In silico identification and functional annotation of universal stress protein (USP) gene family in Chenopodium quinoa

Quinoa is a resilient crop with significant genetic diversity, enabling it to thrive in various climates. This study focuses on the Universal Stress Protein (USP) gene family in quinoa. It helps plants maintain homeostasis in response to drought, high salinity, extreme temperatures, and scavenging reactive oxygen species. The research conducted a genome-wide analysis of C. quinoa USP genes (CqUSPs). The gene structure, distribution of motifs, phylogenetic history, and duplication of CqUSPs were analysed. Analysis of cis-elements, protein-protein interactions, and micro-RNAs that target CqUSPs revealed important insights into the regulatory mechanisms, functional associations and post-transcriptional control of these genes. We have identified 41 sequences inside the allotetraploid genome. Domain architecture helped us understand the multifunctional nature of CqUSPs. Analysis of transcriptome data has demonstrated that the CqUSP gene family plays a role in the defence response to drought and heat stress conditions in quinoa. Protein-protein interaction studies showed their roles in amino acid metabolism, chaperone activity, ubiquitination, and DNA repair mechanisms. This comprehensive study reveals the identification and characterisation of CqUSP genes, offering valuable insights for further exploration of abiotic stress tolerance in quinoa. Additional research, such as expression profiling, might assist in confirming the stress-specific transcriptional regulation of these genes. To the best of our knowledge this the first detailed study conducted on the identification and interaction network of USP gene family in quinoa.