PmiREN: a comprehensive encyclopedia of plant miRNAs

Abstract

MicroRNAs (miRNAs) are small non-coding RNA molecules that function as diverse endogenous gene regulators at the post-transcriptional level. In the past two decades, as research effort on miRNA identification, function and evolution has soared, so has the demand for miRNA databases. However, the current plant miRNA databases suffer from several typical drawbacks, including a lack of entries for many important species, uneven annotation standards across different species, abundant questionable entries, and limited annotation. To address these issues, we developed a knowledge-based database called Plant miRNA Encyclopedia (PmiREN, http://www.pmiren.com/), which was based on uniform processing of sequenced small RNA libraries using miRDeep-P2, followed by manual curation using newly updated plant miRNA identification criteria, and comprehensive annotation. PmiREN currently contains 16,422 high confidence novel miRNA loci in 88 plant species and 3,966 retrieved from miRBase. For every miRNA entry, information on precursor sequence, precursor secondary structure, expression pattern, clusters and synteny in the genome, potential targets supported by Parallel Analysis of RNA Ends (PARE) sequencing, and references is attached whenever possible. PmiREN is hierarchically accessible and has eight built-in search engines. We believe PmiREN is useful for plant miRNA cataloguing and data mining, therefore a resource for data-driven miRNA research in plants.

Transcriptional and post-transcriptional regulation of the miR171-LaSCL6 module during somatic embryogenesis in Larix kaempferi

“…The mature sequences of miR171s from Arabidopsis thaliana (Ath-miR171a, Ath-miR171b, and Ath-miR171c) and Picea abies (Pab-miR171a, Pab-miR171b, and Pab-miR171c) were obtained from PmiREN (https ://www. pmire n.com/) (Guo et al 2019). The sequence of miR171a from Pinus densata (Pde-miR171a) was identified by Hai et al (2017).…”

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

“…To understand the biological signi cance of the RNAseq results, we selected one of the potential miRNA candidates, miR169, which is evolutionarily conserved, reported to be present in various plant species including monocots, dicots, ferns and gymnosperms [68][69][70], and has been shown to be a central regulator of various abiotic stresses, including drought, salt, cold, heat, oxidative and hypoxia [71]. The miR169 family of Arabidopsis has 14 members, that matures into four types of different isoforms, differing only 1 or 2 nucleotides [71].…”

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

“…To understand the biological significance of the RNAseq results, we selected one of the potential miRNA candidates, miR169. The miR169 family is evolutionarily conserved and reported in several plant species (Guo et al 2020;Sunkar and Jagadeeswaran 2008). In addition, miR169 has also been shown to regulate several developmental, abiotic and biotic stress response pathways, including cold stress (Du et al 2017;Li et al 2008;Lee et al 2010;Rao et al 2020;Song et al 2018;Yu et al 2019;Zhao et al 2011, Zhou et al 2008.…”