The complete plastome sequences of nine diploid potato clones

Abstract

Potato (Solanum tuberosum L.) is the world's fourth most important food crop and essential for global food security. The potato chloroplast genomes, the plastomes, are highly conserved and are largely studied for their maternal lineages. In this study, we assembled the complete circular plastome sequences of nine diploid potato clones, with sizes ranging between 155,296 bp and 155,564 bp. Annotation of these plastomes reveals that they each have 141 genes in a similar order. The computational chloroplast DNA typing reveals three plastid DNA types among the nine plastomes and they are grouped according to these types in the phylogeny.

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

“…We assembled the mitogenomes of nine diploid potato clones (mostly S. tuberosum ) for which the plastomes were recently assembled 13 using the pipeline described in Supplementary Fig. S1.…”

“… 3 , 28 We have also found multiple fragments of plastid sequences in each mitogenome, and some of these fragments contained petA, petG, petL, psbJ, psbL and rpl23 genes of plastidial origin. 13 …”

“…The clones are from the breeding collection of Agriculture and Agri-Food Canada and are maintained at the Benton Ridge Substation in Benton, New Brunswick and grown in the greenhouse at the Fredericton Research and Development Centre, Fredericton NB, Canada as described. 13 The potato clones have distinctive tuber size, shape, and disease resistance. The parents of the potato clones are listed on Supplementary Table S1.…”

“…Furthermore, a plastome phylogeny was constructed for the same genomes except Cicero and Désirée (their plastome assemblies are not available) to determine congruency between both phylogenetic trees. 13 , 24 The genome comparisons are visualized using MAUVE v20150226. 25 The cytoplasm types were determined using Insilco PCR experiments.…”

Towards the Well-Tempered Chloroplast DNA Sequences

“…Nowadays, it is common practice to use publicly available data of whole cpDNA genomes in phylogenetic analyses, especially in research involving assembled genomes (e.g., [ 63 , 64 , 65 , 66 , 67 , 68 ]). However, it is expected that the use of misaligned, non-homologous data may lead to erroneous results of phylogenetic analyses.…”