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

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.

本研究针对玉蕊科（Lecythidaceae，巴西坚果科）的10个物种构建了12个转录组，鉴定出一组推定的直系同源核基因座（putatively orthologous nuclear loci），并利用已发表的24个玉蕊科物种的基因组浅层测序（genome skimming）数据，通过计算机模拟（in silico）手段评估了这些基因座的系统发育应用潜力。研究团队使用MarkerMiner工具设计了该批分子标记，并开发了一款名为GoldFinder的全新脚本，用于高效筛选出最适用于测序的标记。本研究在计算机模拟环境下捕获了所有设计完成的354个核基因座，并对拼接后的序列矩阵开展了最大似然法（maximum likelihood）系统发育分析。此外，我们还通过最大似然法构建了单基因树，并基于这些单基因树开展了基于溯祖模型的物种树推断。