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 economically important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strategies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identification 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 identified 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specific 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-specific structural feature of the genus Astrocaryum originated by flip-flop 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.
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Acknowledgements
This research was support by the National Council for Scientific and Technological Development, Brazil (CNPq, Grant 459698/2014-1). We are grateful to INCT-FBN and for the scholarships granted by the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) to ONS, and those granted by the CNPq to ASL, TGP, LMC, EB, EMS, FOP and MR. We are also grateful to the Núcleo de Análise de Biomoléculas (NuBiomol) of the Universidade Federal de Viçosa for providing the software CLC Genomics.
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de Santana Lopes, A., Gomes Pacheco, T., Nascimento da Silva, O. et al. The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a flip-flop recombination between two short inverted repeats. Planta 250, 1229–1246 (2019). https://doi.org/10.1007/s00425-019-03217-z
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DOI: https://doi.org/10.1007/s00425-019-03217-z