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Diverse RNA interference strategies in early-branching metazoans

View ORCID ProfileAndrew D. Calcino, Selene L. Fernandez-Valverde, Ryan J. Taft, Bernard M. Degnan
doi: https://doi.org/10.1101/284349
Andrew D. Calcino
1School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
4Department of Integrative Zoology, University of Vienna, Althanstraße 14A-1090 Vienna, Austria
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Selene L. Fernandez-Valverde
1School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
5CONACYT, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio). CIN-VESTAV, Irapuato, Guanajuato, México
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Ryan J. Taft
2Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
3Illumina Inc, San Diego, California 92122 USA
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Bernard M. Degnan
1School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia
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  • For correspondence: b.degnan@uq.edu.au
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ABSTRACT

Background Micro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians – sponges, ctenophores, placozoans and cnidarians - appears to be more diverse than that of bilaterians, and includes structurally variable miR-NAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans.

Results Here we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queens-landica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. In the ctenophore, the absence of miRNAs is confirmed and an abundance of endo-siRNAs is revealed. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs.

Conclusion Together, these findings suggest that the last common ancestor of animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 19, 2018.
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Diverse RNA interference strategies in early-branching metazoans
Andrew D. Calcino, Selene L. Fernandez-Valverde, Ryan J. Taft, Bernard M. Degnan
bioRxiv 284349; doi: https://doi.org/10.1101/284349
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Diverse RNA interference strategies in early-branching metazoans
Andrew D. Calcino, Selene L. Fernandez-Valverde, Ryan J. Taft, Bernard M. Degnan
bioRxiv 284349; doi: https://doi.org/10.1101/284349

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