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

Fromm, Bastian, Høye, Eirik, Domanska, Diana, Zhong, Xiangfu, Aparicio-Puerta, Ernesto, Ovchinnikov, Vladimir, Umu, Sinan U, Chabot, Peter J +10 more·2022·Nucleic Acids Research
DOI 10.1093/nar/gkab1101PMC PMC8728216
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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/.

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  • MirGeneDB identifies the evolution origin of each miRNA as a node of origin for either the individual miRNA (locus) or the miRNA family (family).

    “MirGeneDB identifies the evolution origin of each miRNA as a node of origin for either the individual miRNA (locus) or the miRNA family (family) [16].”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [16]

  • miRGeneDB has clearly established itself as the resource for bona fide miRNAs, while miRBase still includes scores of dubiously identified miRNAs.

    “miRGeneDB has clearly established itself as the resource for bona fide miRNAs, while miRBase still includes scores of dubiously identified miRNAs [6, 14, 16, 31, 32].”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [16]

  • In total, ∼9 billion of the ∼20 billion trimmed reads of the 2,406 runs mapped to guide and passenger miRNAs covering 89.8% of miRNAs in miRBase and 99.5% of all miRNAs in MirGeneDB2.1.

    “In total, ∼9 billion of the ∼20 billion trimmed reads of the 2,406 runs mapped to guide and passenger miRNAs covering 89.8% of miRNAs in miRBase [15] and 99.5% of all miRNAs in MirGeneDB2.1 (99.8% of mature strands) (Supplementary Table S3) [16].”

    From A curated human cellular microRNAome based on 196 primary cell types (2022) · cites this paper as [16]

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Authors
Fromm, B., Høye, E., Domanska, D., Zhong, X., Aparicio-Puerta, E., Ovchinnikov, V., Umu, S. U., Chabot, P. J., Kang, W., Aslanzadeh, M., Tarbier, M., Mármol-Sánchez, E., Urgese, G., Johansen, M., Hovig, E., Hackenberg, M., Friedländer, M. R., & Peterson, K. J.
Affiliations
  • The Arctic University Museum of Norway, UiT- The Arctic University of Norway , Tromsø, Norway
  • Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital , Oslo, Norway
  • Center for Bioinformatics, Department of Informatics, University of Oslo , Oslo, Norway
  • Department of Biosciences and Nutrition, Karolinska Institute , Huddinge, Sweden
  • Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada , Granada, Spain
  • Computational and Molecular Evolutionary Biology Research Group, School of life sciences, Faculty of Medicine and Health Sciences, University of Nottingham , Nottingham, UK
  • Department of Research , Cancer Registry of Norway, Oslo, Norway
  • Department of Biological Sciences , Dartmouth College, Hanover, USA
  • Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University , Stockholm, Sweden
  • Politecnico di Torino , Torino, Italy
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2021-11-25
Volume
50
Issue
D1
Pages
D204-D210
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkab1101
PMC
PMC8728216
Cited by
167
References
4
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • Tromsø forskningsstiftelse (20_SG_BF)
  • Swedish Research Council
  • ERC (758397)
  • South-Eastern Norway Regional Health Authority (2018014)
  • School of Life Sciences University of Nottingham
  • Spanish Government (AGL2017-88702-C2-2-R)
  • University of Granada (A-BIO-481-UGR18, FEDER 18)
  • National Science Foundation
  • NASA Ames
  • Dartmouth College

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