PmiREN2.0: from data annotation to functional exploration of plant microRNAs

Abstract

Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

“…The paper on BRAD ( 101 ), the dedicated Brassica database, reports a particular focus on synteny analysis tools and looks forward to accommodating the more diverse omics data and pangenome information now becoming available for the Family. Plant ncRNA is covered by returning databases GreeNC ( 102 ), with its focus on lncRNA, and PmiREN ( 103 ) which doubles its content of miRNA entries. The latter offers an impressive array of new features for functional and evolutionary exploration including gene regulatory elements, target annotations, variants and phylogenetic trees.…”

Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication

“…The collapsed miRNAs that existed in at least three samples and expressed at more than 10 TPM in at least one sample were considered as high‐confidence miRNAs, which were compared with miRBase (Kozomara et al., 2019) to identify conserved miRNAs, whereas miRNAs that showed no matches in the miRBase were considered as novel miRNAs. We adopted the existing miRNA ID system in miRBase (Kozomara et al., 2019) and PmiREN2.0 (Guo et al., 2022) for our miRNA nomenclature.…”

“…Comparative studies on miRNA gene evolution in Arabidopsis lyrata and A. thaliana that diverged more than 10 million years ago have discovered numerous less conserved miRNA genes exhibiting high divergence in hairpin structures, processing fidelity, and target complementarity (Ma et al., 2010; Cuperus et al., 2011). With the increasing number of analyses on sRNA sequencing (sRNA‐seq) data, more and more less conserved miRNAs and phasiRNA‐generating loci (PHASs) have been uncovered in diverse species, from green algae to flowering plants (Chavez Montes et al., 2014; Zheng et al., 2015; Lunardon et al., 2020; Baldrich et al., 2022; Chen et al., 2021; Guo et al., 2022). However, whether and how the expression patterns and functions of sRNAs have been changed in shorter evolutionary times such as during crop domestication is unknown.…”

sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms

“…In parallel to software developments, different projects have recently attempted to improve and curate microRNA annotations by removing false positive entries, a known source of bias in downstream results ( 17 ). The metazoan specific MirGeneDB2.1 ( 18 ) and plant specific PmiRen2.0 ( 19 ) are therefore recommended for the correct profiling of bona fide miRNAs using sRNAbench.…”