Identification Of Date Palm (Phoenix Dactvlifera L.) MicroRNAs And Their Expression Profiling During Multi-staged Fruit Development

MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (20 to 24 nt in size), which are derived from single-stranded precursors that form stem-loop secondary structure and common among animals, plants, and even viruses. MiRNAs regulate gene expression by binding to their complementary sequences, leading to either cleavage-induced degradation or translational repression of their target transcripts. MiRNAs have been studied in plants since 2002 and known to play important regulatory roles in plant hormone homeostasis, stress responses, and diverse developmental processes, including seed development, meristem and lateral organ development, root initiation, flowering and sex determination, fruit development, timing and phase transitions. Date palm (Phoenix dactylifera L.), as a socio-cultural symbol for the Arabian Pensinsula, is also an economically important food crop in tropical and subtropical regions. With the development of next-generation sequencing technologies in the past few years, the genomics and transcriptomics studies of date palm (P. dactylifera) have made great progresses. Its high-coverage genome sequences facilitate many aspects of genome-wide studies including miRNA identification. Furthermore, the study of transcriptome profiles for its fruit development and ripening allows direct comparison between miRNAs and their target genes expression.In this study, we report the genome-wide miRNA identification and profiling of miRNAs expressed during P. dactylifera fruit development using a combined strategy—computational prediction and high-throughput miRNA sequencing. We first identified a total of 238 non-redundant conserved miRNAs in P. dactylifera based on the high conservation of known plant miRNAs using the high-quality genome sequences as reference. Through sequencing six small RNA libraries from different P. dactylifera fruit developmental stages, we detected 78 conserved miRNAs expressed during fruit development, and identified 276 novel P. dactylifera-specific FDA miRNAs, several of which were validated using stem-loop RT qPCR. The prediction of miRNA-targeted genes and functional analysis revealed that these FDA miRNAs may participate in regulating carbon metabolism, starch and sucrose metabolism, fructose and mannose metabolism, glycolysis and citrate cycle. Furthermore, by correlating miRNA profiles to those of the corresponding mRNA expression profiles at the different development stages of date palm fruiting, we found 221 FDA miRNAs exhibited a clear negative correlation with their corresponding target genes, which may suggest their direct regulatory roles on mRNA targets. Strikingly, some of these target genes were closely associated with starch and sucrose metabolism and fruit development pathways, indicating that these miRNAs may play important roles in regulating dates sugar accumulation and development.In summary, our study defines a comprehensive set of P. dactylifera genome-wide miRNA distribution and the expression profiles of FDA miRNAs, which provides a basis and data support for further molecular experimentation in assigning discrete functions and mechanisms of these miRNAs in P. dactylifera fruit development.