Complete plastome assemblies from a panel of 13 diverse potato taxa

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.

Complete mitogenome assemblies from a panel of 13 diverse potato taxa

“…Similarly, ADG2 and CHA mitogenomes are grouped together. The nuclear and plastome phylogeny of these 13 accessions was previously determined (Achakkagari et al 2020;Kyriakidou et al 2020), and a similar type of grouping was observed in these potato accessions. Also, a similar grouping of AJH, JUZ, and TBR accessions was observed in the plastome phylogeny.…”

“…chaucha (CHA) (CIP 2021l), and S. tuberosum subsp. tuberosum (TBR) (CIP 2021m)) grown at the International Potato Center (CIP) in Lima, Peru as described (Kyriakidou et al 2020), and sequenced using Illumina PE technology, except BUK2, which was sequenced with 10X Genomics' GemCode technology (https://www.10xgenomics.com/).…”

“…Mitochondrial DNA is maternally inherited and can be used to accurately identify evolutionary relationships. Generating nuclear phylogeny along with organelle phylogeny can be an effective help in understanding the history of hybridization (Achakkagari et al 2020). From the phylogenetic reconstruction, it was observed that GON1, GON2, PHU, STN, BUK1, ADG1, and CUR accessions are grouped together with no significant genetic variation (Figure 1).…”

“…Improving genetic resources helps to better understand the genetic diversity within potato. The current study examines complete mitochondrial genome sequences from 13 accessions of diverse tuber-bearing Solanum taxa (Achakkagari et al 2020).…”

The complete plastome sequences of nine diploid potato clones

“…The plastid DNA sequences (plastomes) of land plants are highly conserved compared to nuclear and mitochondrial DNA, and are extensively studied for their maternal phylogenetic relationships (Hosaka and Hanneman 1988). However, previous studies have shown considerable differences in plastomes and analysis of their complete sequences is important in understanding their diversity and evolutionary links (Hosaka 1986;Hosaka and Hanneman 1988;Chung et al 2006;Achakkagari et al 2020). In this study, a panel of nine diploid potato clones were selected for their unique characteristics such as tuber size, shape and disease resistance.…”