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. 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.