title: Non-coding RNA annotation of the genome of Trichoplax adhaerens.
abstract: 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.
authors.affiliation: Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Hertel
authors.forename: Danielle
authors.initials: D
authors.lastname: de Jong
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.forename: Dominic
authors.initials: D
authors.lastname: Rose
authors.forename: Hakim
authors.initials: H
authors.lastname: Tafer
authors.forename: Andrea
authors.initials: A
authors.lastname: Tanzer
authors.forename: Bernd
authors.initials: B
authors.lastname: Schierwater
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D001483:Base Sequence; D004722:Endoribonucleases / Q000737:chemistry; D016678:Genome; D035683:MicroRNAs / Q000737:chemistry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D054909:Placozoa / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D020733:RNA, Small Cytoplasmic / Q000737:chemistry; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000235:genetics; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D043262:Ribonuclease P / Q000235:genetics; D018271:Signal Recognition Particle / Q000737:chemistry; D012984:Software
chemical_list: C115990:7SL RNA; D035683:MicroRNAs; D012335:RNA, Ribosomal; D020733:RNA, Small Cytoplasmic; D012342:RNA, Small Nuclear; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated; D018271:Signal Recognition Particle; D012343:RNA, Transfer; D004722:Endoribonucleases; C058330:mitochondrial RNA-processing endoribonuclease; D043262:Ribonuclease P