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Open AccessArticle

The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution

1
CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy
2
CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy
3
Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy
*
Authors to whom correspondence should be addressed.
Genes 2018, 9(10), 503; https://doi.org/10.3390/genes9100503
Received: 17 September 2018 / Revised: 11 October 2018 / Accepted: 11 October 2018 / Published: 17 October 2018
(This article belongs to the Special Issue Genomics of Plant Domestication and Crop Evolution)
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. View Full-Text
Keywords: chloroplast genome; pepper; next-generation sequencing; sequence variability; single-nucleotide polymorphism; simple sequence repeats; microsatellites; perfect tandem repeats; molecular markers chloroplast genome; pepper; next-generation sequencing; sequence variability; single-nucleotide polymorphism; simple sequence repeats; microsatellites; perfect tandem repeats; molecular markers
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D’Agostino, N.; Tamburino, R.; Cantarella, C.; De Carluccio, V.; Sannino, L.; Cozzolino, S.; Cardi, T.; Scotti, N. The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution. Genes 2018, 9, 503.

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