The miRNAome of ramie (Boehmeria nivea L.): identification, expression, and potential roles of novel microRNAs in regulation of cadmium stress response

Abstract

BackgroundMicroRNAs (miRNAs) regulate numerous crucial abiotic stress processes in plants. However, information is limited on their involvement in cadmium (Cd) stress response and tolerance mechanisms in plants, including ramie (Boehmeria nivea L.) that produces a number of economic valuable as an important natural fibre crop and an ideal crop for Cd pollution remediation.ResultsFour small RNA libraries of Cd-stressed and non-stressed leaves and roots of ramie were constructed. Using small RNA-sequencing, 73 novel miRNAs were identified. Genome-wide expression analysis revealed that a set of miRNAs was differentially regulated in response to Cd stress. In silico target prediction identified 426 potential miRNA targets that include several uptake or transport factors for heavy metal ions. The reliability of small RNA sequencing and the relationship between the expression levels of miRNAs and their target genes were confirmed by quantitative PCR (q-PCR). We showed that the expression patterns of miRNAs obtained by q-PCR were consistent with those obtained from small RNA sequencing. Moreover, we demonstrated that the expression of six randomly selected target genes was inversely related to that of their corresponding miRNAs, indicating that the miRNAs regulate Cd stress response in ramie.ConclusionsThis study enriches the number of Cd-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in ramie during Cd stress.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1561-5) contains supplementary material, which is available to authorized users.

Integrated miRNA-mRNA analysis reveals the roles of miRNAs in the replanting benefit of Achyranthes bidentata roots

“…Herein, we investigated the regulatory molecular regulator mechanism of the replanting benefit of A. bidentata , we had explored greatly to this number by RNA-seq platform to characterize the root miRNAome of R1 and R2 plants and obtaining > 85 million sRNA clean reads. The results of the present study revealed a range of sRNAs, of length 18–30 nt in length, containing substantially more of 24 nt sRNAs than of 21 nt, similar to the sRNA size distribution of sRNAs in several plant species, including A. thaliana , broccoli and ramie 17 , 19 , 20 . These data suggested that the sequencing results were reliably representative of the endogenous sRNAs in A. bidentata .…”

“…With the development of RNA-seq technology, researchers can easily obtain information on novel and conserved miRNAs from some species and their expression differences among various samples of a species 11 , 15 , 17 . Herein, we investigated the regulatory molecular regulator mechanism of the replanting benefit of A. bidentata , we had explored greatly to this number by RNA-seq platform to characterize the root miRNAome of R1 and R2 plants and obtaining > 85 million sRNA clean reads.…”

“…As their sequences are so highly conserved across the eukaryotes, they are believed to represent an evolutionarily ancient component of gene regulation. To date, numerous studies have demonstrated that miRNA-mediated gene regulation plays an important role in various environmental responses of several plant species, including Arabidopsis thaliana 14 , Populus 15 , wheat 16 and ramie 17 .…”

“…The hypothesis in the present study was that miRNA activity may underlie some at least part of the regulatory mechanism associated with the replanting benefit of A. bidentata . High-throughput RNA sequencing (RNA-seq) technology is a powerful tool that allows concomitant sequencing of millions of sRNAs from a single tissue 10 , 16 , 17 . To date, numerous miRNAs involved in plant environmental responses have been revealed via this technology.…”

Design of a Privacy-Preserving Algorithm for Peer-to-Peer Network Based on Differential Privacy

“…At present, the main privacy-preserving scheme of P2P is anonymous processing of nodes and sensitive edges. It mainly includes the -1 algorithm proposed by Han et al [7], the anonymous node algorithm proposed by Yuan et al [8] and the anonymization privacy-preserving algorithm based on clustering proposed by Zhang et al [9]. But all these algorithms assume the attacker has not fully mastered the sufficient background knowledge.…”