Low base-substitution mutation rate in the germline genome of the ciliate tetrahymena thermophila

Mutation is theultimate sourceof all genetic variation and is, therefore, central toevolutionary change. PreviousworkonParamecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate.Here,we tested the generality of this result among ciliates using Tetrahymena thermophila. We sequenced the genomes of 10 lines of T. thermophila that had each undergone approximately 1,000 generations ofmutation accumulation (MA).Weapplied an existingmutation-calling pipeline and developed a new probabilistic mutation detection approach that directly models the design of anMA experiment and accommodates the noise introduced by mismappedreads.Ourprobabilisticmutation-callingmethodprovides a straightforwardway of estimating thenumber of sites atwhich amutation could have been called if one was present, providing the denominator for ourmutation rate calculations. From these methods, we find that T. thermophila has a germline base-substitution mutation rate of 7.61-10-12 per-site, per cell division,which is consistent with thelowbase-substitutionmutation rate in P. tetraurelia.Over thecourse of the evolution experiment, genomic exclusion lines derived from the MA lines experienced a fitness decline that cannot be accounted for by germline basesubstitutionmutations alone, suggesting that othergenetic or epigenetic factorsmustbeinvolved.Becauseselectioncanonlyoperate to reducemutation rates based upon the "visible"mutational load, asexual reproduction with a transcriptionally silent germlinemay allow ciliates to evolve extremely low germline mutation rates.