment to ensure data security, while allowing multi-user collaboration within local networks and supporting controlled remote access for teams distributed across different regions. Overall, PlantMDCS offers a secure and sustainable framework that integrates data management and analysis within a unified system. This design shifts multi-omics research away from fragmented file-based processing toward persistent, database-driven exploration, thereby enhancing analytical efficiency and reproducibility.