Lateral root (LR) formation promotes plant resistance, whereas high-level ethylene induced by abiotic stress will inhibit LR emergence. Considering that local auxin accumulation is a precondition for LR generation, auxin-induced genes inhibiting ethylene synthesis may thus be important for LR development. Here, we found that auxin response factor 4 (SaARF4) in Sedum alfredii Hance could be induced by auxin. The overexpression of SaARF4 decreased the LR number and reduced the vessel diameters. Meanwhile, the auxin distribution mode was altered in the root tips and PIN expression was also decreased in the overexpressed lines compared with the wild-type (WT) plants. The overexpression of SaARF4 could reduce ethylene synthesis, and thus, the repression of ethylene production decreased the LR number of WT and reduced PIN expression in the roots. Furthermore, the quantitative real-time PCR, chromatin immunoprecipitation sequencing, yeast one-hybrid, and dual-luciferase assay results showed that SaARF4 could bind the promoter of 1-aminocyclopropane-1-carboxylate oxidase 4 (SaACO4), associated with ethylene biosynthesis, and could downregulate its expression. Therefore, we concluded that SaARF4 induced by auxin can inhibit ethylene biosynthesis by repressing SaACO4 expression, and this process may affect auxin transport to delay LR development.

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.