INTERNAL ELIMINATED SEQUENCES INTERRUPTING THE OXYTRICHA-81 LOCUS - ALLELIC DIVERGENCE, CONSERVATION, CONVERSIONS, AND POSSIBLE TRANSPOSON ORIGINS

Internal eliminated sequences (IESs) often interrupt ciliate genes in the silent germline nucleus but are exactly excised and eliminated fro m the developing somatic nucleus from which genes are then expressed. Some long IESs are transposons, supporting the hypothesis that short I ESs are ancient transposon relies. In light of that hypothesis and to explore the evolutionary history of a collection of IESs, we have comp ared various alleles of a particular locus (the 81 locus) of the cilia ted protozoa Oxytricha trifallax and O. fallax. Three short IESs that interrupt two genes of the locus are found in alleles from both specie s, and thus must be relatively ancient, consistent with the hypothesis that short IESs are transposon relies. In contrast, TBE1 transposon i nterruptions of the locus are allele-specific and probably the results of recent transpositions. These IESs (and the TBE1s) are precisely ex cised from the DNA of the developing somatic macronucleus. Each IES in terrupts a highly conserved sequence. A few nucleotides at the ends of each IES are also conserved, suggesting that they interact critically with IES excision machinery. However, most IES nucleotide positions h ave evolved at high rates, showing little or no selective constraint f or function. Nonetheless, the length of each IES has been maintained ( +/-3 bp). While one IES is similar to 33 bp long, three other IESs hav e very similar sizes, similar to 70 bp long. Two IESs are surrounded b y direct repeats of the sequence TTCTT. No other sequence similarities were found between any of the four IESs. However, the ends of one IES do match the inverted terminal repeat consensus sequence of the ''TA' ' IESs of Paramecium. Three O. trifallax alleles appear to have been r ecipients in recent conversion events that could have been provoked by double-strand breaks associated with IES ends subsequent to IES trans position. Our findings support the hypothesis that short IESs evolved from ancient transposons that have lost most of their sequences, excep t those necessary for precise excision during macronuclear development .