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

The tropical tree family Lecythidaceae (order Ericales) 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 Amazonian genera, Lecythis and Eschweilera, are unresolved. In order to develop genetic markers for ecological and evolutionary studies in the family, 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. The B. excelsa plastome contained 160,472 bp and was arranged in a quadripartite structure consisting of a large single copy region (85,830 bp), a small single copy region (16,670 bp), and two inverted repeats (of 27,481 bp each). The coding region ycf1 and the spacer rpl16-rps3 outperformed plastid DNA markers previously used for barcoding and phylogenetics. We identified 456 cpSSRs in the B. excelsa plastome, from which we developed 130 primer pairs. Used in a phylogenetic analysis, the matrix of 24 plastomes showed with 100% bootstrap support that Lecythis and Eschweilera are polyphyletic, indicating the need for more detailed systematics studies of these two important Amazonian tree genera.