MirGeneDB 2.1: toward a complete sampling of all major animal phyla

Abstract

We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.

MicroRNAs are deeply linked to the emergence of the complex octopus brain

“…Massive expansion of the miRNA repertoire in cephalopods (A) Phylogeny of several animal groups with the branch lengths between nodes, or from a node to an extant species, reflecting the gains of miRNA families minus the losses (Methods). Vertical lines at the end of the branches indicate the shared complement of the indicated taxon as deposited in MirGeneDB (46); the other branches lead to single species (sponge: A. queenslandica; sea anemone: N. vectensis; flatworm: S. mediterranea; annelid: C. teleta; oyster: C. gigas; limpet: L. gigantea). (B) Number of miRNA families (excluding species-specific novel families) versus median 3'UTR length in selected animals.…”

“…The O. sinensis transcriptome annotation generated in this study is available as Supplementary Data 1. MiRNA predictions and their corresponding tissue expression patterns for O. vulgaris, O. bimaculoides, E. scolopes and N. pompilius are available at MirGeneDB (46). Author Contributions G.Z.…”

The Small RNA Universe of Capitella teleta

“…miRNAs in C. teleta were investigated using miRDeep2 and standard parameters (Friedländer et al, 2008). Annotations from MirGeneDB were used to guide annotations (Fromm et al, 2021). Novel miRNAs were assessed by manual curation.…”

“…To further examine C. teleta small RNA classes, we first sought to annotate miRNAs using the miRDeep2 algorithm (Supplementary File S2-S8) (Friedländer et al, 2008). In total, ~700 potential miRNAs were found by the method based on alignments from combined small RNA sequencing guided by existing annotations from C. teleta, Eisenia fetida, Crassostrea gigas, and Lottia gigantea (Bhambri et al, 2018;Kozomara et al, 2018;Fromm et al, 2021). Of the 102 annotations in MirGeneDB, 99 were found (Supplementary File S3).…”

No evidence of paralogous loci or new bona fide microRNAs in telomere to telomere (T2T) genomic data

“…While miRBase used to be a repository for published miRNA candidates, where authors could submit their published miRNA candidates (Griffiths-Jones 2004), MirGeneDB uses a uniform system for microRNA annotation & nomenclature, based on next generation sequencing detectable criteria of miRNA biogenesis to arrive at bona fide miRNA complements for metazoan species (Fromm et al 2015; Fromm et al 2020; Fromm et al 2021).…”