Abstract
Members of the genus Capsicum are of great economic importance, including both wild forms and cultivars of peppers and chilies. The high number of potentially informative characteristics that can be identified through next-generation sequencing technologies gave a huge boost to evolutionary and comparative genomic research in higher plants. Here, we determined the complete nucleotide sequences of the plastomes of eight Capsicum species (eleven genotypes), representing the three main taxonomic groups in the genus and estimated molecular diversity. Comparative analyses highlighted a wide spectrum of variation, ranging from point mutations to small/medium size insertions/deletions (InDels), with accD, ndhB, rpl20, ycf1, and ycf2 being the most variable genes. The global pattern of sequence variation is consistent with the phylogenetic signal. Maximum-likelihood tree estimation revealed that Capsicum chacoense is sister to the baccatum complex. Divergence and positive selection analyses unveiled that protein-coding genes were generally well conserved, but we identified 25 positive signatures distributed in six genes involved in different essential plastid functions, suggesting positive selection during evolution of Capsicum plastomes. Finally, the identified sequence variation allowed us to develop simple PCR-based markers useful in future work to discriminate species belonging to different Capsicum complexes.
Highlights
In recent decades, plastid DNA markers were used either to infer species-level phylogenetic and phylogeographic relationships in plants or to identify species via barcoding approaches [1,2,3]
Sequencing of the eleven Capsicum genotypes produced 5,634,814–404,910,769 base pairs of high-quality plastid reads with per-base mean coverage ranging from 26 to 2581
The C. chacoense genotype examined here can be unequivocally assigned as a sister to the CB complex, with the results of Walsh and Hoot [20], and ruling out the previous hypothesis by Ince, Karaca, and Onus [19], who postulated C. chacoense as a sort of bridge placement between the complexes: annuum (CA) and C. chacoense is the basal species in the clade, including the CB complex; it is expected to share some plesiomorphic traits with the CA complex
Summary
Plastid DNA (cpDNA) markers were used either to infer species-level phylogenetic and phylogeographic relationships in plants or to identify species via barcoding approaches [1,2,3]. CpDNA sequence divergence is often unable to provide adequate resolution of genetic differences at the intra-specific level because of its slow evolutionary rate, chloroplast DNA-based molecular markers, such as microsatellites and tandem repeats, are widely exploited to reveal inter-specific variation [4,5,6]. The genus Capsicum (Solanaceae), native to South and Central America and the southern. Capsicum-specific starch fossils, found at seven sites from the Bahamas to southern Peru, dating 6000 years before first contact with Europeans, clearly demonstrate that members of the genus Capsicum were extensively cultivated initially in the Americas and, after Columbus, were dispersed around the World [18]. Plants of the genus Capsicum show an entire cup-shaped calyx, a unique trait among Solanaceae flowers and only shared with flowers of the genus Lycianthes [15]
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