m6A profile of soybean tissues

Soybean is a critical source of vegetable protein, yet its proteome remains under-characterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D-data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity, with significant differences in protein-transcript abundance across organs. We also map N6-methyladenosine (m6A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of proteome and m6A methylome identifies novel regulator in m6A methylation. This comprehensive proteomic and m6A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement. Overall design: Different tissues from wild-type SoyC11 soybeans (Glycine max) were used and collected for proteome, m6A methylome and transcriptome analysis. The seedlings were grown in the greenhouse at 25?. Mature plants were grown in soybean field located in Shijiazhuang (37°6'25?N, 114°42'47?E), Hebei province, China. Seeds of the soybean germinated in sterilized water for 1 days, the imbibition seeds (ISD) were transferred to soil. At V1 stage, unifoliolate leaf (ULF), seedling stem (SM), root (RT_V1), seedling cotyledon (CT_V1) and trifoliolate leaf (TLF) were collected. The flowers (FL_R2) were collected at R2 stage in soybean field, the roots (RT_R5) and the root nodules (RTN) at R5 stage, the pod (Pod) at R6 stage, green seed (GSD) at R7, mature seed (MSD) at R8 stage.