Genome-Wide Identification of MicroRNAs and Their Targets in the Leaves and Fruits of Eucommia ulmoides Using High-Throughput Sequencing

Abstract

MicroRNAs (miRNAs), a group of endogenous small non-coding RNAs, play important roles in plant growth, development, and stress response processes. Eucommia ulmoides Oliver (hardy rubber tree) is one of the few woody plants capable of producing trans-1, 4-polyisoprene (TPI), also known as Eu-rubber, which has been utilized as an industrial raw material and is extensively cultivated in China. However, the mechanism of TPI biosynthesis has not been identified in E. ulmoides. To characterize small RNAs and their targets with potential biological roles involved in the TPI biosynthesis in E. ulmoides, in the present study, eight small RNA libraries were constructed and sequenced from young and mature leaves and fruits of E. ulmoides. Further analysis identified 34 conserved miRNAs belonging to 20 families (two unclassified families), and 115 novel miRNAs seemed to be specific to E. ulmoides. Among these miRNAs, fourteen conserved miRNAs and 49 novel miRNAs were significantly differentially expressed and identified as Eu-rubber accumulation related miRNAs. Based on the E. ulmoides genomic data, 202 and 306 potential target genes were predicted for 33 conserved and 92 novel miRNAs, respectively; the predicted targets are mostly transcription factors and functional genes, which were enriched in metabolic pathways and biosynthesis of secondary metabolites. Noticeably, based on the expression patterns of miRNAs and their target genes in combination with the Eu-rubber accumulation, the negative correlation of expression of six miRNAs (Eu-miR14, Eu-miR91, miR162a, miR166a, miR172c, and miR396a) and their predicted targets serving as potential regulators in Eu-rubber accumulation. This study is the first to detect conserved and novel miRNAs and their potential targets in E. ulmoides and identify several candidate genes potentially controlling rubber accumulation, and thus provide molecular evidence for understanding the roles of miRNAs in regulating the TPI biosynthesis in E. ulmoides.

Identification, expression analysis, and potential roles of microRNAs in the regulation of polysaccharide biosynthesis in Polygonatum cyrtonema Hua

“…Analysis of conserved miRNAs revealed that miR159a_1, miR168a-5p, and miR166g-3p were highly expressed in all tissues. Among these miRNAs, miR159a_1showed the highest expression level in leaves, which was consistent with expression pattern of Eucommia ulmoides[ 17]. In rhizomes, expression levels of miR160, miR160e-5p, miR8175, miR319c_2, miR319b_1, miR319a_1, miR319a-3p, and miR319_1 were up-regulated and those of miR167d-5p, miR171b_2, miR397a_3, and miR160a-5p were significantly down-regulated compared with leaves and flowers.…”

Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses

“…Two distinct pathways i.e., the MEP pathway and the MVA pathway play key roles in the synthesis of IPP which is the precursor of polyisoprene [ 6 , 39 ]. Pyruvate is a primary material in the MEP pathway [ 5 , 40 ].…”

“…It is a Tertiary relict species that has been a well-known medicinal plant in China for >2000 years [ 3 ]. Recently, the high productivity of gutta, i.e., trans -1,4-polyisoprene (TPI) in E. ulmoides has attracted broad attention [ 4 , 5 , 6 ]. E. ulmoides therefore has the potential to replace the commonly known para -rubber tree ( Hevea brasiliensis from the Euphorbiaceae, which only grows in tropical zones) because of its wide distribution in the subtropical and temperate ecozones and good resistance [ 7 , 8 ].…”

“…Sexual dimorphism such as differences in the morphology and physiology is commonly present in the dioecious plants, which may be related to the DEGs [ 37 , 38 ] or other genetic and epigenetic factors between the male and female individuals. In plants, isopentenyl diphosphate (IPP) is the precursor of polyisoprene, which is synthesized in two distinct pathways, i.e., the methylerythritol phosphate (MEP) pathway in the plastids and the mevalonate (MVA) pathway in the cytoplasm [ 6 , 39 ]. Gutta i.e., TPI, is formed by successive condensation of the IPP into a trans -structure [ 5 ].…”

Genome‐wide screening of long non‐coding RNAs involved in rubber biosynthesis in Eucommia ulmoides

“…To date, studies have primarily focused on the underlying protein-coding genes involved in Eu-rubber biosynthesis (Suzuki et al 2012;Wuyun et al 2018), whereas little is known about the non-coding RNAs (ncRNAs) involved in this process (Wang et al 2016). Transcriptome analyses, based on deep sequencing, have revealed that more than 90% of the genome can be transcribed into ncRNAs (Kapranov et al 2007), which are classified as small ncRNAs (sncRNAs), or long ncRNAs (lncRNAs), based on length (Brosnan and Voinnet 2009).…”