In Silico Prediction of Small Open Reading Frames from Intergenic Regions of Cucumis sativus L. Var. Hardwickii

Abstract

Small open reading frames play important roles in growth and development regulation in plant species. However, their sequences and functions remain poorly understood in many plant species including Cucumis sativus which is Asia's fourth most important vegetable. The breeding of climate-resilient cucumbers is of great importance to ensure their sustainability under extreme climate conditions. In this study, we aim to predict the intergenic sORFs from C. sativus var. hardwickii and determine their expression profiles in transcriptome datasets. We identified a total of 50,191 coding sORFs from var. hardwickii genome. In addition, 1,311 transcribed sORFs were detected in RNA-seq datasets of var. hardwickii and shared homology to sequences deposited in the cucumber EST database, and among these, 91 transcribed sORFs with translation potential were detected. The findings of this study provide insight into sequence diversity and expression patterns of sORFs in C. sativus, which could help in developing climate-resilient cucumbers.