The exon/intron organisation of homologous nuclear genes was compared in several yeast species. CLUSTALX multiple alignments were performed to verify the degree of conservation of the homologues and to reconstruct a virtual (scaffold) gene, exhibiting the probable ancestral intron arrangement. Intron position was defined at the nucleotide level making it possible to determine whether the intron is at an identical position (same codon and same phase) or not in the homologues.
In the cases herein illustrated, some intron positions were found divergent in homologues sharing a high degree of sequence conservation, suggesting that these positions may result either from intron sliding or intron gain events [Bon et al., 2003].
Intron sliding is defined as the relocation of a pre-existing intron over short distances in the course of gene evolution [Rogozin et al., 2000, Trends Genet., 16, 430-432]. Although it is now admitted that intron sliding by one or two bases is a real phenomenon, it remains relatively rare and probably occurs in less than 5% of all introns [Stoltzfus et al., 1997, Proc. Natl. Acad. Sci. USA, 94, 10739-10744; Rogozin et al., 2000; Boudet et al., 2001, Genome Res., 11, 2101-2114].
This implies that most of these discordant intron positions should be attributed to independent intron insertion events rather than intron sliding events [Bon et al., 2003].
The YFL037w scaffold gene contains 6 introns of which i2 position is absent in the S. pombe YFL037w gene, but present in C. albicans and P. sorbitophila.
Different scenario were proposed to explain the absence of this intron position in S. pombe:
SC: S. cerevisiae; CA: C. albicans; PA: P. angusta and SP: S. pombe.