Landscape of novel smORFs predicted from crop genomes with evolutionary and functional analysis

Numerous small open reading frames (smORFs) and related smORF-encoded peptides (SEPs) have been identified in model plants. However, a genome-wide overview of smORFs has yet to be established in plants, especially in crops. Here, we predicted millions of novel smORFs in Arabidopsis and 14 commonly cultivated crops by bioinformatic approaches. We found that the smORFs may reflect recurrent polyploidy events and genome rearrangements during evolution, and some smORFs are under strong purifying selection. About 70 % of orthogroups contain SEPs from one species, while 0.1 % of orthogroups contain SEPs from all species. Orthogroup size variation suggests that species-specific features are shaped by factors, including evolutionary relationship, genome size, and genome duplication. DNA repair and translation are major functions of conserved SEPs. Species-specific functions were also observed, such as salt stress responses in Brassica. Our work provides a valuable resource of smORFs and SEPs, offering insights into the understanding of their characteristics.