Inst. f. Informatik   
Uni Leipzig

Bioinformatics Preprint 05-021

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[Supplementary Material]

The Expansion of the Metazoan MicroRNA Repertoire

Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried,
Andrea Tanzer, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler,
and The Students of Bioinformatics Computer Labs 2004 and 2005:
Sten Heinze, Alexander ''muppet'' Donath, Sven Findeß, Stephanie Keller, Kevin Peter,
Julian Jöris, Jokab Mühmel, Marco Dienelt (in Leipzig),
Martina Hödl, Bernhard Wurzinger, Camille Stephan-Otto Attolini, Ulrich Omasits,
Sebastian Krüttner, Regina Anzengruber, Daniela Lenek, Gregor Neumayr,
Reinhard Wohlfart (in Vienna).


MicroRNAs have been identified as crucial regulators in both animals and plants. Here we report on a comprehensive comparative study of all known miRNA families in animals. We expand the MicroRNA Registry 6.0 by more than 1000 new homologs of miRNA precursors whose expression has been verified in at least one species. Using this uniform data basis we analyze their evolutionary history in terms of individual gene phylogenies and in terms of preservation of genomic nearness across species. This allows us to reliably identify microRNA clusters that are derived from a common transcript. We identify three episodes of microRNA innovation that correspond to major developmental innovations: A class of about 20 miRNAs is common to protostomes and deuterostomes and might be related to the advent of bilaterians. A second large wave of innovations maps to the branch leading to the vertebrates. The third significant outburst of miRNA innovation coincides with placental (eutherian) mammals. In addition, we observe the expected expansion of the microRNA inventory due to genome duplications in early vertebrates and in an ancestral teleost. The non-local duplications in the vertebrate ancestor are predated by local (tandem) duplications leading to the formation of about a dozend ancient microRNA clusters.

Keywords: Micro RNA, Evolution, Gene phylogenies, Genome duplication.


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