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Background  Two categories of introns are known, a common U2 type and a rare U12 type. These two types of introns are removed by distinct spliceosomes. The phylogenetic distribution of spliceosomal RNAs that are characteristic of the U12 spliceosome, i.e. the U11, U12, U4atac and U6atac RNAs, suggest that U12 spliceosomes were lost in many phylogenetic groups. We have now examined the distribution of U2 and U12 introns in many of these groups.    Results  U2 and U12 introns were predicted by making use of available EST and genomic sequences. The results show that in species or branches where U12 spliceosomal components are missing, also U12 type of introns are lacking. Examples are the choanoflagellate  Monosiga brevicollis ,  Entamoeba histolytica , green algae, diatoms, and the fungal lineage Basidiomycota. Furthermore, whereas U12 splicing does not occur in  Caenorhabditis elegans , U12 introns as well as U12 snRNAs are present in  Trichinella spiralis , which is deeply branching in the nematode tree. A comparison of homologous genes in  T. spiralis  and  C. elegans  revealed different mechanisms whereby U12 introns were lost.    Conclusions  The phylogenetic distribution of U12 introns and spliceosomal RNAs give further support to an early origin of U12 dependent splicing. In addition, this distribution identifies a large number of instances during eukaryotic evolution where such splicing was lost.

U12 type introns were lost at multiple occasions during evolution