Hiding in plain sight: advances in discovery and functional description of plant sORF-encoded peptides

Short open reading frames (sORFs) and sORF-encoded peptides (SEPs) have confounded functional geneticists, as sORFs do not fit historical definitions of protein-coding genes. Evading traditional prediction and detection techniques, plant SEP genes have long been neglected in functional studies, but those that have been identified have proven to play numerous critical biological roles. Recent advances in transcriptomics and proteomics have led to the identification of hundreds of putative sORFs and SEPs in plants, some positioned within genes traditionally thought to be non-coding, highlighting a portion of the proteome that has gone unnoticed thus far. In this review, we examine the historical approaches to answering questions on gene function, how they have impacted and continue to impact sORF and SEP identification, and how they have evolved with technological advancements and developments in the field. Additionally, we emphasize the need for functional validation of putative SEPs in an era of high throughput and -omics based approaches, and discuss potential options for such pursuits. The definition, identification, and characterization of SEPs will ultimately allow for more accurate genomic resources and improved tools with which to develop them, pushing towards a more complete understanding of the functional genome.