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.
Highlights
Peppers are a major global crop and one of the top five most abundant vegetables in China[1] that are cultivated as food, as a source of spices, and for pharmaceutical and ornamental purposes[2]
The plastome consists of 79 protein-coding genes, 30 tRNA genes, and 8 rRNA genes
In the case in which each sample was assigned to a species/variety according to their herbarium labels, the plastome length showed high levels of size variation between and within each species/variety, which was in contrast to the anticipated results (Supplementary Fig. 1 and Supplementary Table 1)
Summary
Peppers are a major global crop and one of the top five most abundant vegetables in China[1] that are cultivated as food, as a source of spices, and for pharmaceutical and ornamental purposes[2]. The Capsicum genus consists of ~32 wild and five cultivated species[3]. Given the continuing confusion regarding the best method to identify the traditionally recognized domesticated species of Capsicum, several key features have been proposed (e.g., seed color, corolla color and pattern, filament color, and the number of flowers per node) to distinguish the five cultivated Capsicum species[5]. Those key features have been widely evaluated in phenotypic, chromosomal, and hybridization studies[6,7]. The triple origin of the domesticated Capsicum species was confirmed by
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
