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. 2009 Apr;37(5):1602-15.
doi: 10.1093/nar/gkn1084. Epub 2009 Jan 16.

Non-coding RNA annotation of the genome of Trichoplax adhaerens

Jana Hertel  1 , Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, Peter F Stadler
Affiliations

Non-coding RNA annotation of the genome of Trichoplax adhaerens

Jana Hertel et al. Nucleic Acids Res. 2009 Apr.

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.

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Figures

Figure 1.
Figure 1.
(a) Histogram of score distribution for U4atac, U17 and RNase MRP. (b) Fitting the GotohScan score distribution of U4atac to known density functions.
Figure 2.
Figure 2.
Trichoplax pre-rRNA cluster reconstructed from previously published sequences L10828, Z22783, AY652578 (SSU), AY303975, AY652583 (LSU), U65478 (internal spacers and 5.8S) and Triad1 genomic sequence. Blast hits of the pre-rRNA to the Triad1 genome assembly are shown below as in the JGI genome browser.
Figure 3.
Figure 3.
RNA secondary structures of major spliceosomal (U1, U2, U4, U5, U6) and minor spliceosomal (U11, U12, U4atac, U5, U6atac) snRNAs. For U4/U6 and U4atac/U6atac the interaction structures computed by means of RNAcofold are shown. The 5 nt insert (relative to other metazoa) is highlighted in the U12.
Figure 4.
Figure 4.
Secondary structure of T. adhaerens RNase MRP RNA inferred from the multiple alignment of metazoan RNase MRP RNAs provided in the Electronic Supplement.
Figure 5.
Figure 5.
Structural alignments of the Trichoplax RNase P RNA, SRP RNA and U3 snoRNA sequences with the corresponding Rfam alignments as computed by infernal. The first line contains the structure annotation of the two sequences that are aligned in the second and fourth line. Line three in-between describes the sequence conservation and the type of substitution.
Figure 6.
Figure 6.
Top: secondary structure model of a novel H/ACA snoRNA (l.h.s.) and the best snoplex prediction of its targets sites in the rRNA operon (r.h.s.). Below: alignment of U18 snoRNA sequences from several Metazoa. Boxes and the conserved target binding site are indicated.
Figure 7.
Figure 7.
Distribution of RNAz classification score for known (true positive) (black) all predictions (grey), and only those that are identified as coding or repetitive (maroon). Note the logarithmic scale: there are more than 100 non-annotated predictions with a classification confidence above 99%.
See this image and copyright information in PMC

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