Genome-Wide Identification and Profiling of Novel and Conserved Mirnas during Formation of an Epigenetic Memory in Norway Spruce Embryos

Epigenetic memory in Norway spruce permanently affect the timing of bud burst and bud set, vitally important adaptive traits, in this long-lived forest species. MicroRNAs (miRNAs), a class of small noncoding RNA molecules have recently drawn attention for their prominent role in development and epigenetic regulations.

We prepared 18 small RNA libraries from embryogenic tissues of two individuals at three stages of maturation grown up in vitro at three culturing temperatures (18, 23 and 28°C). Obtained libraries were sequenced in duplicate on PGM™ (Ion Torrent™) system and analyzed using CLC genomic workbench.

In this study, we report the identification of more than 1100 novel and conserved miRNAs in Norway spruce derived from 1050 precursors. We found high amount of isomiRs and high redundancy of putative miRNA genes in released Norway spruce genome v1. Based on identified miRNAs we studied their expression patterns in dependence on the temperature prevailing during somatic embryogenesis growth and leading to establishing of epigenetic marks. Distinct temperature dependent expression patterns were determined for most of analyzed miRNAs. miRNAs are targeting the large amounts of spruce genes with a wide range of functions, including genes involved in epigenetic regulation.