Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates

Abstract

Although plant mitochondrial genomes typically show low rates of sequence evolution, levels of divergence in certain angiosperm lineages suggest anomalously high mitochondrial mutation rates. However, de novo mutations have never been directly analyzed in such lineages. Recent advances in high-fidelity DNA sequencing technologies have enabled detection of mitochondrial mutations when still present at low heteroplasmic frequencies. To date, these approaches have only been performed on a single plant species (Arabidopsis thaliana). Here, we apply a high-fidelity technique (Duplex Sequencing) to multiple angiosperms from the genus Silene, which exhibits extreme heterogeneity in rates of mitochondrial sequence evolution among close relatives. Consistent with phylogenetic evidence, we found that S. latifolia maintains low mitochondrial variant frequencies that are comparable to previous measurements in Arabidopsis. Silene noctiflora also exhibited low variant frequencies despite high levels of historical sequence divergence, which supports other lines of evidence that this species has reverted to lower mitochondrial mutation rates after a past episode of acceleration. In contrast, S. conica showed much higher variant frequencies in mitochondrial (but not in plastid) DNA, consistent with an ongoing bout of elevated mitochondrial mutation rates. Moreover, we found an altered mutational spectrum in S. conica heavily biased towards AT→GC transitions. We also observed an unusually low number of mitochondrial genome copies per cell in S. conica, potentially pointing to reduced opportunities for homologous recombination to accurately repair mismatches in this species. Overall, these results suggest that historical fluctuations in mutation rates are driving extreme variation in rates of plant mitochondrial sequence evolution.

Reassessing Banana Phylogeny and Organelle Inheritance Modes Using Genome Skimming Data

“…Organellar genomes of sperm cells have low copy numbers and may exert stronger genetic bottleneck compared to egg cells, eventually leading to genetic drifts and elevated rates of nucleotide substitutions (Greiner et al, 2015). Additionally, low genome copy numbers also disrupt DNA repairs through recombination, resulting in accumulations of mismatches, as proposed in the Silene conica mitogenomes (Broz et al, 2021).…”

A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA

“…This is especially pertinent in species with very high or very low mutation rates or show unusual biases in genetic variability. Indeed, recent work in A. thaliana linked mismatch repair with the low mutation rate seen in this species, and three species of angiosperm genus Silene with notably different mutation rates showed corresponding patterns in somatic mtDNA mutations ( 55 , 74 ), lending credence to the idea that studying somatic mutagenic processes can inform on evolutionary and population level patterns. A systematic analysis of somatic mutations in species with unusual genome composition or SNP patterns may provide insight into how and why these species deviate so significantly from related species and clues to their natural history.…”

Rapid shifts in mitochondrial tRNA import in a plant lineage with extensive mitochondrial tRNA gene loss

“…Despite this generally low mutation rate, some plant lineages have experienced a recent and dramatic acceleration in mutation rates in their mitogenomes, including multiple species in Silene (Mower, et al 2007;Broz, et al 2021). This accelerated rate may have then facilitated a rapid replacement of mt-tRNA genes in some plant lineages.…”

“…Leaf tissue was collected from a single hermaphrodite plant that had been crossed to the F2 generation and grown under standard greenhouse conditions at the University of Virginia. Genomic DNA was extracted with a modified CTAB protocol (Doyle and Doyle 1987) (Broz, et al 2021).…”