Abstract
Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable of processing long reads. The mitogenome contains all genes typical for plant mitochondrial genomes and long inserts of plastid origin (~6.4% of the total mitogenome length). Using this new information, we characterized the genetic diversity of mitochondrial and plastid genomes in 11 buckwheat cultivars compared with the ancestral subspecies, F. esculentum ssp. ancestrale. We found it to be surprisingly low within cultivars: Only three to six variations in the mitogenome and one to two in the plastid genome. In contrast, the divergence with F. esculentum ssp. ancestrale is much higher: 220 positions differ in the mitochondrial genome and 159 in the plastid genome. The SNPs in the plastid genome are enriched in non-synonymous substitutions, in particular in the genes involved in photosynthesis: psbA, psbC, and psbH. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program.
Highlights
In contrast to plastid genomes, plant mitochondrial genomes are usually large and complex.They are shaped by multiple structural changes, including rearrangements, duplications, and horizontal gene transfer (HGT) from nuclear and plastid genomes and, in rare cases, from other plant species [1,2].This complexity leads to the under-representation of the plant mitochondrial genome sequences compared to the plastome sequences
Despite plenty of evidence that plant mitogenomes can exist in the form of multiple circles and even non-circular forms due to intramolecular recombination mediated by the repeats [14], the single circular molecule, which includes all the subcircles, is usually recovered in the genome assemblies
We found that many structural variants, predominantly chromosome merges, are associated with the repeats (Table S1). This shows that the buckwheat mitochondrial genome undergoes recombination, which generates a diversity of subgenomic forms
Summary
In contrast to plastid genomes, plant mitochondrial genomes are usually large and complex. They are shaped by multiple structural changes, including rearrangements, duplications, and horizontal gene transfer (HGT) from nuclear and plastid genomes and, in rare cases, from other plant species [1,2]. This complexity leads to the under-representation of the plant mitochondrial genome sequences compared to the plastome sequences. The cytoplasmic male sterility (CMS) is associated with rearrangements in the mitochondrial genome. We generated the reference genome sequence for the buckwheat mitochondrial genome and studied the diversity of the mitochondrial and plastid genome in 11 buckwheat cultivars (nine Russian, one Japanese, and one Canadian) and the ancestral subspecies, F. esculentum ssp. ancestrale
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