Non-coding RNAs in Ciona intestinalis

Motivation: The analysis of animal genomes showed that only a minute part of their DNA codes for proteins. Recent experimental results agree, however, that a large fraction of these genomes are transcribed and hence are probably functional at the RNA level. A computational survey of vertebrate genomes has predicted thousands of previously unknown ncRNAs with evolutionarily conserved secondary structures. Extending these comparative studies beyond vertebrates is difficult, however, since most ncRNAs evolve quickly at the sequence level while conserving their characteristic secondarystructures. Results: We report on a computational screen of structured ncRNAs in the urochordate lineage based on a comparison of the genomic data from Ciona intestinalis , Ciona savignyi and Oikopleura dioica . We predict >1000 ncRNAs with an evolutionarily conserved RNA secondary structure. Of these, about a quarter are located in introns of known protein coding sequences. A few RNA motifs can be identified as known RNAs, including ∼300 tRNAs, some 100 snRNA genes and a few microRNAs and snoRNAs