Post‐transcriptional adaptation of the aquatic plant Spirodela polyrhiza under stress and hormonal stimuli

Summary The Lemnaceae family comprises aquatic plants of angiosperms gaining attention due to their utility in wastewater treatment, and rapid production of biomass that can be used as feed, fuel, or food. Moreover, it can serve as a model species for neotenous growth and environmental adaptation. The latter properties are subject to post‐transcriptional regulation of gene expression, meriting investigation of how mi RNA s in Spirodela polyrhiza , the most basal and most thoroughly sequenced member of the family, are expressed under different growth conditions. To further scientific understanding of its capacity to adapt to environmental cues, we measured mi RNA expression and processing of their target sequences under different temperatures, and in the presence of abscisic acid, copper, kinetin, nitrate, and sucrose. Using two small RNA sequencing experiments and one degradome sequencing experiment, we provide evidence for 108 mi RNA s. Sequencing cleaved mRNA s validated 42 conserved mi RNA s with 83 targets and 24 novel mi RNA s regulating 66 targets and created a list of 575 predicted and verified targets. These analyses revealed condition‐induced changes in mi RNA expression and cleavage activity, and resulted in the addition of stringently reviewed mi RNA s to mi RB ase. This combination of small RNA and degradome sequencing provided not only high confidence predictions of conserved and novel mi RNA s and targets, but also a view of the post‐transcriptional regulation of adaptations. A unique aspect is the role of miR156 and miR172 expression and activity in its clonal propagation and neoteny. Additionally, low levels of 24 nt sRNA s were observed, despite the lack of recent retrotransposition.