Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences.
Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences.
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DOI：
10.1371/journal.pone.0268847
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发表时间：
2023
期刊：
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
--
作者：
细菌系统发育分析通常基于细菌的16S rRNA基因序列来探索不同细菌种类和属之间的进化关系；然而，这些结果受到镶嵌现象、基因组内异质性和难以区分亲缘种的限制。在这项研究中，我们的目的是基于不同细菌物种的K-mer谱，对大肠杆菌、志贺氏菌、耶尔森氏菌、克雷伯氏菌和奈瑟氏菌进行全基因组比较，构建系统发育树。五核苷酸频率分析（512模式，每个5个核苷酸）进行区分高度相似的物种。此外，尽管在系统发育树上与肠出血性大肠杆菌密切相关，但阿尔伯氏杆菌菌株与大肠杆菌和志贺氏菌有明显的区别。此外，我们基于叶绿体基因组中五聚体频率的Ipomoea物种系统发育树与先前报道的形态相似性相关。此外，支持向量机根据大肠杆菌和志贺氏菌的五核苷酸谱对它们的基因组进行了清晰的分类。这些结果表明，基于五聚体或六聚体的系统发育分析是一种有用的微生物系统发育研究方法。此外，我们还引入了一个R应用程序Phy5，该应用程序基于全基因组的五聚体谱比较生成系统发育树。Phy5的在线版本可在https://phy5.shinyapps.io/Phy5R/访问，命令行版本Phy5cli可在https://github.com/YoshioNakano2021/phy5下载。
Bacterial phylogenetic analyses are commonly performed to explore the evolutionary relationships among various bacterial species and genera based on their 16S rRNA gene sequences; however, these results are limited by mosaicism, intragenomic heterogeneity, and difficulties in distinguishing between related species. In this study, we aimed to perform genome-wide comparisons of different bacterial species, namely Escherichia coli, Shigella, Yersinia, Klebsiella, and Neisseria spp., based on their K-mer profiles to construct phylogenetic trees. Pentanucleotide frequency analyses (512 patterns of 5 nucleotides each) were performed to distinguish between highly similar species. Moreover, Escherichia albertii strains were clearly distinguished from E. coli and Shigella, despite being closely related to enterohemorrhagic E. coli in the phylogenetic tree. In addition, our phylogenetic tree of Ipomoea species based on pentamer frequency in chloroplast genomes was correlated with previously reported morphological similarities. Furthermore, a support vector machine clearly classified E. coli and Shigella genomes based on their pentanucleotide profiles. These results suggest that phylogenetic analyses based on penta- or hexamer profiles are a useful methodology for microbial phylogenetic studies. In addition, we introduced an R application, Phy5, which generates a phylogenetic tree based on genome-wide comparisons of pentamer profiles. The online version of Phy5 can be accessed at https://phy5.shinyapps.io/Phy5R/ and its command line version Phy5cli can be downloaded at https://github.com/YoshioNakano2021/phy5.
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