Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex.
Dense infraspecific sampling reveals rapid and independent trajectories of plastome degradation in a heterotrophic orchid complex.
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DOI：
10.1111/nph.15072
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发表时间：
2018-05
期刊：
影响因子：
--
通讯作者：
Sass C
中科院分区：
文献类型：
--
作者：
Barrett CF;Wicke S;Sass C
异养植物为研究改变的选择机制对基因组进化的影响提供了极好的机会。异养植物的叶绿体基因组(质体组)研究往往基于一个或几个高度分化的物种或序列作为整个谱系的代表，因此遗漏了重要的进化-短暂事件。在这里，我们提出了第一次亚种下分析任何异养植物的质体体进化。通过结合基因组浏览和有针对性的序列捕获，我们解决了关于地理范围内无叶兰花(Corallorhiza Striata)复合体的质体退化程度和速率的假设。原口动物为卷曲线虫和濒临灭绝的本特勒线虫之间的相互单系关系和证据提供了强有力的支持。塑性体的退化是广泛的，在几百万年的时间里迅速发生，有证据表明该复合体的两个主要分支之间的替换率不同。基因组浏览和靶向序列捕获在总体覆盖深度上有很大不同，靶向序列捕获数据集的深度随着GC含量的不同而在整个质体组中变化很大。这些发现将有助于填补异养叶绿体基因组进化模型中的知识空白，并对未来异养生物的研究具有指导意义。
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.
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