We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.
CVTree方法是我们课题组开发的，基于全基因组的原核生物亲缘关系与分类的研究方法。它无需序列比对且具有种以下分辨能力。在本文中，我们利用CVTree网络服务器，基于“万量级”的原核生物全基因组构建亲缘关系树。系统研究了十个科与一个目的下级分类单元的亲缘关系，并将其与基于16S rRNA亲缘关系树的研究结果进行一一比对。我们发现，虽然当前分类系统越来越多的依赖基于16S rRNA 序列分析的结果，但是基于全基因组的CVTree方法的结果与分类系统更加一致，特别是在种的级别上。这说明CVTree方法，合理利用了全基因组序列中物种信息，避免了基于16S rRNA序列联配方法，由于信息量有限而导致的种级别的分辨能力不足的缺陷。我们相信，随着基因组测序越来越便捷，原核生物的亲缘关系与分类系统的研究将需要越来越多的考虑基于全基因组的研究结果，而CVTree方法将是一件非常有力的研究工具，为原核生物学家在这些研究中提供帮助。





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