Novel class of 31-nt small longer RNAs (slRNAs) in embryos of Norway spruce are differentially expressed during epitype inducing conditions

Here, we performed sRNA profiling to elucidate a more complete picture of the gymnosperm sRNA population than previously reported. We detected novel sRNA with length around 30-35nt in our raw sequencing data. These median length 31nt small longer RNAs (slRNAs) were then found to be most abundant in developing embryos, but not in vegetative plant tissues. The in-silico analysis indicates that these slRNA match to transfer RNAs (tRNA) and other non-coding transcripts and thus may target other non-coding RNAs (including tRNAs) or target repetitive elements such as transposons. Among the slRNAs, tRNA-derived sequences from Asp, Glu and His iso-acceptors were in majority and these sequences showed 3-prime or 5-prime- bias dependent on iso-acceptor type putatively targeted.This slRNA sized fraction was not only detected in a number of gymnosperm but also in Arabidopsis thaliana seeds suggesting these might be conserved type sRNAs between gymnosperm and angiosperm plant species. slRNA levels differed significantly between tissue type and developmental stage and interestingly their expression was affected by environmental changes, i.e., epitype inducing (EpI) temperature conditions, in our study. These slRNAs add to the complexity of the small RNA world and could play a role in epigenetic regulation of gene expression in plants.