title: Hypervariable and highly divergent intron-exon organizations in the chordate Oikopleura dioica.
abstract: Oikopleura dioica is a pelagic tunicate with a very small genome and a very short life cycle. In order to investigate the intron-exon organizations in Oikopleura, we have isolated and characterized ribosomal protein EF-1alpha, Hox, and alpha-tubulin genes. Their intron positions have been compared with those of the same genes from various invertebrates and vertebrates, including four species with entirely sequenced genomes. Oikopleura genes, like Caenorhabditis genes, have introns at a large number of nonconserved positions, which must originate from late insertions or intron sliding of ancient insertions. Both species exhibit hypervariable intron-exon organization within their alpha-tubulin gene family. This is due to localization of most nonconserved intron positions in single members of this gene family. The hypervariability and divergence of intron positions in Oikopleura and Caenorhabditis may be related to the predominance of short introns, the processing of which is not very dependent upon the exonic environment compared to large introns. Also, both species have an undermethylated genome, and the control of methylation-induced point mutations imposes a control on exon size, at least in vertebrate genes. That introns placed at such variable positions in Oikopleura or C. elegans may serve a specific purpose is not easy to infer from our current knowledge and hypotheses on intron functions. We propose that new introns are retained in species with very short life cycles, because illegitimate exchanges including gene conversion are repressed. We also speculate that introns placed at gene-specific positions may contribute to suppressing these exchanges and thereby favor their own persistence.
authors.affiliation: Sars Centre for Marine Molecular Biology, Bergen High Technology Centre, Thormoehlensgt 55, 5020 Bergen, Norway.
authors.forename: Rolf B
authors.initials: RB
authors.lastname: Edvardsen
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Lerat
authors.forename: Anne Dorthea
authors.initials: AD
authors.lastname: Maeland
authors.forename: Mette
authors.initials: M
authors.lastname: Flåt
authors.forename: Rita
authors.initials: R
authors.lastname: Tewari
authors.forename: Marit F
authors.initials: MF
authors.lastname: Jensen
authors.forename: Hans
authors.initials: H
authors.lastname: Lehrach
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Hee-Chan
authors.initials: HC
authors.lastname: Seo
authors.forename: Daniel
authors.initials: D
authors.lastname: Chourrout
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019143:Evolution, Molecular; D005091:Exons / Q000502:physiology*; D014644:Genetic Variation; D018398:Homeodomain Proteins / Q000235:genetics; D007438:Introns / Q000502:physiology*; D008969:Molecular Sequence Data; D020648:Peptide Elongation Factor 1 / Q000235:genetics; D010802:Phylogeny; D012269:Ribosomal Proteins / Q000235:genetics; D016415:Sequence Alignment; D014404:Tubulin / Q000235:genetics; D014561:Urochordata / Q000235:genetics*
chemical_list: D018398:Homeodomain Proteins; D020648:Peptide Elongation Factor 1; D012269:Ribosomal Proteins; D014404:Tubulin