Complete plastome assemblies from a panel of 13 diverse potato taxa

PLoS One. 2020 Oct 8;15(10):e0240124. doi: 10.1371/journal.pone.0240124. eCollection 2020.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Plant / genetics
  • Evolution, Molecular
  • Genes, Plant
  • INDEL Mutation
  • Phylogeny
  • Plastids / genetics*
  • Polymorphism, Single Nucleotide
  • Solanum / classification
  • Solanum / genetics*
  • Solanum tuberosum / classification
  • Solanum tuberosum / genetics

Substances

  • DNA, Plant

Grants and funding

The authors acknowledge funding through a Nouvelles Initiatives (Project International) grant from the Centre SÈVE (Fonds de recherche du Québec - Nature et technologies (FRQ-NT) to M.V.S., N.A., D.E., and H.H.T.; Compute/Calcul Canada Resource Allocations for Research Portals and Platforms (The Potato Genome Diversity Portal), a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (NSERC) and a Génome Québec (GQ-AAC-2019-2) award to M.V.S.; A-base funding from Agriculture and Agri-Food Canada to H.H.T. from the Management Directed Genomics Call. The authors also gratefully acknowledge the support of the CGIAR Genebank Platform and appreciatively express thanks to the financial support for the sequencing by GIZ on behalf of the Federal Ministry of Economic Cooperation and Development, Germany. The funders had no role in the study design, data collection and analysis, decision to publish or preparation of the manuscript.