Hypermutability of integrated sequences of viral origin in a chlorarachniophyte

Abstract

Mutations provide the raw material for evolution, but mutation rates are not uniform across genomes. Using a mutation accumulation experiment in the marine phytoplankton Bigelowiella natans , we found extreme local variation in mutation rate: over 1,000-fold differences across its nuclear genome. While the baseline single-nucleotide mutation rate is approximately 3.5 × 10 –10 per site per generation, a common value for unicellular species, two genomic regions derived from integrated viruses exhibit strikingly elevated rates of about 6 × 10 –7 . These two regions show a distinctive mutational signature with almost exclusively T/A→C/G transitions, a pattern also found in other non-eukaryote-derived sequences in B. natans , contrary to the usual GC to AT mutation bias. Notably, hypermutation occurs only on TpA dinucleotides, and only in a subset of experimental lines, suggesting a regulated process rather than random genomic instability. We propose that B. natans targets invading DNA through localized hypermutation, reminiscent of deamination-based antiviral defense systems in animals. This prompts the idea of genome editing as a recurring immune strategy in eukaryotes.