Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae)
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ORIGINAL ARTICLE
Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae) Túlio Gomes Pacheco1 · Gleyson Morais da Silva1 · Amanda de Santana Lopes1 · José Daniel de Oliveira1 · Juliana Marcia Rogalski2 · Eduardo Balsanelli3 · Emanuel Maltempi de Souza3 · Fábio de Oliveira Pedrosa3 · Marcelo Rogalski1 Received: 17 March 2020 / Accepted: 8 July 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Main conclusion Complete plastome sequence of Tropaeolum pentaphyllum revealed molecular markers, hotspots of nucleotide polymorphism, RNA editing sites and phylogenetic aspects Abstract Tropaeolaceae Juss. ex DC. comprises approximately 95 species across North and South Americas. Tropaeolum pentaphyllum Lam. is an unconventional and endangered species with occurrence in some countries of South America. Although this species presents nutritional, medicinal and ornamental uses, genetic studies involving natural populations or promising genotypes are practically non-existent. Here, we report the nucleotide sequence of T. pentaphyllum plastome. It represents the first complete plastome sequence of the family Tropaeolaceae to be fully sequenced and analyzed in detail. The sequencing data revealed that the T. pentaphyllum plastome is highly similar to the plastomes of other Brassicales. Notwithstanding, our analyses detected some specific features concerning events of IR expansion and structural changes in some genes such as matK, rpoA, and rpoC2. We also detected 251 SSR loci, nine hotspots of nucleotide polymorphism, and two specific RNA editing sites in the plastome of T. pentaphyllum. Moreover, plastid phylogenomic inference indicated a closed relationship between the families Tropaeolaceae and Akaniaceae, which formed a sister group to Moringaceae–Caricaceae. Finally, our data bring new molecular markers and evolutionary features to be applied in the natural population, germplasm collection, and genotype selection aiming conservation, genetic diversity evaluation, and exploitation of this endangered species. Keywords Organelle DNA · Molecular markers · Extranuclear inheritance · Brassicales · Plastid evolution · Neglected crops Communicated by Anastasios Melis.
Introduction
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00425-020-03427-w) contains supplementary material, which is available to authorized users.
The family Tropaeolaceae Juss. ex DC. comprises approximately 95 species of the Americas. The family represents annual or perennial climbing or prostate herbs that contain rhizomes and tubers with an odor of mustard oils (Andersson and Andersson 2000; Bayer and Appel 2003; Edger et al. 2018). Tropaeolaceae is neotropical and most species occur in areas with a higher altitude of South America, with less frequency and abundance of species in North America (Bayer and Appel 2003; Souza and Lorenzi 2008; CardinalMcTeague et al. 2016). The first infrageneric classification (Cronquist 1988) divided
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