Rates and spectra of de novo structural mutations inChlamydomonas 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 algaChlamydomonas reinhardtii. The SM rate is highly variable between strains and between MA lines, and SMs represent a substantial proportion of all mutations in both strains (CC-1952 6%; CC-2931 12%). The SM spectra differ 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, whereas in CC-1952 a Dualen LINE was associated with 87% of duplications. Other SMs, notably 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

“…Second, many of the mutations were complex and featured large InDels or duplications at their repair points, potentially indicating a deficiency in DSB repair. High rates of deletions, duplications, and rearrangements have recently been documented in the Chlamydomonas field isolate CC-2931, however this was partly attributed to TE activity and similar patterns of mutational complexity at repair points were not observed ( López-Cortegano et al 2022 ).…”

Replitrons: a new group of eukaryotic transposons encoding HUH endonuclease

“…In a recent mutation accumulation experiment of C. reinhardtii strain CC-2931, six de novo insertions of a 3.6 kb unclassified TE were observed via PacBio sequencing of experimental lines (López-Cortegano et al 2022). An additional 44 insertions of an associated ∼910 bp nonautonomous element were also observed.…”

“…As introduced, Replitron-1 was discovered as an active TE in a mutation accumulation experiment, where replicate lines of C. reinhardtii strain CC-2931 were each maintained by single cell descent for ∼1,050 generations (López-Cortegano et al 2022). The ancestor of the experiment and eight of these replicate lines were sequenced with PacBio long reads at sufficient coverages to produce genome assemblies, enabling de novo insertions to be precisely characterised by comparison between the ancestral and derived assemblies.…”

“…The Replitron-1 sequence and predicted Replitron-1 transposase gene and protein were determined by López-Cortegano et al (2022). I downloaded all eukaryotic genome assemblies available from NCBI on 2021/06/03.…”

“…The cause of these non-canonical Helitron insertion signatures is unknown. Notably, Replitron-1 and Replitron-N1 were also associated with the breakpoints of several translocations in the mutation accumulation experiment (López-Cortegano et al 2022). These breakpoints always specifically coincided with the transposon right ends, and it was hypothesised that the transposition machinery may cause double-strand breaks, in contrast to the expected ssDNA activity of an HUH endonuclease.…”