RT Journal Article SR Electronic T1 Low base-substitution mutation rate in the germline genome of the ciliate Tetrahymena thermophila JF bioRxiv FD Cold Spring Harbor Laboratory SP 025536 DO 10.1101/025536 A1 Hongan Long A1 David J. Winter A1 Allan Y-C. Chang A1 Way Sun A1 Steven H. Wu A1 Mariel Balboa A1 Ricardo B.R. Azevedo A1 Reed A. Cartwright A1 Michael Lynch A1 Rebecca A. Zufall YR 2016 UL http://biorxiv.org/content/early/2016/04/27/025536.abstract AB Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium 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 of mutation accumulation (MA). We developed a new probabilistic mutation detection approach that directly models the design of an MA experiment and accommodates the noise introduced by mismapped reads and also applied an existing mutation-calling pipeline. 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 the low base-substitution mutation rate in P. tetraurelia. Over the course of the evolution experiment, genomic exclusion lines derived from the MA lines experienced a fitness decline that cannot be accounted for by germline base-substitution mutations alone, suggesting that other genetic or epigenetic factors must be involved. Because selection can only operate to reduce mutation rates based upon the “visible” mutational load, asexual reproduction with a transcriptionally silent germline may allow ciliates to evolve extremely low germline mutation rates.