Identification of miRNAs and Their Target Genes in Peach (Prunus persica L.) Using High-Throughput Sequencing and Degradome Analysis

Abstract

MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development.

In-silico identification of miRNAs and their regulating target functions in Ocimum basilicum

“…Uracil was dominant in the first position of mature miRNA sequence (Table 1), suggesting its important role in miRNA mediated regulation in plants (Zhang et al, 2008;Unver et al, 2010;Dhandapani et al, 2011;Luo et al, 2013). In the case of pre-miRNA, predominance of Adenine and Uracil was observed, which is in accordance to the earlier report in Gossypium arboretum L. and Brassica rapa L. (Dhandapani et al, 2011;Wang et al, 2012).…”

Identification of miRNAs and their targets involved in the secondary metabolic pathways of Mentha spp.

“…Uracil was the predominant base in the mature miRNA sequences as reported in earlier studies (Zhang et al, 2008;Unver et al, 2010;Dhandapani et al, 2011;Luo et al, 2013).…”

Deletion of the miR172 target site in a TOE‐type gene is a strong candidate variant for dominant double‐flower trait in Rosaceae

“…Conversely, in N. benthamiana transgenic plants overexpressing Arabidopsis AP2, mRNA levels are controlled by endogenous miR172 via transcript cleavage (Mlotshwa et al ., ). In peach, the Prupe.6G242400 transcript cleavage by miR172 has been confirmed both experimentally (Gao et al ., ) and by degradome sequencing (Luo et al ., ). Future work aimed at assessing Prupe .6G242400 peptide accumulation may help to determine the effect of the ΔCter mutation on the final protein levels.…”