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

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 NCBIdeposited 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.