Published online 5 July 2006
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis
1 Department of Zoology, Graduate School of Science, Kyoto University Sakyo, Kyoto 606-8502, Japan 2 Montreal Neurological Institute and Department of Biology, McGill University 3801 University St. Montreal, Quebec, Canada H3A 2B4 3 CREST, Japan Science Technology Agency Kawaguchi, Saitama, 330-0012, Japan
*To whom correspondence should be addressed. Tel: +81-75-753-4095; Fax: +81-75-705-1113; Email: yutaka{at}ascidian.zool.kyoto-u.ac.jp
Received March 25, 2006. Accepted May 19, 2006.
Although spliced leader (SL) trans-splicing in the chordates was discovered in the tunicate Ciona intestinalis there has been no genomic overview analysis of the extent of trans-splicing or the make-up of the trans-spliced and non-trans-spliced gene populations of this model organism. Here we report such an analysis for Ciona based on the oligo-capping full-length cDNA approach. We randomly sampled 2078 5'-full-length ESTs representing 668 genes, or 4.2% of the entire genome. Our results indicate that Ciona contains a single major SL, which is efficiently trans-spliced to mRNAs transcribed from a specific set of genes representing 
50% of the total number of expressed genes, and that individual trans-spliced mRNA species are, on average, 2–3-fold less abundant than non-trans-spliced mRNA species. Our results also identify a relationship between trans-splicing status and gene functional classification; ribosomal protein genes fall predominantly into the non-trans-spliced category. In addition, our data provide the first evidence for the occurrence of polycistronic transcription in Ciona. An interesting feature of the Ciona polycistronic transcription units is that the great majority entirely lack intercistronic sequences.
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