Low copy numbers for mitochondrial DNA moderates the strength of nuclear-cytoplasmic incompatibility in plants

Mitochondrial DNA and the largest nuclear-mitochondrial DNA in Arabidopsis can be separated by their methylation levels

Methylation of cytosines in plant mitochondrial DNA (mtDNA) has been a controversial issue. Results supporting mtDNA methylation may have been subject to contamination due to the presence of nuclear sequences originating from the mitochondrial genome called nuclear mitochondrial insertions (NUMT). In Arabidopsis (Arabidopsis thaliana) Columbia 0 (Col-0), the largest NUMT, located on Chromosome 2, is nearly twice the size of the entire mitochondrial genome and exhibits a sequence almost identical to the mitochondrial genome, albeit with shuffling and repeats. In the presence of such high similarity, it is challenging to eliminate interference when determining mtDNA methylation levels. Here, we applied a methyl-CpG-binding domain (MBD) protein-based affinity assay to separate total DNA, applied next-generation sequencing to the pre- and postseparation DNA samples, and examined the single nucleotide polymorphism (SNP) sites between NUMT and mtDNA. The results revealed successful separation of methylated and non-methylated DNA within the total DNA, with simultaneous separation achieved between NUMT DNA and mtDNA. These results suggest that our method can achieve separation based on the differential methylation levels of the whole lengths of NUMT and mtDNAs. The bisulfite sequencing results for the postseparation DNA samples suggest that mtDNA exhibits not only a lack of CpG methylation but also an absence of CHH and CHG methylation. In contrast, the NUMT shows high levels of methylation across all 3 contexts, at least in the Col-0 accession.

The evolutionarily diverged single-stranded DNA-binding proteins SSB1/SSB2 differentially affect the replication, recombination and mutation of organellar genomes in Arabidopsis thaliana

Single-stranded DNA-binding proteins (SSBs) play essential roles in the replication, recombination and repair processes of organellar DNA molecules. In Arabidopsis thaliana, SSBs are encoded by a small family of two genes (SSB1 and SSB2). However, the functional divergence of these two SSB copies in plants remains largely unknown, and detailed studies regarding their roles in the replication and recombination of organellar genomes are still incomplete. In this study, phylogenetic, gene structure and protein motif analyses all suggested that SSB1 and SSB2 probably diverged during the early evolution of seed plants. Based on accurate long-read sequencing results, ssb1 and ssb2 mutants had decreased copy numbers for both mitochondrial DNA (mtDNA) and plastid DNA (ptDNA), accompanied by a slight increase in structural rearrangements mediated by intermediate-sized repeats in mt genome and small-scale variants in both genomes. Our findings provide an important foundation for further investigating the effects of DNA dosage in the regulation of mutation frequencies in plant organellar genomes.

RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola

Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.