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The plastome sequence of the endemic Amazonian conifer, Retrophyllum piresii (Silba) C.N.Page, reveals different recombination events and plastome isoforms

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Abstract

Retrophyllum piresii (Podocarpaceae) is an endemic conifer species from the Brazilian Amazonian Region, and very few data related to ecological and genetic characteristics of this species are available. Plastome sequencing is an efficient tool to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as to probe the structural and functional evolution of plants. Usually, the plastome of photosynthetic land plants is quadripartite, with two copies of the inverted repeats (IRs) separating the small and large single-copy regions. However, in gymnosperms, IR can vary from large in size to completely absent, being constituted principally by transfer RNA (tRNA) genes, or a part of sequence of other genes. Here, we sequenced and characterized the complete plastome of R. piresii. This plastome was determined to be 133,291 bp (~480-fold coverage), presenting a total of 120 identified genes, of which 118 were single copy and two genes, trnN-GUU and trnD-GUC, were found to be duplicated and occurring as inverted and directed repeat (DR) sequences, respectively. These repeated regions presented recombinationally active sites, resulting in an IR-mediated inversion and a DR-mediated deletion. However, the isoform resulted from DR-mediated deletion may result in unviable plastome, with deletion of photosynthetic and expression machinery-related genes.

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Acknowledgments

This work was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), and Fundação de Amparo à Pesquisa e Inovação do Estado de Santa Catarina (FAPESC 14848/2011-2, 3770/2012, and 2780/2012-4). The authors thank Prof. Dr. Willian Antônio Rodrigues for the information related to the species, Angelo Schuabb Heringer and Ramon Felipe Scherer for collecting the plant material, and Museu Paraense Emílio Goeldi for kindly providing the plant material.

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    Authors and Affiliations

    1. Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga, 1346, ZC: 88040-900, Florianópolis, Santa Catarina, Brazil

      Leila do Nascimento Vieira, Hugo Pacheco de Freitas Fraga, Karina Goulart dos Anjos, Rubens Onofre Nodari & Miguel Pedro Guerra

    2. Departamento de Biologia Vegetal, Univesidade Federal de Viçosa, Avenida Peter Henry Rolfs s/n, ZC: 36570-000, Viçosa, Minas Gerais, Brazil

      Marcelo Rogalski

    3. Instituto Carlos Chagas, Fundação Oswaldo Cruz, Rua Professor Algacyr Munhoz Mader, 3775, bloco C 81350010, Curitiba, Paraná, Brazil

      Helisson Faoro & Gisele Fernanda Assine Picchi

    4. Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Rua Coronel Francisco H. dos Santos s/n, ZC: 81531-980, Curitiba, Paraná, Brazil

      Helisson Faoro, Fábio de Oliveira Pedrosa & Emanuel Maltempi de Souza

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    1. Leila do Nascimento Vieira
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    Correspondence to Miguel Pedro Guerra.

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    Communicated by Y. Tsumura

    Leila do Nascimento Vieira and Marcelo Rogalski contributed equally to this work.

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    do Nascimento Vieira, L., Rogalski, M., Faoro, H. et al. The plastome sequence of the endemic Amazonian conifer, Retrophyllum piresii (Silba) C.N.Page, reveals different recombination events and plastome isoforms. Tree Genetics & Genomes 12, 10 (2016). https://doi.org/10.1007/s11295-016-0968-0

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