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Non-coding RNA annotation of the genome of Trichoplax adhaerens

: Hertel, J.; Jong, D. de; Marz, M.; Rose, D.; Tafer, H.; Tanzer, A.; Schierwater, B.; Stadler, P.F.

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Nucleic Acids Research 37 (2009), No.5, pp.1602-1615
ISSN: 0305-1048
ISSN: 0301-5610
ISSN: 1362-4962
Journal Article, Electronic Publication
Fraunhofer IZI ()

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 ncRNAsin particular rRNAs, tRNAs and some snRNAswe 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.