In silico expression profiling and function prediction of transcribed small open reading frames from Cucumis sativus var. hardwickii PI183967 in C. sativus var. sativus

Abstract

Cucumis sativus is one of the most cultivated and consumed plants worldwide. To meet the demanding requirements following the rise in population, it is important to maintain and enhance the growth and development of this crop. Recent findings suggest that small open reading frames (sORFs) are associated not only with plant growth but with plant stress responses, especially in the case of drought and salt stress conditions. Hence, in this present study, we aim to determine the function and expression profile reflected in Cucumis sativus var. hardwickii PI183967 sORFs in the variety C. sativus var. sativus through transcriptomic analyses of publicly available RNA-seq datasets of var. sativus. We managed to obtain 14,799 transcribed sORF from the transcriptome datasets of var. sativus. Among these, only 689 (4.66%) transcribed sORF have translational potential. We were able to unveil the roles of transcribed sORFs associated with biological processes (reproductive process, immune response, and multicellular organism reproduction), molecular functions (transferase activity, catalytic activity, acting on a protein, hydrolase activity, and oxidoreductase activity), and cellular component (cytoplasm). KEGG pathway analysis revealed that the transcribed sORFs were significantly enriched in two of the KEGG Ontology (KO) terms, namely, plant-pathogen interaction and plant hormone signal transduction. Results from this study aid the understanding of sORF roles in Cucumis sativus and pave the way for future attempts to utilize these sORFs involved in stress responses to enhance the quality of the crop.