Cao Ruixin, Tong Shuyan, Luan Tianjing, Zheng Hanyun, Zhang Wei
Marine College, Shandong University, 180 Wenhua Xilu, Weihai 264209, China.
Plants (Basel). 2022 Mar 30;11(7):929. doi: 10.3390/plants11070929.
A compensatory base change (CBC) that coevolves in the secondary structure of ribosomal internal transcribed spacer 2 (ITS2) influences the estimation of genetic distance and thus challenges the phylogenetic use of this most popular genetic marker. To date, however, the CBC effect on ITS2 genetic distance is still unclear. Here, ITS2 sequences of 46 more recent angiosperm lineages were screened from 5677 genera and phylogenetically analyzed in sequence-structure format, including secondary structure prediction, structure-based alignment and sequence partition of paired and unpaired regions. ITS2 genetic distances were estimated comparatively by using both conventional DNA substitution models and RNA-specific models, which were performed in the PHASE package. Our results showed that the existence of the CBC substitution inflated the ITS2 genetic distances to different extents, and the deviation could be 180% higher if the relative ratio of substitution rate in ITS2 secondary structure stems was threefold higher than that in the loops. However, the CBC effect was minor if that ratio was below two, indicating that the DNA model is still applicable in recent lineages in which few CBCs occur. We thus provide a general empirical threshold to take account of CBC before ITS2 phylogenetic analyses.
核糖体内部转录间隔区2（ITS2）二级结构中共同进化的补偿性碱基变化（CBC）会影响遗传距离的估计，从而对这一最常用遗传标记在系统发育分析中的应用提出了挑战。然而，迄今为止，CBC对ITS2遗传距离的影响仍不明确。在此，我们从5677个属中筛选了46个近代被子植物谱系的ITS2序列，并以序列-结构形式进行了系统发育分析，包括二级结构预测、基于结构的比对以及配对和非配对区域的序列划分。通过使用传统的DNA替代模型和RNA特异性模型，在PHASE软件包中对ITS2遗传距离进行了比较估计。我们的结果表明，CBC替代的存在会不同程度地夸大ITS2遗传距离，如果ITS2二级结构茎中替代率的相对比率比环中高三倍，偏差可能会高出180%。然而，如果该比率低于2，CBC效应则较小，这表明DNA模型在几乎没有CBC发生的近代谱系中仍然适用。因此，我们提供了一个通用的经验阈值，以便在进行ITS2系统发育分析之前考虑CBC的影响。
