Complete mitogenome assemblies from a panel of 13 diverse potato taxa

Abstract

Mitochondrial DNA is maternally inherited and is shown to affect nuclear-cytoplasmic interactions in potato. Analyzing the mitogenome helps understand the evolutionary relationships and improve breeding programs in potato. We report complete mitogenome sequences from a panel of 13 potato accessions of various taxa. Each mitogenome has three independent circular molecules, except one of the S. bukasovii sample BUK2, which has a single circular molecule. Each mitogenome code for 37 non-redundant protein-coding genes, three rRNAs, 20 tRNAs, and 19 hypothetical open reading frames. Phylogenetic analysis reveals congruency between plastome and mitogenome phylogeny.

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

“…Annotation of each mitogenome revealed a conserved set of genes that are common in potato mtDNA. 2 Each mitogenome contains five ATP synthases ( atp1, atp4, atp6, atp8 , atp9 ), nine NADH dehydrogenases ( nad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9 ), 11 ribosomal proteins ( rps1, rps3, rps4, rps10, rps12, rps13, rps19, rpl2, rpl5, rpl10, rpl16 ), four cytochrome C biogenesis group genes ( ccmB, ccmC, ccmFC, ccmFN ), three cytochrome c oxidases ( cox1, cox2, cox3 ), two succinate dehydrogenases ( sdh3, sdh4 ), one cytcochrome c reductase ( cob ), one maturase ( matR ), and a transport membrane protein ( mttB ). All 10 mitogenomes have a functional cob gene while a truncated cob gene copy is also present in all but the OKA15 mitogenome.…”

“…First, the reads were aligned to a reference set created by concatenating the publicly available potato mitochondrial genome sequences [GenBank acc. MW122949-MW122985 , MN104801-MN104803 , MN114537-MN114539 ] 2 , 3 using minimap2 v2.17. 15 Mapped reads with a minimum alignment length of 2 kb were extracted and assembled using Canu v2.1.1.…”

“…A phylogenetic tree was constructed from the coding sequences of the 33-common protein-coding genes ( atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, ccmFc, ccmFn, cob, cox1, cox2, cox3, matR, mttB, nad3, nad4L, nad6, nad7, nad9, rpl10, rpl16, rpl2, rpl5, rps1, rps10, rps12, rps13, rps19, rps3, rps4, sdh3, sdh4 ) for each clone. In addition, the same 33 genes from 13 published mitogenomes of a panel of diverse taxa, 2 , 21 and two S. tuberosum cultivars (Cicero and Désirée) 3 were included for this phylogenetic study. The coding sequences were extracted and concatenated from each mitogenome and used in constructing the phylogenetic tree.…”

“…Recently, three individual molecules in each of 12 potato accessions from diverse taxa were reported. 2 Similarly, Varré et al 3 reported three autonomous molecules with two circular and one linear DNA for two Solanum tuberosum cultivars, and Cho et al 12 reported five circular DNA molecules in S. tuberosum with shared sequences between three of them. Given the diversity within the potato mitogenome, it is necessary to utilize the latest technologies to better understand its landscape of genetic variation, evolution and structural rearrangements.…”

“…The potato mitochondrial genome is also complicated and often reported as a multichromosomal type architecture with both circular and linear DNA molecules. 2 , 3 It was shown to exist in the form of multiple individual molecules, and occasionally with shared sequences between them. Recently, three individual molecules in each of 12 potato accessions from diverse taxa were reported.…”