Long‐read sequencing characterizes mitochondrial and plastid genome variants in Arabidopsis msh1 mutants

Abstract

SUMMARY The abundant repeats in plant mitochondrial genomes can cause rapid genome rearrangements and are also a major obstacle in short‐read sequencing studies. Nuclear‐encoded proteins such as MSH1 are known to suppress the generation of repeat‐associated mitochondrial genome variants, but our understanding of these mechanisms has been constrained by the limitations of short‐read technologies. Here, we used highly accurate long‐read sequencing (PacBio HiFi) to characterize mitochondrial and plastid genome variants in Arabidopsis thaliana msh1 mutant individuals. The HiFi reads provided a global view of recombination dynamics with detailed quantification of parental and crossover recombination products for both large and small repeats. We found that recombination breakpoints were distributed relatively evenly across the length of repeated sequences and detected widespread internal exchanges of sequence variants between pairs of imperfect repeats in the mitochondrial genome of msh1 mutants. Long‐read assemblies of mitochondrial genomes from seven other A. thaliana wild‐type accessions differed by repeat‐mediated structural rearrangements similar to those observed in msh1 mutants, but they were all in a simple low‐heteroplasmy state. The Arabidopsis plastid genome generally lacks small repeats and exhibited a very different pattern of variant accumulation in msh1 mutants compared with the mitochondrial genome. Our data illustrate the power of HiFi technology in studying repeat‐mediated recombination in plant organellar genomes and improved the sequence resolution for recombinational processes suppressed by MSH1. Plant organellar genomes can undergo rapid rearrangements. Long‐read sequencing provides a detailed and quantitative view of mitochondrial and plastid genome variants normally suppressed by MSH1, advancing our understanding of plant organellar genome dynamics.

Nanopore Sequencing Technology as an Emerging Tool for Diversity Studies of Plant Organellar Genomes

“…This technology also adeptly resolves structural variations and recombination events, providing a more comprehensive understanding of plant mitochondrial DNA. A recent studies highlights the efficacy of long-read sequencing in unravelling the intricacies of plant mitochondrial genomes, reflecting its growing importance in plant genomics research [26,27].…”

Exploring the unexplored : Unravelling the cyto-nuclear interactions in Arabidopsis thaliana to improve photosynthesis

“…We report that while mitochondrial genomes are known to be highly dynamic in structure (Xu et al, 2015;Gualberto and Newton, 2017;Zou et al, 2022), the neighbour-joining trees of the mitochondria and chloroplast genomes are highly correlated. The high correlation suggests that both organellar genomes have been inheriting together in the A. thaliana population, implying that paternal transmission of organelles does not strongly influence organellar inheritance in A. thaliana.…”

“…The structure of the mitochondrial genome is known to be more dynamic than the structure of the chloroplast genome (Xu et al, 2015;Gualberto and Newton, 2017). This results in extensive interspecies modification of the mitochondrial genome structure (Zou et al, 2022), and therefore…”

“…Recently, major rearrangements and increased point mutations in the mitochondrial genomes were found to occur in msh1 mutants. The MUTS HOMOLOG 1 (MSH1) gene encodes a protein involved in recombination surveillance and repair of organellar genomes in A. thaliana (Wu et al, 2020;Chustecki et al, 2022;Zou et al, 2022). According to Zou et al, 2022, the rearrangements observed in msh1 mutants are more or less evenly spread over the mitochondrial genome.…”

“…The MUTS HOMOLOG 1 (MSH1) gene encodes a protein involved in recombination surveillance and repair of organellar genomes in A. thaliana (Wu et al, 2020;Chustecki et al, 2022;Zou et al, 2022). According to Zou et al, 2022, the rearrangements observed in msh1 mutants are more or less evenly spread over the mitochondrial genome. However, upon closer inspection of these data, the Col-0 genome region covering the location where orf225Staro-2 resides in the Staro-2 genome, shows a relatively high number of rearrangements.…”