G3 (Bethesda). 2025 Dec 29. pii: jkaf310. [Epub ahead of print]
Spontaneous mutations display biases in their relative frequencies with important consequences for genome structure and composition. While laboratory studies have provided important insights into the spontaneous mutation spectrum, laboratory environments for optimal growth may engender biases that are not representative of natural populations. We analyzed the mitochondrial genomes of 1,524 Caenorhabditis elegans natural isolates comprising 531 unique isotypes to investigate mtDNA polymorphism in the wild. Ancestral reconstruction was used to polarize 2,464 variants (88 indels, 2,376 SNPs) and the results were compared to mutations identified in experimental lines under relaxed selection. MtDNA variant distribution in natural isolates is strongly dependent on site-degeneracy in a manner consistent with purifying selection. There is significant variation in the proportion of synonymous and nonsynonymous polymorphism between genes. Specifically, ETC complex I genes are enriched for nonsynonymous polymorphism. The probability of synonymous mutation is higher at sites with neighboring G/C nucleotides and the per gene synonymous polymorphism is negatively correlated with A+T-content at the 1st and 2nd codon positions. Furthermore, the 5' and 3' ends of genes have both higher A+T-content and less synonymous polymorphism than central regions. There is evidence of natural selection for preferred codons. We identify the first cases of large heteroplasmic mtDNA structural variants in C. elegans natural isolates, comprising deletions and duplications. Although some patterns of mtDNA mutational bias are similar between laboratory and natural populations, there exist significant differences. In particular, G/C → T/A transversions typically associated with oxidative damage and 8-oxoguanine are strikingly rarer at four-fold degenerate sites in natural populations relative to laboratory populations suggesting that the latter are more prone to mtDNA oxidative damage. Hence, mutational spectra observed in laboratory strains may differ in important aspects from those of natural populations.
Keywords:
C. elegans
; codon usage bias; heteroplasmy; mtDNA; natural isolates; selection