Conserved and Novel miRNA Annotation in Bats

Conserved noncoding RNA genes were annotated using the Infernal pipeline^{95 (link)}. To gain insights into the evolution of conserved miRNA families along the bat lineages, we performed two analyses that investigate (i) expansion or contraction of members with miRNA gene families, and (ii) gain or loss of miRNA gene families. To explore variation in miRNA sequence unique to bats, we aligned and investigated single-copy miRNA genes across these 48 taxa. We developed a pipeline to predict the gene targets of candidate miRNAs and the biological processes in which they are potentially engaged. To identify novel miRNAs evolved in bats, we sequenced small RNA libraries from brain, kidney and liver for all six bat species using Illumina miRNA-seq. We carried out a comprehensive pipeline to identify novel miRNA commonly shared by the ancestral bat lineage. We further used luciferase assays^{96 (link),97 (link)} to test the functionality of candidate miRNAs in vitro. A full description is provided in Supplementary Note 5.

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Jebb D., Huang Z., Pippel M., Hughes G.M., Lavrichenko K., Devanna P., Winkler S., Jermiin L.S., Skirmuntt E.C., Katzourakis A., Burkitt-Gray L., Ray D.A., Sullivan K.A., Roscito J.G., Kirilenko B.M., Dávalos L.M., Corthals A.P., Power M.L., Jones G., Ransome R.D., Dechmann D.K., Locatelli A.G., Puechmaille S.J., Fedrigo O., Jarvis E.D., Hiller M., Vernes S.C., Myers E.W, & Teeling E.C. (2020). Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583(7817), 578-584.

Publication 2020

miRNA-seq

Biological processes Brain Evolution Gene Kidney Liver Luciferase Mirnas Noncoding rna

Corresponding Organization :

Other organizations : Max Planck Institute of Molecular Cell Biology and Genetics, University College Dublin, Max Planck Institute for Psycholinguistics, Medawar Building for Pathogen Research, University of Oxford, Texas Tech University, Center for Systems Biology Dresden, Stony Brook University, John Jay College of Criminal Justice, University of Bristol, Max Planck Institute of Animal Behavior, Université de Montpellier, Institut des Sciences de l'Evolution de Montpellier, Rockefeller University

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Protocol cited in 2 other protocols

Variable analysis

independent variables

Expansion or contraction of members with miRNA gene families
Gain or loss of miRNA gene families

dependent variables

Evolution of conserved miRNA families along the bat lineages
Sequence variation in single-copy miRNA genes across 48 taxa
Identification of novel miRNAs evolved in bats
Functionality of candidate miRNAs in vitro

control variables

Positive controls: luciferase assays to test the functionality of candidate miRNAs in vitro
Negative controls: not explicitly mentioned

Annotations

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