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Nucleic Acids Research Advance Access published online on January 16, 2009
Nucleic Acids Research, doi:10.1093/nar/gkn1084
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Non-coding RNA annotation of the genome of Trichoplax adhaerens

Jana Hertel1, Danielle de Jong2, Manja Marz1, Dominic Rose1, Hakim Tafer3, Andrea Tanzer1,3,4, Bernd Schierwater2 and Peter F. Stadler1,3,5,6,*

1Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, 2Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, 3Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, 4Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, 5RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and 6Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA

*To whom correspondence should be addressed. Tel: +49 341 97 16686; Fax: +49 341 97 16679; Email: jana{at}bioinf.uni-leipzig.de

Received November 13, 2008. Revised December 22, 2008. Accepted December 23, 2008.

A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs—in particular rRNAs, tRNAs and some snRNAs—we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome.


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