Evolution and assembly of an extremely scrambled gene

The process of gene unscrambling in hypotrichous ciliates represents one of nature's ingenious solutions to the problem of gene assembly. With some es sential genes scrambled in as many as 51 pieces, these ciliates rely on seq uence and structural cues to rebuild their fragmented genes and genomes. He re we report the complex pattern of scrambling in the DNA polymerase alpha gene of Stylonychia lemnae, The germline (micronuclear) copy of this gene i s broken into 48 pieces with 47 dispersed over two loci, with no asymmetry in the placement of coding segments on either strand. Direct repeats presen t at the boundaries between coding and noncoding sequences provide pointers to help guide assembly of the functional (macronuclear) gene. We investiga te the evolution of this complex gene in three hypotrichous species.