Fujita Med J
Department of Microbiology, Fujita Health University, School of Medicine, Toyoake, Aichi, Japan.
Published: February 2024
Objectives: 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 spp., a complex taxonomic group consisting of 30 species.
Methods: Data from 335 publicly available 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.
Results: The phylogenetic tree constructed with OSNA successfully delineated the majority of species of the genus 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.
Conclusions: We propose that OSNA is a useful tool in predicting the taxonomic classification of complex bacterial genera.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10847635 | PMC |
http://dx.doi.org/10.20407/fmj.2023-007 | DOI Listing |
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Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia 46022, Spain.
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