Plastome sequences of the subgenus Passiflora reveal highly divergent genes and specific evolutionary features

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Plastome sequences of the subgenus Passiflora reveal highly divergent genes and specific evolutionary features Túlio Gomes Pacheco1 · Amanda de Santana Lopes1 · Juliana Fátima Welter1 · Karla Suemy Clemente Yotoko2 · Wagner Campos Otoni3 · Leila do Nascimento Vieira4 · Miguel Pedro Guerra4 · Rubens Onofre Nodari4 · Eduardo Balsanelli5 · Fábio de Oliveira Pedrosa5 · Emanuel Maltempi de Souza5 · Marcelo Rogalski1  Received: 21 February 2020 / Accepted: 7 June 2020 © Springer Nature B.V. 2020

Abstract Key Message  Phylogenetic aspects, hotspots of nucleotide divergence, highly divergent genes, and specific RNA editing sites have been identified and characterized in the plastomes of the subgenus Passiflora. Abstract  The genus Passiflora comprises more than 500 species across five subgenera: Astrophea, Decaloba, Deidamioides, Passiflora, and Tetrapathea. The most economically relevant species belong to the subgenus Passiflora, whose genetic pool and diversity among wild species remain poorly characterized. Similarly, little is known about the interspecific relationships within the subgenus Passiflora and the genetic causes of nuclear-cytoplasmic incompatibility observed in interspecific hybrids. Here, we report the complete nucleotide sequences of six plastomes belonging to species of the subgenus Passiflora, with the aim of better understanding the evolution of the plastome in this subgenus. Complete plastome sequences revealed five hotspots of nucleotide polymorphism: three intergenic regions and two coding sequences. Moreover, among 70 RNA editing sites predicted in our analysis for the subgenus Passiflora, 38 were not shared by all analyzed species, highlighting their species-specific occurrence. Furthermore, phylogenies based on plastid sequences accurately resolved most relationships between species and suggested a non-monophyletic origin of three super-sections of the subgenus Passiflora, previously defined solely based on morphological traits. Finally, our findings identified putative candidates, including predicted RNA editing sites and the coding sequences of accD and clpP genes, responsible for nuclear-cytoplasmic incompatibility in the interspecific hybrids of Passiflora. Keywords  Passifloraceae · Organelle DNA · Genetic incompatibility · Plastome evolution · Polymorphism hotspots

Introduction The genus Passiflora comprises more than 500 species and is the largest within the pantropical family Passifloraceae (MacDougal and Feuillet 2004; Rocha et al. 2020). Its center of diversity in the Neotropics accounts for approximately 95% of all Passiflora species in South America, with some Túlio Gomes Pacheco and Amanda de Santana Lopes contributed equally to this work. Electronic supplementary material  The online version of this article (https​://doi.org/10.1007/s1110​3-020-01020​-z) contains supplementary material, which is available to authorized users. * Marcelo Rogalski [email protected] Extended author information available on the last page of the article

species found also in the Old World, Southeast Asia