Jana Hertel (1), Danielle de Jong (2), Manja Marz (1), Dominic Rose (1), Hakim Tafer (3), Andrea Tanzer (1,3,4), Bernd Schierwater (2) and Peter F. Stadler (1,3,5,6,*)

Non-Coding RNA annotations of the genome of Trichoplax adhaerens

Nucleic Acids Research, 2009, 1–14

doi:10.1093/nar/gkn1084

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

ABSTRACT
A detailed annotation of non-protein coding RNAs
is typically missing in initial releases of newly
sequenced genomes. Here we report on a compre-
hensive 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 eume-
tazoan sequences. Interestingly, most ncRNAs,
including the pol-III transcripts, appear as single-
copy genes or with very small copy numbers in the
Trichoplax genome.