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

Abstract

miRNAs are a class of non-coding endogenous small RNAs. They play vital roles in plant growth, development, and response to biotic and abiotic stress by negatively regulating genes. Mulberry trees are economically important species with multiple uses. However, to date, little is known about mulberry miRNAs and their target genes. In the present study, three small mulberry RNA libraries were constructed and sequenced using high-throughput sequencing technology. Results showed 85 conserved miRNAs belonging to 31 miRNA families and 262 novel miRNAs at 371 loci. Quantitative real-time PCR (qRT-PCR) analysis confirmed the expression pattern of 9 conserved and 5 novel miRNAs in leaves, bark, and male flowers. A total of 332 potential target genes were predicted to be associated with these 113 novel miRNAs. These results provide a basis for further understanding of mulberry miRNAs and the biological processes in which they are involved.

Identification and characterization of microRNAs in Humulus lupulus using high-throughput sequencing and their response to Citrus bark cracking viroid (CBCVd) infection

“…Their response to CBCVd-infection was also investigated, delivering valuable information for gaining in-depth knowledge of the function and regulatory mechanisms of miRNAs in the CBCVd-defence response. Comparison of sequencing data of the two libraries showed that sRNAs of 21-nt and 24-nt formed two major classes, consistent with the distribution patterns of sRNAs in other plant species [29, 30]. However, their distributions were significantly different between two analysed libraries.…”

“…The approach has been successfully used to discover novel miRNAs (which are generally expressed at a lower level), due to its ability to generate millions of reads randomly and independently with a determined length, which is implausible to identify by sequencing a low number of clones (sRNA library sequencing) or in situ hybridization-based methods (sRNA Northern blot and miRNA array analyses) [22]. Over the past years, high-throughput sequencing technologies have been implemented to investigate miRNAs across different plant species such as maize [23], potato [24], peanut [25], barley [26], soybean [27], Chinese cabbage [28], mulberry [29] and tobacco [30]. …”

Human Genes Are In Silico Potential Targets For Rice miRNA

“…However, seven miRNA families, miR482, miR529, miR858, miR4376, miR4414, miR4995, and miR5523, were found in only one or two plant species. The present data indicated that the conserved miRNA families (miR156, miR166, miR167, miR168, and miR535) miR159, miR160, miR164, miR169, miR171, miR172, miR390, miR396, miR397, miR529 and miR4376, miR162, miR393, miR395, miR398, miR399, miR408 and miR4414 miR319, miR482, miR827, miR828, miR858, miR2111, miR4995 and miR5523 were expressed across a vast range exceeded in all three tissues (Jia et al, 2014). In African rice Oryza glaberrima ( ogl), some miRNAs such as ogl-miR156l, ogl-miR166c, ogl-miR166k, ogl-miR168a, ogl-miR167i, ogl-miR171f, ogl-miR1846d of the control library and ogl-miR408, ogl-miR528, ogl-miR156, ogl-miR390, and ogl-miR396c of the treated library had higher reads than their complementary strand.…”

Evaluation of reference genes for quantitative real‐time PCR analysis of messenger RNAs and microRNAs in rainbow trout Oncorhynchus mykiss under heat stress

“…Analysis of gene expression patterns under heat stress can help us to understand the mechanisms of heat stress in O. mykiss and improve their ability to resist heat stress. QRT‐PCR has the advantages of high sensitivity, repeatability and specificity and has become an important research method for gene expression analysis (Candar‐Cakir et al ., ; Chávez‐Hernández et al ., ; Jia et al ., ; Kou et al ., ; Li et al ., ; Maroufi et al ., ; Shi & Chiang, ). For quantitative analysis, ideal reference genes can reduce experimental error and ensure the accuracy and reliability of screening results (Li et al ., ).…”

“…Oncorhynchus mykiss is an economically important cold water fish species throughout the world (Palti et al, 2011) -Cakir et al, 2016;Chávez-Hernández et al, 2015;Jia et al, 2014;Kou et al, 2012;Li et al, 2015;Maroufi et al, 2010;Shi & Chiang, 2005). For quantitative analysis, ideal reference genes can reduce experimental error and ensure the accuracy and reliability of screening results (Li et al, 2015).…”