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bioRxiv · 10.1101/192112

Comparative analysis of 24 chloroplast genomes yields highly informative genetic markers for the Brazil nut family (Lecythidaceae)

Thomson, A. M.·Vargas, O. M.·Dick, C. W.
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Abstract

O_LIPremise of the study: The tropical tree family Lecythidaceae has enormous ecological and economic importance in the Amazon basin. Lecythidaceae species can be difficult to identify without molecular data, however, and phylogenetic relationships within and among the most diverse genera are poorly resolved.\nC_LIO_LIMethods: To develop informative genetic markers for Lecythidaceae, we used genome skimming to assemble de novo the full plastome of the Brazil nut tree (Bertholletia excelsa) and 23 other Lecythidaceae species. Indices of nucleotide diversity and phylogenetic signal were used to identify regions suitable for genetic marker development.\nC_LIO_LIResults: The B. excelsa plastome contained 160,472 bp and was arranged in a quadripartite structure. Using the 24 plastome alignments, we developed primers for 10 coding and non-coding DNA regions containing exceptional nucleotide diversity and phylogenetic signal. We additionally developed 19 chloroplast simple sequence repeats (cpSSRs) for population-level studies.\nC_LIO_LIDiscussion: The coding region ycf1 and the spacer rpl16-rps3 outperformed plastid DNA markers previously used for barcoding and phylogenetics. Used in a phylogenetic analysis, the matrix of 24 plastomes showed with 100% bootstrap support that Lecythis and Eschweilera are polyphyletic. The plastomes and primers presented in this study will facilitate a broad array of ecological and evolutionary studies in Lecythidaceae.\nC_LI

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Thomson, A. M., Vargas, O. M., Dick, C. W.. 2017-09-21. Comparative analysis of 24 chloroplast genomes yields highly informative genetic markers for the Brazil nut family (Lecythidaceae). https://doi.org/10.1101/192112

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