Genome-wide identification and expression profiling of the 20 S proteasome gene family in sugarcane under cold stress

The 20 S proteasome is an evolutionarily conserved and essential protein complex in plant cells, consisting of α and β subunits organized into stacked ring structures, and it plays a central role in maintaining protein quality control, regulating signaling pathways and the cell cycle, and enabling cellular responses to environmental stress. However, our understanding of the 20 S proteasome gene family in sugarcane is still limited. In this study, a comprehensive genome-wide analysis of the 20 S proteasome gene family was performed in Saccharum spontaneum (AP85-441), including chromosomal localization, gene structure, conserved motif composition, phylogenetic relationships, and expression profiling. A total of 57 of 20 S proteasome genes were identified, comprising 28 α-subunit (ScPA) and 29 β-subunit (SsPB) genes distributed across 20 chromosomes. Phylogenetic analysis grouped these genes into seven clades and revealed a high degree of sequence homology with corresponding genes from rice and sorghum. The conserved motif and cis-element analyses revealed that ScPAs and SsPBs genes were involved in hormone signaling pathways such as ethylene (ET) and abscisic acid (ABA), as well as abiotic stress responsiveness. The analysis of RNA-seq and protein-seq datasets demonstrated that the 57 20 S proteasome genes exhibited distinct expression patterns across leaves, stems, and roots, and were involved in responses to cold stress, ET, and ABA. Additionally, the cultivar GT28 was used to clone the SoPAA1 (GenBank accession KC794940) gene, which codes for a 247-amino acid protein and showed higher levels of expression in the cold-tolerant cultivar than in the cold-sensitive cultivar. These findings show that SoPAA1 is a key positive regulator of the cold stress response, and it provides a promising candidate gene for breeding cold-resistant sugarcane.