Target sequence capture in the Brazil nut family (Lecythidaceae): marker selection and in silico capture from genome skimming data. Lecythidaceae

We generated twelve transcriptomes for ten species of the Brazil nut family (Lecythidaceae), identified a set of putatively orthologous nuclear loci and evaluated, in silico, their phylogenetic utility using published genome skimming data of 24 Lecythidaceae species. We designed the markers using MarkerMiner, and developed a new script, GoldFinder, to efficiently sub-select the best makers for sequencing. We captured, in silico, all 354 nuclear loci designed and performed maximum likelihood phylogenetic analysis on the concatenated sequence matrix. We also calculated individual gene trees with maximum likelihood and used them for a coalescent-based species tree inference.