Origins of recently gained introns in Caenorhabditis

1. 

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   Fig. 1.

   Identifying novel introns. To ensure that a putative novel intron was almost certainly caused by insertion rather than by deletion, we drew phylogenetic trees of the gene and its animal and nematode orthologs. We required that there be at least three nodes between the gene and the outgroup. We also required that, in a protein alignment of the gene and its orthologs, ≥5/10-aa residues on either side of the intron be identical or well conserved among the animal genomes.

   
   
2. 

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   Fig. 2.

   Exon splice site consensus of novel introns in C. elegans and C. briggsae, compared with the consensus for control sets of introns from each genome. Numbers show the percentage of introns in each group that have the indicated base at each position.

   
   
3. 

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   Fig. 3.

   Dot matrix comparison of introns in C. briggsae gene CBG18597. Intron 3 is novel and has similarity to intron 1. The plot was made by dotter (34), with min = 0 and max = 100 in the greyramp tool.