Tracing the origin of the rocoto chile (Capsicum pubescens):insights through RAD-seq data

Abstract

The hot chile Capsicum pubescens is cultivated mainly in the highlands of Central-South America. Unlike other cultivated chiles, C. pubescens is known only as a cultigen and not in the wild. The affinities and origin of this species are puzzling; the purple species from central Andes have been proposed as its ancestors but C. pubescens forms an isolated monotypic clade in phylogenetic reconstructions. To better understand C. pubescens origin and affinities, the RAD-sequencing approach was followed using samples from C. pubescens, the purple species, and other species across Capsicum. The data filtered were analysed by Maximum Likelihood methods. A highly resolved phylogenetic reconstruction was obtained. Capsicum pubescens samples are resolved as a monophyletic group, sister the purple species, which in turn form a strong monophyletic group; this assemblage is sister to the clade that includes the other cultivated chiles and their wild relatives, altogether in the most derived branches of Capsicum. In contrast to previous studies, by using data from the whole genome it is proposed that C. pubescens is not an isolated lineage but closely related to the purple species, although they are clearly distinct clades, therefore none of the latter or any extant species would be its ancestor.