Vol.:(0123456789) 1 3 Planta https://doi.org/10.1007/s00425-019-03217-z ORIGINAL ARTICLE The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a fip‑fop recombination between two short inverted repeats Amanda de Santana Lopes 1  · Túlio Gomes Pacheco 1  · Odyone Nascimento da Silva 1  · Leonardo Magalhães Cruz 2  · Eduardo Balsanelli 2  · Emanuel Maltempi de Souza 2  · Fábio de Oliveira Pedrosa 2  · Marcelo Rogalski 1 Received: 2 May 2019 / Accepted: 18 June 2019 © Springer-Verlag GmbH Germany, part of Springer Nature 2019 Abstract Main conclusion The plastomes of Astrocaryum murumuru and A. aculeatum revealed a lineage-specific structural feature originated by flip-flop recombination, non-synonymous substitutions in conserved genes and several molecular markers. Abstract Astrocaryum murumuru Mart. and A. aculeatum G.Mey. are two palm species of Amazon forest that are economi- cally important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strate- gies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identifcation and characterization of molecular markers are essential to assess the genetic diversity of natural populations of both species. Therefore, we sequenced and characterized in detail the plastome of both species. We compared both species and identifed 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specifc RNA editing site found in the ccsA gene, which is exclusive to A. murumuru. Moreover, the structural analysis in the plastomes of both species revealed a 4.6-kb inversion encompassing a set of genes involved in chlororespiration and plastid translation. This 4.6-kb inversion is a lineage-specifc structural feature of the genus Astrocaryum originated by fip-fop recombination between two short inverted repeats. Furthermore, our phylogenetic analysis using whole plastomes of 39 Arecaceae species placed the Astrocaryum species sister to Acrocomia within the tribe Cocoseae. Finally, our data indicated substantial changes in the plastome structure and sequence of both species of the genus Astrocaryum, bringing new molecular markers, several structural and evolving features, which can be applied in several areas such as genetic, evolution, breeding, phylogeny and conservation strategies for both species. Keywords Palm tree · Horizontal gene transfer · Plastome evolution · Plastid SSRs · Plastid SNPs Introduction The palm family (Arecaceae) comprises 188 genera and approximately 2585 species distributed throughout tropi- cal and subtropical ecosystems with great ecological and economical importance (Dransfeld et al. 2008; Palmweb, http://www.palmweb.org/). The genus Astrocaryum G. Mey. contains 40 species, which are divided into three subgenera, Astrocaryum, Munbaca and Monogynanthus (Kahn 2008). In the Amazon region we can highlight two species of genus Astrocaryum, A. murumuru Mart. (subgenus Monogynan- thus) and A. aculeatum G.Mey (subgenus Astrocaryum), which are economically important as source of food, oil and raw material for several applications (Clement et al. 2005; Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00425-019-03217-z) contains supplementary material, which is available to authorized users. * Marcelo Rogalski rogalski@ufv.br 1 Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil 2 Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil