Rates and spectra of de novo structural mutation in Chlamydomonas reinhardtii

Abstract

Genetic variation originates from several types of spontaneous mutation, including single nucleotide substitutions, short insertions and deletions (INDELs), and larger structural changes. Structural mutations (SMs) drive genome evolution and are thought to play major roles in evolutionary adaptation, speciation and genetic disease, including cancers. Sequencing of mutation accumulation (MA) lines has provided estimates of rates and spectra of single nucleotide and INDEL mutations in many species, yet the rate of new SMs is largely unknown. Here, we use long-read sequencing to determine the full mutation spectrum in MA lines derived from two strains (CC-1952 and CC-2931) of the green alga Chlamydomonas reinhardtii. The SM rate is highly variable between strains and MA lines, and SMs represent a substantial proportion of all mutations in both strains (CC-1952 6%; CC-2931 12%). The SM spectra also differs considerably between the two strains, with almost all inversions and translocations occurring in CC-2931 MA lines. This variation is associated with heterogeneity in the number and type of active transposable elements (TEs), which comprise major proportions of SMs in both strains (CC-1952 22% and CC-2931 38% of SMs). In CC-2931, a Crypton and a previously undescribed type of DNA element caused 71% of chromosomal rearrangements, while in CC-1952 a Dualen LINE was associated with 87% of duplications. Other SMs, notably many large duplications in CC-2931, were likely products of various double-strand break repair pathways. Our results demonstrate that diverse types of SMs occur at substantial rates and support prominent roles for SMs and TEs in evolution.

The Chlamydomonas Genome Project, version 6: Reference assemblies for mating-type plus and minus strains reveal extensive structural mutation in the laboratory

“…Recent work has in fact demonstrated that an unexpectedly large proportion of mutations in Chlamydomonas are beneficial under laboratory conditions, potentially due to many genes being dispensable in such an artificial environment (Böndel et al 2019;Böndel et al 2022). It has also been estimated that ~5-10% of all de novo mutations in Chlamydomonas experimental lines are >50 bp (López-Cortegano et al 2022), supporting a prominent role for structural evolution in the laboratory. The implications of "laboratory domestication" have been considered in other model systems such as Caenorhabditis elegans (Sterken et al 2015), and laboratory mutations should be carefully considered when evaluating experimental results.…”

“…MSAT-11_cRei arrays consist of a 1.9 kb tandemly repeated monomer and are present on chromosomes 7 and 12 in all three available genomes, with two additional unique insertions in CC-1690 (not shown). Similarly, MSAT-11_cRei de novo insertions have recently been observed in experimental lines of the field isolate CC-2931(López-Cortegano et al 2022. There are very few observations of de novo satellite dissemination and its mechanisms are generally unclear (Ruiz-Ruano et al 2016), although rolling circle replication and reinsertion via extrachromosomal circular DNA intermediates has been proposed (Navrátilová et al 2008).…”

The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory

“…Recent work has in fact demonstrated that an unexpectedly large proportion of mutations in Chlamydomonas are beneficial under laboratory conditions, potentially due to many genes being dispensable in such an artificial environment (Böndel et al 2019; Böndel et al 2022). It has also been estimated that ∼5-10% of all de novo mutations in Chlamydomonas experimental lines are >50 bp (López-Cortegano et al 2022), supporting a prominent role for structural evolution in the laboratory. The implications of “laboratory domestication” have been considered in other model systems such as Caenorhabditis elegans (Sterken et al 2015), and laboratory mutations should be carefully considered when evaluating experimental results.…”

Causes of Mutation Rate Variability in Plant Genomes

“…Still, the mutation rates of structural variants, especially complex ones such as inversions, remain difficult to measure. The emergence of long-read sequencing technologies, such as circular consensus sequencing of single molecules up to tens of kilobases, may shed new light on mutation rates of complex structural variants and transposable element dynamics (66,75).…”