Genomic analysis in Entamoeba reveals intron gain and unbiased intron loss, transformed splicing signals, and a coevolved snRNA.

The intron-exon structures of nuclear genes show striking diversity across eukaryotes. Several independent lineages have undergone convergent evolution including widespread loss of introns and transformed cis splicing signals. The causes and mechanisms of these changes remain mysterious: (i) transformation of splicing signals could reflect either selective loss of suboptimal introns or coevolution of introns and splicing machinery; and (ii) corresponding changes in the splicing machinery remain poorly characterized. A promising model to study these questions is Entamoeba. Analysis of five Entamoeba species revealed low intron densities, nearly universal atypical 5 splice sites and 3 intronic sequences. A flexible search for U1 snRNA genes revealed a modified 5-AACAAAC-3 recognition sequence, affording complete Watson-Crick basepairing potential with the atypical 5 splice site and extended basepairing potential. A U1 candidate in the related species Mastigamoeba balumuthi revealed a separate modification complimenting a different atypical consensus splice site. Genome-wide study of intron loss and gain revealed that introns with suboptimal splicing motifs were no more likely to be lost, suggesting against genome-wide homogenization of intron splicing motifs by selective intron loss. Unexpectedly, this analysis also revealed widespread intron gain in Entamoeba invadens. In total, the current analyses: (i) provide the most direct available evidence of coevolution of spliceosomal introns and splicing machinery; (ii) illuminate the evolutionary forces responsible for concerted intron loss and splicing motif transformation; and (iii) reveal widespread intron gain in an otherwise highly reduced lineage.