MBE Advance Access published online on December 21, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj084
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1 Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
* To whom correspondence should be addressed. Recent studies indicate that many introns, as well as the complex spliceosomal mechanism to remove them, were present early in eukaryotic evolution. This study examines intron and exon characteristics from annotations of whole genomes to investigate the intron-recognition mechanism. Exon-definition uses the exon as the unit of recognition, placing length constraints on the exon but not on the intron (allowing it a greater range of lengths). In contrast, intron-definition uses the intron itself as the unit of recognition and thus removes constraints on internal exon length forced by the use of an exon-definition mechanism. Thus intron and exon lengths within a genome can reflect the constraints imposed by its splicing. This study shows that it is possible firstly to recover valid intron and exon information from genome annotation. We then compare internal intron and exon information from a range of eukaryotic genomes and investigate possible evolutionary length constraints on introns and exons and how they can impact on the intron-recognition mechanism. Results indicate that exon-definition based mechanisms may predominate in vertebrates although the exact system in fish is expected to show some differences with the better characterised system from mammals. We also raise the possibility that the last common ancestor of plants and animals contained some type of exon-definition, and that this mechanism was replaced in some genes and lineages by intron-definition, possibly as a result of intron loss and/or intron shortening.
Accepted December 14, 2005
Research Article
Investigating the Intron Recognition Mechanism in Eukaryotes
Lesley Collins 1 *
and
David Penny 1
Lesley Collins, E-mail: L.J.Collins{at}massey.ac.nz
Abstract 
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