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

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.

Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

“…While the chloroplast genome is generally viewed as highly conserved and little changed, our and other findings 2 , suggest that even at the population level the chloroplast genomes contain ample SNPs for resolving population structure. More work is needed to place these population level differences in context through intensively sampled sister-species comparative studies and data partitioning to understand how these changes may lead to functional changes between populations including the evolution of cytonuclear conflict in hybrids 67 .…”

“…The use of complete chloroplast genomes in studies of plant biodiversity has provided an important advancement over previous methods because of the conserved gene content, mainly uniparental inheritance, and very low rates of recombination helping to reduce problems such as incomplete lineage sorting found among nuclear markers 1 , 2 . As with the nucleus and mitochondria, the chloroplast controls essential and specialized cellular functions, mainly photosynthesis, with coding genes retained in this genome distinct to this cellular compartment 3 .…”

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

“…ex A. St.-Hil. & Girard (Silva et al, 2019), Capsicum annuum L. (Magdy et al, 2019), Holcoglossum Schltr. spp.…”

Variabilidad del fruto en el ecotipo ají “charapita” (Capsicum frutescens L.) de la Amazonía peruana

“…El ají (Capsicum spp.) tiene actividad antioxidante (Loizzo et al, 2015;Ridzuan et al, 2019;Alam et al, 2018;Carvalho et al, 2015;Sarpras et al, 2019); acumulación de metabolitos como prolina, capsaicina y fenilalanina en la etapa madura (Kim et al, 2020); altas concentraciones de vitamina A, C y ácido fólico (Kantar et al, 2016;Keles et al, 2016;Mamedov et al, 2017;Zhera et al, 2017;Korkutata y Kavaz, 2015;Szafirowska y Elkner, 2015), por lo cual se considera como favorable para desarrollar alimentos, especia (Magdy et al, 2019) y productos nutraceúticos (Tejada-Tovar et al, 2017).…”