PT - JOURNAL ARTICLE AU - Igor Fesenko AU - Ilya Kirov AU - Andrey Kniazev AU - Regina Khazigaleeva AU - Vassili Lazarev AU - Daria Kharlampieva AU - Ekaterina Grafskaia AU - Viktor Zgoda AU - Ivan Butenko AU - Georgy Arapidi AU - Anna Mamaeva AU - Vadim Ivanov AU - Vadim Govorun TI - Distinct types of short open reading frames are translated in plant cells AID - 10.1101/213736 DP - 2017 Jan 01 TA - bioRxiv PG - 213736 4099 - http://biorxiv.org/content/early/2017/11/03/213736.short 4100 - http://biorxiv.org/content/early/2017/11/03/213736.full AB - Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in atleast one of ten plant species examined. Mass spectrometry analysis of proteomic and peptidomic datasets suggested that 602 sORFs located on distinct parts of mRNAs and long non-coding RNAs (lncRNAs) are translated, including 74 conservative sORFs. Combined analysis of the translation of the sORFs and the main ORF from a single gene suggested the existence of bi- and poly-cistronic mRNAs with tissue-specific expression. Alternative splicing is likely involved in the excision of translatable sORFs from such transcripts. We identified a group of sORFs homologous to known protein domains and suggested they function as small interfering peptides. Functional analysis of a candidate lncRNA-encoded peptide showed it to be involved in regulating growth and differentiation in moss. The high evolutionary rate and wide translation of sORFs suggest that they may provide a reservoir of potentially active peptides and their importance as a raw material for gene evolution. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.