MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D116 - D128

Published: Nov. 30, 2024

Abstract We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to new server and creation computational mirror, we have expanded database with addition 33 invertebrate species, including representatives 5 previously unsampled phyla, 6 mammal species. now contains entries for 21 822 genes (5160 these from species) belonging 1743 families. The inclusion species allowed us refine both evolutionary node appearance number genes/families, as well MirGeneDB’s phylogenetically informed nomenclature system. Updated covariance models all families, along smallRNA read data are downloadable. These enhanced annotations will allow researchers analyze properties such secondary structure features their biogenesis within robust phylogenetic context without plagued numerous false positives negatives. In light improvements, 3.0 assume responsibility naming conserved novel metazoan microRNAs. is part RNAcentral Elixir Norway publicly freely available at mirgenedb.org.

Language: Английский

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A genome resource for the marine annelidPlatynereis dumerilii

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 23, 2024

The marine annelid

Language: Английский

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Analysis of miRNAs in milk of four livestock species

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: Sept. 14, 2024

Language: Английский

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Substantial hierarchical reductions of genetic and morphological traits in the evolution of rotiferan parasites

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 4, 2024

Abstract Figure Graphical abstract During the last 800 million years of evolution animals radiated into a vast range diversity species and disparity forms lifestyles. The process involved near hierarchical increase in complexity from life with few cell types to organisms many hundreds cell-types. However, neither genome size nor number protein-coding genes can explain these differences their biological basis remains elusive. Yet, recent studies have suggested that is closely linked acquisition class protein coding gene-regulators called microRNAs. In regressive approach, investigate association between loss organismal microRNAs, we here studied Syndermata, an invertebrate group including free-living rotifers (Monogononta, Bdelloidea), epibiotic Seisonidea endoparasitic Acanthocephala. Genomic, transcriptomic morphological characterization comparisons across 25 syndermatan revealed strong correlation decreasing complexity. extends ∼85% microRNAs ∼50% BUSCO Acanthocephala, most reduced studied. Together, ∼400 ∼10 metazoan core gene losses went along one microRNA family loss. Furthermore, ∼4 families or ∼34 associated lost feature. These are first quantitative insights regulatory impact on organismic as predictable consequence parasites.

Language: Английский

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Commentary: Environmental RNA and the assessment of organismal function in the field

Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology, Journal Year: 2024, Volume and Issue: unknown, P. 111036 - 111036

Published: Sept. 1, 2024

Language: Английский

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Editorial

Zoologica Scripta, Journal Year: 2024, Volume and Issue: 53(6), P. 753 - 753

Published: July 19, 2024

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