The complete mitogenome assemblies of 10 diploid potato clones reveal recombination and overlapping variants

Abstract

The potato mitogenome is complex and to understand various biological functions and nuclear-cytoplasmic interactions, it is important to characterize its gene content and structure. In this study, the complete mitogenome sequences of nine diploid potato clones along with a diploid Solanum okadae clone were characterized. Each mitogenome was assembled and annotated from Pacific Biosciences (PacBio) long-reads and 10X genomics short reads. The results show that each mitogenome consists of multiple circular molecules with similar structure and gene organization, though two groups (clones 07506-01, DW84-1457, 08675-21, and H412-1 in one group, and clones W5281-2, 12625-02, 12120-03, and 11379-03 in another group) could be distinguished, and two mitogenomes (clone 10908-06 and OKA15) were not consistent with those or with each other. Significant differences in the repeat structure of the ten mitogenomes were found, as was recombination events leading to multiple sub-genomic circles. Comparison between individual molecules revealed a translocation of ∼774 bp region located between a short repeat of 40 bp in molecule 3 of each mitogenome, and an insertion of the same in the molecule 2 of the 10908-06 mitogenome. Finally, phylogenetic analyses revealed a close relationship between the mitogenomes of these clones and previously published potato mitogenomes.

Discovery of a novel mitochondrial DNA molecule associated with tetrad pollen sterility in potato

“…There is a truncated copy of cob ( ψcob ) between rpl5-ψrps14 and rps10 in cv. Désirée [ 9 ] and in nine diploid breeding clones except S. okadae [ 13 ]. Like in S. okadae , there was no cob -like sequence in this region in our materials.…”

“…In the present study, only M03 was retained as a single molecule in all the clones, whereas M01 and M02 were rearranged intensively by inversions, translocations, and duplications and formed one to six contigs in each clone. Structural variability via repeat sequences is remarkably large in plant mitogenomes [ 8 , 13 ]. The larger number of contigs was constructed for 17H117-9 and 17H131, probably because branching molecules often caused sequence termination at the ends of these contigs [ 9 , 13 ].…”

“…Structural variability via repeat sequences is remarkably large in plant mitogenomes [ 8 , 13 ]. The larger number of contigs was constructed for 17H117-9 and 17H131, probably because branching molecules often caused sequence termination at the ends of these contigs [ 9 , 13 ].…”

“…In this recombinant-type molecule, a novel intergenic sequence between rpl5-ψrps14 and nad6 was found. rpl5-ψrps14 and nad6 are often located in different molecules [ 9 , 13 ]. Seven contigs assembled in the present study were terminated with rpl5-ψrps14 , rps10 , or nad6 .…”

“…Some genes are duplicated via repeat sequences in several species, but the number of core genes is similar across all accessions. Another study by Achakkagari et al [ 13 ] revealed that each mitogenome in nine diploid potato clones (mostly S. tuberosum ) and a wild diploid species ( S. okadae ) consisted of multiple circular molecules with similar structures and gene organization. On the other hand, comparing the mitogenomes of wild and cultivated potatoes, researchers detected DNA polymorphisms in several genes, such as atp6 , nad3 , rps10 , cob , and rpl5-ψrps14 [ 14 ], which allowed classification of mitochondrial DNA into α, β and γ types [ 15 ].…”