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- Title
The plastome sequence of the endemic Amazonian conifer, Retrophyllum piresii (Silba) C.N.Page, reveals different recombination events and plastome isoforms.
- Authors
do Nascimento Vieira, Leila; Rogalski, Marcelo; Faoro, Helisson; Pacheco de Freitas Fraga, Hugo; Goulart dos Anjos, Karina; Assine Picchi, Gisele Fernanda; Onofre Nodari, Rubens; de Oliveira Pedrosa, Fábio; Maltempi de Souza, Emanuel; Pedro Guerra, Miguel
- 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.
- Subjects
ENDEMIC species; HOMOLOGOUS recombination; PLANT evolution; TRANSFER RNA; CHLOROPLAST DNA; GYMNOSPERMS
- Publication
Tree Genetics & Genomes, 2016, Vol 12, Issue 1, p1
- ISSN
1614-2942
- Publication type
Article
- DOI
10.1007/s11295-016-0968-0