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. 2020 May 12;9(5):618.
doi: 10.3390/plants9050618.

Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat

Maria D Logacheva  1   2 , Mikhail I Schelkunov  1   2 , Aleksey N Fesenko  3 , Artem S Kasianov  1 , Aleksey A Penin  1
Affiliations

Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat

Maria D Logacheva et al. Plants (Basel). .

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.

Keywords: buckwheat; genetic diversity; long reads; mitochondrial genome; plastid genome; targeted assembly.

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Conflict of interest statement

References

Figures

Figure 1
Figure 1
Map of the buckwheat mitochondrial genome representing genes and repeats. Genes shown in the outer circle are transcribed clockwise; in the inner circle, counterclockwise. Repeats with length >500 bp and similarity >95% are represented.
Figure 2
Figure 2
Phylogenetic tree based on maximum likelihood analysis of a concatenated data set of mitochondrial gene sequences. Branch lengths are proportional to the number of substitutions; bootstrap support values are equal to 100, unless otherwise specified.
See this image and copyright information in PMC

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