Ciliates, microbial eukaryotes that contain separate germline and somatic
nuclei, provide a near perfect system in which to study mutation. During
vegetative growth, the ciliate germline genome is duplicated but not expressed.
Thus, mutations can accrue over many rounds of cell division without being
exposed to natural selection, allowing the full range of spontaneous mutations
to be studied. However, detecting these mutations through short read sequencing
is particularly difficult. A lack of complete reference genomes, the
binuclear nature of ciliates and the large number of genomic
rearrangements that occur during ciliate development all contribute to a high
error-rate when using traditional mutation detection methods.
Using a novel approach to mutation detection, we have estimated the mutation rate
for the ciliate Tetrahymena thermophila and found that it is one of the lowest
if not the lowest ever recorded. The only other ciliate for which a direct
estimate of the mutation rate is available, Paramecium tetraurelia, is among the
very few species with a comparable rate.Here we describe the unique challenges
associated with taking whole genome approaches to ciliates, and how they can be
overcome. We also propose and test mechanistic and evolutionary hypotheses that
might explain the low mutation rates observed in this group.