Altered expression profiles of microRNA families during de-etiolation of maize and rice leaves

BACKGROUND: MicroRNAs (miRNAs) are highly conserved small non-coding RNAs that play important regulatory roles in plants. Although many miRNA families are sequentially and functionally conserved across plant kingdoms (Dezulian et al. in Genome Biol 13, 2005), they still differ in many aspects such as family size, average length, genomic loci etc. (Unver et al. in Int J Plant Genomics, 2009). RESULTS: In this study, we investigated changes of miRNA expression profiles during greening process of etiolated seedlings of Oryza sativa (C(3)) and Zea mays (C(4)) to explore conserved and species-specific characteristics of miRNAs between these two species. Futhermore, we predicted 47 and 42 candidate novel miRNAs using parameterized monocot specific miRDeep2 pipeline in maize and rice respectively. Potential targets of miRNAs comprising both mRNA and long non-coding RNA (lncRNA) were examined to clarify potential regulation of photosynthesis. Based on our result, two putative positive Kranz regulators reported by Wang et al. (2010) were predicted as potential targets of miR156. A few photosynthesis related genes such as sulfate adenylytransferase (APS3), chlorophyll a/b binding family protein etc. were suggested to be regulated by miRNAs. However, no C(4) shuttle genes were predicted to be direct targets of either known or candidate novel miRNAs. CONCLUSIONS: This study provided the comprehensive list of miRNA that showed altered expression during the de-etiolation process and a number of candidate miRNAs that might play regulatory roles in C(3) and C(4) photosynthesis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13104-016-2367-x) contains supplementary material, which is available to authorized users.