Running Head Two Scrambled Genes Intertwined on Two Loci

be.oxfordjournals.org/ D ow nloaded from The germline micronuclear genome of some ciliated protists can be scrambled, with coding segments disordered relative to the expressed macronuclear genome. Here we report a surprisingly complex pair of genes that assemble from interwoven segments on two germline loci in the ciliate Uroleptus. This baroque organization requires two scrambled genes to be disentangled from each other from two clusters in the genome, one containing segments 1-2-4-5-6-8-11-13-15-16 and the other 7-9-3-10-12-14, with pieces 1-5 comprising the first gene and 6-16 the second gene. Both genes remain linked in the somatic genome on a 1.5 kb "nanochromosome". This study is the first to reveal that two genes can become scrambled during evolution with their coding segments intertwined. These twin scrambled genes underscore the beauty and exceptions of protist genome architecture, pointing to the critical need for evolutionary biologists to survey protist genomes broadly. Main Text Ciliates possess two types of nuclei, a germline micronucleus and a somatic macronucleus that develops from a copy of the germline after cell mating. In spirotrichous ciliates, massive deletion and rearrangement of the 1-2.5 Gb germline genome constructs a ~50 Mb set of approximately 2 kb tiny chromosomes (Prescot