PDF(Pubmed)
Abstract：
UNASSIGNED: Taxonomic assignment based on whole-genome sequencing data facilitates clear demarcation of species within a complex genus. Here, we applied a unique pan-genome phylogenetic method, open reading frame (ORF)-based binarized structure network analysis (OSNA), for taxonomic inference of Aeromonas spp., a complex taxonomic group consisting of 30 species.
UNASSIGNED: Data from 335 publicly available Aeromonas genomes, including the reference genomes of 30 species, were used to build a phylogenetic tree using OSNA. In OSNA, whole-genome structures are expressed as binary sequences based on the presence or absence of ORFs, and a tree is generated using neighbor-net, a distance-based method for constructing phylogenetic networks from binary sequences. The tree built by OSNA was compared to that constructed by a core-genome single-nucleotide polymorphism (SNP)-based analysis. Furthermore, the orthologous average nucleotide identity (OrthoANI) values of the sequences that clustered in a single clade in the OSNA-based tree were calculated.
UNASSIGNED: The phylogenetic tree constructed with OSNA successfully delineated the majority of species of the genus Aeromonas forming conspecific clades for individual species, which was corroborated by OrthoANI values. Moreover, the OSNA-based phylogenetic tree demonstrated high compositional similarity to the core-genome SNP-based phylogenetic tree, supported by the Fowlkes-Mallows index.
UNASSIGNED: We propose that OSNA is a useful tool in predicting the taxonomic classification of complex bacterial genera.
UNASSIGNED: Data from 335 publicly available Aeromonas genomes, including the reference genomes of 30 species, were used to build a phylogenetic tree using OSNA. In OSNA, whole-genome structures are expressed as binary sequences based on the presence or absence of ORFs, and a tree is generated using neighbor-net, a distance-based method for constructing phylogenetic networks from binary sequences. The tree built by OSNA was compared to that constructed by a core-genome single-nucleotide polymorphism (SNP)-based analysis. Furthermore, the orthologous average nucleotide identity (OrthoANI) values of the sequences that clustered in a single clade in the OSNA-based tree were calculated.
UNASSIGNED: The phylogenetic tree constructed with OSNA successfully delineated the majority of species of the genus Aeromonas forming conspecific clades for individual species, which was corroborated by OrthoANI values. Moreover, the OSNA-based phylogenetic tree demonstrated high compositional similarity to the core-genome SNP-based phylogenetic tree, supported by the Fowlkes-Mallows index.
UNASSIGNED: We propose that OSNA is a useful tool in predicting the taxonomic classification of complex bacterial genera.
摘要：
■基于全基因组测序数据的分类分配有助于对复杂属中的物种进行清晰的划分。这里,我们应用了一种独特的全基因组系统发育方法，基于开放阅读框(ORF)的二值化结构网络分析(OSNA)，用于气单胞菌属的分类学推断。,由30种组成的一个复杂的分类群。
■来自335个公开可用的气单胞菌基因组的数据，包括30个物种的参考基因组，用于使用OSNA构建系统发育树。在OSNA,基于ORF的存在或不存在，全基因组结构被表达为二元序列，并且使用邻居网生成树，从二元序列构建系统发育网络的基于距离的方法。将OSNA构建的树与基于核心基因组单核苷酸多态性（SNP）的分析构建的树进行比较。此外，计算了基于OSNA的树中聚集在单个进化枝中的序列的直系同源平均核苷酸同一性(OrthoANI)值.
■用OSNA构建的系统发育树成功地描绘了气单胞菌属的大多数物种，这些物种形成了单个物种的特定进化枝，这得到了OrthoANI值的证实。此外，基于OSNA的系统发育树与基于核心基因组SNP的系统发育树表现出高度的组成相似性，由Fowlkes-Mallows索引支持。
■我们建议OSNA是预测复杂细菌属分类学分类的有用工具。
■来自335个公开可用的气单胞菌基因组的数据，包括30个物种的参考基因组，用于使用OSNA构建系统发育树。在OSNA,基于ORF的存在或不存在，全基因组结构被表达为二元序列，并且使用邻居网生成树，从二元序列构建系统发育网络的基于距离的方法。将OSNA构建的树与基于核心基因组单核苷酸多态性（SNP）的分析构建的树进行比较。此外，计算了基于OSNA的树中聚集在单个进化枝中的序列的直系同源平均核苷酸同一性(OrthoANI)值.
■用OSNA构建的系统发育树成功地描绘了气单胞菌属的大多数物种，这些物种形成了单个物种的特定进化枝，这得到了OrthoANI值的证实。此外，基于OSNA的系统发育树与基于核心基因组SNP的系统发育树表现出高度的组成相似性，由Fowlkes-Mallows索引支持。
■我们建议OSNA是预测复杂细菌属分类学分类的有用工具。
