Department of Computer Science, University of Central Florida, Orlando, FL, USA.
Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, FL, USA.
Sci Rep. 2022 Aug 25;12(1):14550. doi: 10.1038/s41598-022-18762-z.
Universal single-copy genes (USCGs) are widely used for species classification and taxonomic profiling. Despite many studies on USCGs, our understanding of USCGs in bacterial genomes might be out of date, especially how different the USCGs are in different studies, how well a set of USCGs can distinguish two bacterial species, whether USCGs can separate different strains of a bacterial species, to name a few. To fill the void, we studied USCGs in the most updated complete bacterial genomes. We showed that different USCG sets are quite different while coming from highly similar functional categories. We also found that although USCGs occur once in almost all bacterial genomes, each USCG does occur multiple times in certain genomes. We demonstrated that USCGs are reliable markers to distinguish different species while they cannot distinguish different strains of most bacterial species. Our study sheds new light on the usage and limitations of USCGs, which will facilitate their applications in evolutionary, phylogenomic, and metagenomic studies.
通用单拷贝基因（USCGs）被广泛用于物种分类和分类学分析。尽管已经有很多关于 USCGs 的研究，但我们对细菌基因组中 USCGs 的理解可能已经过时，特别是不同研究中 USCGs 的差异、一组 USCGs 区分两种细菌物种的能力、USCGs 是否可以区分细菌物种的不同菌株等方面。为了填补这一空白，我们研究了最新的完整细菌基因组中的 USCGs。结果表明，尽管这些 USCG 来自高度相似的功能类别，但不同的 USCG 集合却存在很大的差异。我们还发现，尽管 USCG 几乎在所有细菌基因组中只出现一次，但在某些基因组中，每个 USCG 都会出现多次。我们证明，USCGs 是区分不同物种的可靠标记，但不能区分大多数细菌物种的不同菌株。我们的研究揭示了 USCGs 的使用和局限性，这将有助于它们在进化、系统基因组学和宏基因组学研究中的应用。
