Complete plastome assemblies from a panel of 13 diverse potato taxa
Citation
Achakkagari, S.R., Kyriakidou, M., Tai, H.H., Anglin, N.L., Ellis, D., Strömvik, M.V. (2020). Complete plastome assemblies from a panel of 13 diverse potato taxa. PLoS ONE, [online] 15(10 October), http://dx.doi.org/10.1371/journal.pone.0240124
Plain language summary
All organisms are composed of cells that have DNA encoding the genes that control all the functions of the organism. Most of the DNA is in a part of the cell called the nucleus and this DNA is called the nuclear genome. There are also other parts of the cell called plastids. A very special plastid, called a chloroplast, is involved in photosynthesis in plants. Photosynthesis is process where light energy from the sun converts carbon dioxide into sugars. Chloroplasts also have a small amount of DNA that mostly encodes genes that function in photosynthesis. The chloroplast DNA is called the plastome. The plastome sequence of potato and 12 other species (also referred to as taxa at gene banks) that are closely related to potato. Five different types of plastomes were found. These 13 species were grouped based on the similarity of plastome sequences. The groupings were mostly the same as previous groupings based on nuclear genomes, but with some differences. These differences reflected the parental origins of nuclear and chloroplast genomes, where nuclear genomes are from both parents and chloroplast genomes are of maternal origin. The study provided knowledge on chloroplast DNA, and information the similarities and differences of the 13 species.
Abstract
The chloroplasts are a crucial part of photosynthesizing plant cells and are extensively utilized in phylogenetic studies mainly due to their maternal inheritance. Characterization and analysis of complete plastome sequences is necessary to understand their diversity and evolutionary relationships. Here, a panel of thirteen plastomes from various potato taxa are presented. Though they are highly similar with respect to gene order and content, there is also a great extent of SNPs and InDels between them, with one of the Solanum bukasovii plastomes (BUK2) having the highest number of SNPs and InDels. Five different potato plastome types (C, S, A, W, W2) are present in the panel. Interestingly, the S. tuberosum subsp. tuberosum (TBR) accession has a W-type plastome, which is not commonly found in this species. The S-type plastome has a conserved 48 bp deletion not found in other types, which is responsible for the divergence of the S-type from the C-type plastome. Finally, a phylogenetic analysis shows that these plastomes cluster according to their types. Congruence between the nuclear genome and the plastome phylogeny of these accessions was seen, however with considerable differences, supporting the hypothesis of introgression and hybridization between potato species.