Deep sequencing discovery of novel and conserved microRNAs in strawberry (Fragaria×ananassa)

Abstract

In plants, microRNAs (miRNAs) play a critical role in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice. Deep sequencing technologies have facilitated identification of species-specific or lowly expressed as well as conserved or highly expressed miRNAs in plants. In this research, we used Solexa sequencing to discover new miRNAs in cultivated strawberry (Fragaria×ananassa). A total of 23,282 ,309 reads representing 22,500 ,402 distinct sequences were obtained from a short RNA library generated from small RNAs extracted from strawberry fruit tissues. On the basis of sequence similarity and hairpin structure prediction, we found that 156,639 reads representing 153 sequences have good matches to known miRNAs. We also identified 37 novel miRNA candidates. These sequences had not been previously described in other plant species. Potential target genes were predicted for the majority of and novel miRNAs. These results show that regulatory miRNAs exist in the agriculturally important cultivated strawberry and may play an important role in its growth, development and response to disease.

Identification of the Conserved and Novel miRNAs in Mulberry by High-Throughput Sequencing

“…However, the size distribution pattern of male mulberry flowers was different. The most common size for small RNAs in male flower tissue was 21 nt, which was consistent with Fragaria × ananassa and Pinus contorta [34], [35].…”

Identification of microRNAs and their targets in Finger millet by high throughput sequencing

“…The sequencing resulted in 20,512,196 raw reads, after filtering out adapter contaminants, low-quality reads and Rfam contaminants 7,755,160 unique reads were got and the percentage of putative small RNA reads were 73% (Table 1). The most abundant sRNAs range from 21-24 nt (Chi et al, 2011;Xu et al, 2013), and the 21 nt sRNAs represented the most abundant followed by 24 nt which was in agreement with previous reports (Morin et al, 2008;Ge et al, 2012) (Fig. 1).…”

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

“…The relative concentrations of these novel putative miRNAs were mostly lower than those of conserved miRNAs measured in the same samples. A similar situation was observed previously for novel miRNAs isolated in this and other plant species (Mica et al, 2010;Li et al, 2011;Ren et al, 2012;Ge et al, 2013). Moreover, since miRNAs belonging to lowabundance categories have emerging big roles in plant developmental processes (Wang and Guo, 2015), we hypothesize that the analyzed novel miRNAs that are less abundant than conserved miRNAs could function to modulate the cross talk between plant development and the abiotic stress response.…”