The evolutionary origin of a complex scrambled gene

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Abstract
Some species of ciliates undergo massive DNA elimination and genome rearrangement to construct gene-sized “chromosomes” in their somatic nucleus. An example is the extensively scrambled DNA polymerase α gene that is broken into 48 pieces and distributed over two unlinked loci in Stylonychia . To understand the emergence of this complex phenomenon during evolution, we examined DNA polymerase α genes in several earlier diverging species, representing evolutionary intermediates. Mapping these data onto an evolutionary tree suggests that this gene became extensively fragmented and scrambled over evolutionary time through a series of steps, each leading to greater complexity. Our results also suggest a possible mechanism for intron loss by deletion of intron sequences as DNA during development of the somatic nucleus.