Horticulture Research (Sep 2019)

Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species

  • Mahmoud Magdy,
  • Lijun Ou,
  • Huiyang Yu,
  • Rong Chen,
  • Yuhong Zhou,
  • Heba Hassan,
  • Bihong Feng,
  • Nathan Taitano,
  • Esther van der Knaap,
  • Xuexiao Zou,
  • Feng Li,
  • Bo Ouyang

DOI
https://doi.org/10.1038/s41438-019-0191-x
Journal volume & issue
Vol. 6, no. 1
pp. 1 – 15

Abstract

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Abstract Pepper species (Capsicum spp.) are widely used as food, spice, decoration, and medicine. Despite the recent old-world culinary impact, more than 50 commercially recognized pod types have been recorded worldwide from three taxonomic complexes (A, B, and P). The current study aimed to apply a pan-plastome approach to resolve the plastomic boundaries among those complexes and identify effective loci for the taxonomical resolution and molecular identification of the studied species/varieties. High-resolution pan-plastomes of five species and two varieties were assembled and compared from 321 accessions. Phyloplastomic and network analyses clarified the taxonomic position of the studied species/varieties and revealed a pronounced number of accessions to be the rare and endemic species, C. galapagoense, that were mistakenly labeled as C. annuum var. glabriusculum among others. Similarly, some NCBI-deposited plastomes were clustered differently from their labels. The rpl23-trnI intergenic spacer contained a 44 bp tandem repeat that, in addition to other InDels, was capable of discriminating the investigated Capsicum species/varieties. The rps16-trnQ/rbcL-accD/ycf3-trnS gene set was determined to be sufficiently polymorphic to retrieve the complete phyloplastomic signal among the studied Capsicum spp. The pan-plastome approach was shown to be useful in resolving the taxonomical complexes, settling the incomplete lineage sorting conflict and developing a molecular marker set for Capsicum spp. identification.