Coevolution of genomic intron number and splice sites

Spliceosomal intron numbers and boundary sequences vary dramatically in eukaryotes. We found a striking correspondence between low intron number and strong sequence conservation of 5′ splice sites (5′ss) across eukaryotic genomes. The phylogenetic pattern suggests that ancestral 5′ss were relatively weakly conserved, but that some lineages independently underwent both major intron loss and 5′ss strengthening. It seems that eukaryotic ancestors had relatively large intron numbers and ‘weak’ 5′ss, a pattern associated with frequent alternative splicing in modern organisms.