Genome-Wide Analysis of Soybean Vacuolar Processing Enzyme Gene Family Reveals Their Roles in Plant Development and Response to Stress Conditions

Vacuolar processing enzymes (VPEs) are important proteases for the processing and maturation of vacuolar proteins. The VPEs in model plant Arabidopsis have been well researched. However, less is known about this gene family in the crop plant soybean (Glycine max). This study performed genome-wide identification of soybean VPE genes and 7 members were isolated. Their sequence information was firstly collected, and then phylogenetic relationship, chromosome distribution, gene duplication, conserved motifs as well as gene structure were analyzed for further insight into this gene family. The 7 GmVPEs were located on 6 chromosomes, and their encoding proteins were classified into three groups. Collinearity analysis indicated that 5 GmVPEs were involved in gene duplication events and they have undergone purifying selection during evolution. Conserved motif and gene structure analysis revealed the similarity and diversity among the sequences of different GmVPEs. To uncover the possible functions of soybean VPEs, cis-acting elements and TF binding sites on their promoters were identified, the results implied soybean VPE genes might participate in various biological processes and transcriptional regulation pathways. Through analyzing the RNA-Seq data, expression of the soybean VPE genes were found to exhibit spatiotemporal differences, with some being expressed almost ubiquitously, while others being expressed uniquely in seed. Finally, the expression profile analysis indicated that two VPE members, namely GmVPE4 and GmVPE7, likely play key roles in plant response to both biotic and abiotic stresses.