Data from: Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex

Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events. Here we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhiza striata) across its geographic range. Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of substitution among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content. These findings will help fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.异养植物为探究选择压力改变对基因组进化的影响提供了绝佳的研究契机。此前针对异养植物的质体基因组（plastome）研究，往往以单个或少数高度趋异的物种/序列作为某一完整支系的代表，因此遗漏了诸多重要的进化过渡事件。本研究首次针对任意异养植物开展质体基因组进化的种内分析。通过结合基因组浅层测序（genome skimming）与靶向序列捕获（targeted sequence capture）技术，我们针对分布于其整个地理分布范围的无叶兰复合体——珊瑚兰属条纹珊瑚兰（Corallorhiza striata），探究了与其质体基因组降解程度及速率相关的科学假说。质体基因组数据为卷叶珊瑚兰（C. involuta）与濒危物种本特利珊瑚兰（C. bentleyi）之间的系统发育关系提供了强力支持，并证实了二者的互惠单系性。质体基因组降解现象极为显著，可在数百万年的较短时间尺度内快速发生，且该复合体的两个主要演化支间存在替换速率差异。基因组浅层测序与靶向序列捕获的整体覆盖深度差异显著，其中靶向序列捕获数据集的覆盖深度在质体基因组范围内随GC含量变化呈现剧烈波动。本研究结果填补了异养植物质体基因组进化模型中的认知空白，可为后续异养生物相关研究提供重要参考。