Ubiquitin-like SUMO protease expansion in rice (Oryza sativa L.)

SUMOylation is a protein post-translational modification that is essential for plant growth and response to changing environments. However, past work in this area has mainly focused on simple sequence similarity methods for discovering SUMOylation genes, often using orthologue mapping from yeast (Saccharomyces cerevisiae) or Arabidopsis (Arabidopsis thaliana). In this work, we employed a range of computational techniques and approaches to describe and characterize the SUMOylation machinery in Asian rice (Oryza sativa), a globally important stable crop, and where the SUMOylation system has been shown to play key roles in responses to biotic and abiotic stresses. We describe and analyze the Ubiquitin-Like Protease (ULP) system at the phylogenetic, transcriptional, and protein structural levels, with a focus on the rice reference genome, a well-annotated rice population reference panel (RPRP), and wild rice genomes. Our analysis revealed the expansion of ULPs in the reference genome and RPRP set (32-45 ULPs) compared to wild rice (9-36 ULPs), raising an intriguing hypothesis about the expansion of the ULP family being driven by selective breeding pressure. We provide evidence of potential functional ULPs and their possible roles in biotic and abiotic stress responses in cultivated rice. These insights offer valuable resources for future rice breeding and crop improvement.