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

Autor:	Fromm B; The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway.; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Høye E; Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.; Institute of Clinical Medicine, University of Oslo, Oslo, Norway., Domanska D; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.; Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway., Zhong X; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden., Aparicio-Puerta E; Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.; Biotechnology Institute, CIBM, Granada, Spain.; Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain., Ovchinnikov V; Computational and Molecular Evolutionary Biology Research Group, School of life sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK., Umu SU; Department of Research, Cancer Registry of Norway, Oslo, Norway., Chabot PJ; Department of Biological Sciences, Dartmouth College, Hanover, USA., Kang W; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.; Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden., Aslanzadeh M; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Tarbier M; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.; Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden., Mármol-Sánchez E; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.; Centre for Palaeogenetics, Stockholm, Sweden., Urgese G; Politecnico di Torino, Torino, Italy., Johansen M; Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway., Hovig E; 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., Hackenberg M; Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.; Biotechnology Institute, CIBM, Granada, Spain.; Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain., Friedländer MR; Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden., Peterson KJ; Department of Biological Sciences, Dartmouth College, Hanover, USA.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2022 Jan 07; Vol. 50 (D1), pp. D204-D210.
DOI:	10.1093/nar/gkab1101
Abstrakt:	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/. (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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