GFAP is a gene functional annotation tool for myriad plant studies.

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.

Phosphorus (P), an essential macronutrient, is crucial for plant growth and development. However, available inorganic phosphate (Pi) is often scarce in soil, and its limited mobility exacerbates P deficiency in plants. Plants have developed complex mechanisms to adapt to Pi-limited soils. The root, the primary interface of the plant with soil, plays an essential role in plant adaptation to Pi-limited soil environments. Root system architecture significantly influences Pi acquisition via the dynamic modulation of primary root and/or crown root length, lateral root proliferation and length, root hair development, and root growth angle in response to Pi availability. This review focuses on the physiological, anatomical, and molecular mechanisms underpinning changes in root development in response to Pi starvation in cereals, mainly focusing on the model monocot plant rice (Oryza sativa). We also review recent efforts to modify root architecture to enhance P uptake efficiency in crops and propose future research directions aimed at the genetic improvement of Pi uptake and use efficiency in crops based on root system architecture.

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

Plant research faces persistent challenges in integrating heterogeneous data and ensuring compatibility across diverse analytical pipelines. The limited automation of existing tools often results in fragmented workflows, reducing analytical efficiency and reproducibility. To address these limitations, we developed SPDEv3.0 as a fully integrated bioinformatics platform with a graphical user interface, consolidating more than 130 functions across seven logically connected modules. SPDEv3.0 streamlines key tasks such as gene family identification, primer design, and genome feature extraction through high-level automation, enabling users to perform complex bioinformatic workflows with minimal manual intervention. For instance, collinearity analysis between Arabidopsis thaliana and A. halleri can be completed in under 2 min using only genome and annotation files, with all intermediate steps executed automatically. In addition, SPDEv3.0 offers over 30 customizable visualization functions, including genomic feature mapping, domain structure illustration, heatmaps, Circos plots, and statistical charting, all designed to help users generate publication-ready figures without coding. A total of 40 classical breeding methods have been implemented in SPDEv3.0, all of which support automated computation following user data input. Benchmarking across a range of plant genomes (including those exceeding 14 Gb) demonstrates SPDEv3.0's robust performance, scalability, and practical utility. By integrating high automation, module interoperability, and extensive visualization capacity, SPDEv3.0 provides a powerful and accessible solution for modern plant genomics and breeding research.

The selection of superior lines is extremely important to improve the utilization rate and economic value of bamboo. In this research, 120 anther-regenerated bamboo lines were planted in the field, and the survival rate reached 84.2% one year after planting. During five years of observations, we continuously measured and recorded the number of shoots and the size of the new bamboo of these regenerated lines. The results showed that there were considerable differences in culm size and growth rate among the different lines. After comprehensive evaluation, we found that one of the lines (P82) had obvious advantages in culm size and growth rate compared with the others. The chromosome ploidy of line P82 and the other three lines (P38, P84, and P34) was detected. It was found that P82 was hexaploid, while the other three lines were dodecaploid. Nutritional components of the P82 shoots were further detected. The results showed that the content of soluble sugar was 1.4%, the content of free amino acid was 3.5 g·kg⁻¹ (FW, fresh weight), and the content of protein was 14.8 g·kg⁻¹ (FW), and there were no significant differences compared with the local wild mature bamboo. Anatomical analysis showed that the vascular bundle size of the line P82 (hexaploid) was significantly larger than that of line P38 (dodecaploid), and the length of parenchyma cells in the culm wall of line P82 was similar to that of line P38, however, the cell width of line P82 was significantly wider than that of line P38. In this study, the breeding of superior lines of regenerated bamboo plants from an anther culture was realized, which provided an example for a new method for selecting superior lines from an anther culture, and also enriched the resources of superior lines of D. latiflorus.