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

Pepper species ( 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, , that were mistakenly labeled as var. among others. Similarly, some NCBI-deposited plastomes were clustered differently from their labels. The 23-I intergenic spacer contained a 44 bp tandem repeat that, in addition to other InDels, was capable of discriminating the investigated species/varieties. The 16-Q/L-D/3-S gene set was determined to be sufficiently polymorphic to retrieve the complete phyloplastomic signal among the studied 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 spp. identification.