Conservation and Diversity of miRNAs in Seeds of Gymnosperm Species

Micro RNAs are important regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in animal and plant species. Here we report a comprehensive analysis of sRNAs and miRNAs from 9 gymnosperm species (Welwitschia, Araucaria, Cykas, Efedra, Ginko, Gnetum, Sciadopitys, Spruce and Pine) and Arabidopsis as representative of angiosperm species, based on NGS results from 10 sRNA libraries.

In all gymnosperm seeds were found one predominant class of 21 nucleotides sRNAs followed by second predominant class of 24 nucleotides sRNAs and additional length classes of 31-34 nucleotides sRNAs.

Using miRBase mature sequences as a reference, we identified 899 conserved miRNAs combined into 65 conserved miRNA families. From which, 16 miRNA families were considered as highly conserved, they were presented in all studied gymnosperm species and Arabidopsis. Additionally, using the set of novel spruce miRNAs defined earlier in Norway spruce embryos, we defined 174 novel conserved miRNAs, which were presented more than in 2 gymnosperm species. We applied diverse profiling methods to examine size distribution and sequence conservation between species for defined miRNAs.

For conserved miRNAs, we defined 8485 miRNA–target pairs, combining 772 miRNAs and 2496 putative target gene models. Among the putative targets were found following gene families: TIR and NBS-LRR protein genes, protein kinases, PPR and TPR repeat, Clathrins/VPS, mTERFs, Multicopper oxidases, Myb-like, SPB, F-box, AP2 domain protein genes and many others. 466 gene models were unknowns. General characterization of conserved miRNA families’ targets was presented.

This study provides new insights on gymnosperms miRNAs, and a foundation for future studies.