Illustrator 2023

Multiple sequence alignments were performed and visualized in Jalview (v.2.11.2.6) using the MUSCLE algorithm with default parameters. The displayed results were enhanced using Adobe Illustrator 2023. The brighter the colour, the more conserved the site. In addition, we used ESPript 3.0 to help with visualization.

The crystal structures of CsRAS (PDB ID: 6MK2) and AtHCT (PDB ID: 5KJU) were downloaded from Uniprot (https://www.uniprot.org/ (accessed on 12 July 2022)). All ligands were drawn using ChemBio3D Ultra 14.0 and saved in PDB format. Due to an incorrect connection between the Arg-355 and the Tyr-302 in the rank1 output of MlAT6, the rank2 output was selected for docking. Docking was performed using AutoDock4, and the results were analysed using AutoDockTools (v.1.5.6). We employed a semi-flexible docking method where the protein was treated as rigid, except for Arg-355 in MlAT6, which was set as a flexible amino acid residue. The grid covered the active cavity with an appropriate cube size. Docking conformations were generated using a Lamarckian genetic algorithm (LGA), and the results were ordered based on the interaction energy between the substrate and target protein, from lowest to highest. Low-energy conformations were our focus. In addition, references in the literature provided positions and conformations for some active residues of acyltransferases. All results were visualized on PyMOL, including aligned structures, measured distances, calculated RMSD, labelled residues, and figure preparation. Finally, Adobe Illustrator 2023 was used to combine and enhance these images.

All .treefile outputs from IQ-Tree 2 were imported into FigTree v1.4.4 for visualization and coloring. Branch support values and labels were added manually in Adobe Illustrator 2023.

The values presented in the figures and tables are given as means ± standard errors. One-way analysis of variance (ANOVA) tests was used to examine the significant changes in soil P fractions, enzyme activities and the microbial gene abundance, citrus growth parameters and citrus P uptake under CK, Leg and Non-Leg treatments in P-surplus and P-deficient soils, respectively. Spearman correlation analysis was conducted to reveal the relationship between soil P fractions, the δ¹⁸O_P values of P_i pools and phosphatase activities, P-cycling gene relative abundance in P-surplus and P-deficient soils, respectively. All the statistics analysis were performed with IBM SPSS Statistics 22.0.
To evaluate the direct and indirect factors (including green manure addition, soil phosphatase activities and P-cycling genes abundances) affecting soil P sources transformation and citrus P uptake under different treatments in P-surplus and P-deficient soils, partial least squares path models (PLS-PM) were constructed using the R 4.2.3 packages “vegan” and “plspm”. And all figures in the present study were plotted using GraphPad Prism 8.0 and Adobe Illustrator 2023.

All .treefile outputs from IQ-Tree 2 were imported into FigTree v1.4.4 for visualization and coloring. Branch support values and labels were added manually in Adobe Illustrator 2023.

Raw micrographs and immunoblot scans were adjusted with the Levels tool and cropped in Adobe Photoshop 2023 and 2021, respectively. For immunofluorescence micrographs, images from the same biological replicate were scaled to identical settings. For GFP immunoprecipitation assays, GFP-RNF138 ubiquitylation was quantified from densitometry readings of immunoblots with Image Studio software (LI-COR Biosciences). HA signal from immunoprecipitates was normalized to the GFP signal immunoprecipitated. All graphs were generated in Prism 9 (GraphPad) and display the mean with error bars showing the standard deviation. Unless indicated otherwise, ordinary one-way ANOVA with Šídák's multiple comparisons test was performed to determine statistical significance. Asterisks depict statistically significant differences: ns (not significant), ∗ (p ≤ 0.05), ∗∗ (p ≤0.01), ∗∗∗ (p < 0.001), ∗∗∗∗ (p < 0.0001). Figures were arranged and labeled using Adobe Illustrator 2023.