MirGeneDB 2.0: the metazoan microRNA complement

Abstract

Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database - MirGeneDB - to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.

Identification of Differentially Expressed MicroRNAs and Their Potential Target Genes in Adipose Tissue from Pigs with Highly Divergent Backfat Thickness

“…Although miRBase does have some weaknesses, it has been used widely for identifying porcine miRNA and is a popular and reliable platform for miRNA researches [16,17,29,30]. Although MiRgeneDB (https://mirgenedb.org/) [31] and miRCarta (https://mircarta.cs.uni-saarland.de/) [32] provide more accurate and reliable miRNA annotations, miRNAs from porcine species are not included in the current MiRgeneDB. MiRCarta currently has miRNAs from 148 species, including 390 mature porcine miRNA sequences.…”

Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1

“…The percentage of the sncRNA reads mapping to the oyster genome ranged from 90.7 to 97.1%, whereas only a small fraction of the reads mapped to the OsHV-1 genome (0.03-0.07%, Table 1). Overall, 46% of the sncRNA reads mapped to the 151 C. gigas miRNA precursors retrieved from MirGeneDB v.2.0 [44], showing a clear 22-nt peak (Fig. 2c).…”

“…By using only the 151 miRNA predictions available for oyster in the MirGeneDB [44], we adopted a conservative Table 3 Putative miRNA-mRNA interactions. The possible miRNA-mRNA interactions are listed for the DE-miRNAs and for other miRNAs of interests.…”

“…FastQC (https://www.bioinformatics.babraham.ac.uk/projects/ fastqc/) was used to verify the absence of sequencing adaptors as well as to verify the quality statistics of each dataset. The clean reads were uploaded in CLC Genomic Workbench v.12.0 (Qiagen, US), they were size selected (18-40 nt) and mapped on the oyster and OsHV-1 reference genomes (GCA_000297895 [49] and MG561751 (OsHV-1) [73], respectively) as well as on the predicted oyster miRNA precursors obtained from MirGeneDB (http://mirgenedb.org/) [44], applying 0.9 and 1 for similarity and length fraction parameters, respectively. The mapping graphs of the 151 oyster miRNA precursors were manually inspected to verify the presence of the minimal annotation criteria.…”

Exploring Non‐Coding RNAs in RNAcentral

“…It is important to view sequence reports for all ncRNAs in a genomic region of interest. For example, the genome browser shows another precursor microRNA sequence (URS0000EFBE70_9606) in the same region provided by MirGeneDB (Fromm et al, 2020;Fig. 2C).…”