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Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed une...

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Autores principales: Mohammed, Jaaved, Flynt, Alex S., Panzarino, Alexandra M., Mondal, Md Mosharrof Hossein, DeCruz, Matthew, Siepel, Adam, Lai, Eric C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749182/
https://www.ncbi.nlm.nih.gov/pubmed/29233922
http://dx.doi.org/10.1101/gr.226068.117
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author Mohammed, Jaaved
Flynt, Alex S.
Panzarino, Alexandra M.
Mondal, Md Mosharrof Hossein
DeCruz, Matthew
Siepel, Adam
Lai, Eric C.
author_facet Mohammed, Jaaved
Flynt, Alex S.
Panzarino, Alexandra M.
Mondal, Md Mosharrof Hossein
DeCruz, Matthew
Siepel, Adam
Lai, Eric C.
author_sort Mohammed, Jaaved
collection PubMed
description To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.
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spelling pubmed-57491822018-07-01 Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus Mohammed, Jaaved Flynt, Alex S. Panzarino, Alexandra M. Mondal, Md Mosharrof Hossein DeCruz, Matthew Siepel, Adam Lai, Eric C. Genome Res Research To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death using our annotation and a phylogenetic model for estimating rates of miRNA turnover. We observed striking differences in birth and death rates across miRNA classes defined by biogenesis pathway, genomic clustering, and tissue restriction, and even identified flux heterogeneity among Drosophila clades. In particular, distinct molecular rationales underlie the distinct evolutionary behavior of different miRNA classes. Mirtrons are associated with high rates of 3′ untemplated addition, a mechanism that impedes their biogenesis, whereas TRC miRNAs appear to evolve under positive selection. Altogether, these data reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution. Cold Spring Harbor Laboratory Press 2018-01 /pmc/articles/PMC5749182/ /pubmed/29233922 http://dx.doi.org/10.1101/gr.226068.117 Text en © 2018 Mohammed et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Research
Mohammed, Jaaved
Flynt, Alex S.
Panzarino, Alexandra M.
Mondal, Md Mosharrof Hossein
DeCruz, Matthew
Siepel, Adam
Lai, Eric C.
Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
title Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
title_full Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
title_fullStr Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
title_full_unstemmed Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
title_short Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
title_sort deep experimental profiling of microrna diversity, deployment, and evolution across the drosophila genus
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749182/
https://www.ncbi.nlm.nih.gov/pubmed/29233922
http://dx.doi.org/10.1101/gr.226068.117
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