Comparative analyses of whole-genome protein sequences from multiple organisms

Abstract Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are different than most other whole-genome methods, because they are based on...

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Autores principales:	Makio Yokono, Soichirou Satoh, Ayumi Tanaka
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/16656572c4ac44f09059ab5223ee6e71
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spelling	oai:doaj.org-article:16656572c4ac44f09059ab5223ee6e712021-12-02T12:32:59ZComparative analyses of whole-genome protein sequences from multiple organisms10.1038/s41598-018-25090-82045-2322https://doaj.org/article/16656572c4ac44f09059ab5223ee6e712018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-25090-8https://doaj.org/toc/2045-2322Abstract Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are different than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method. Our method correctly reconstructs the phylogenetic tree of in silico evolved E. coli proteomes. We applied the method to reconstruct a whole-proteome phylogeny of 1,087 species from all three domains of life, Bacteria, Archaea, and Eucarya. Our tree was automatically reconstructed without any human decisions, such as the selection of organisms. The tree exhibits a concentric circle-like structure, indicating that all the organisms have similar total branch lengths from their common ancestor. Branching patterns of the members of each phylum of Bacteria and Archaea are largely consistent with previous reports. The topologies are largely consistent with those reconstructed by other methods. These results strongly suggest that this approach has sufficient taxonomic resolution and reliability to infer phylogeny, from phylum to strain, of a wide range of organisms.Makio YokonoSoichirou SatohAyumi TanakaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-10 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Makio Yokono Soichirou Satoh Ayumi Tanaka Comparative analyses of whole-genome protein sequences from multiple organisms
description	Abstract Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are different than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method. Our method correctly reconstructs the phylogenetic tree of in silico evolved E. coli proteomes. We applied the method to reconstruct a whole-proteome phylogeny of 1,087 species from all three domains of life, Bacteria, Archaea, and Eucarya. Our tree was automatically reconstructed without any human decisions, such as the selection of organisms. The tree exhibits a concentric circle-like structure, indicating that all the organisms have similar total branch lengths from their common ancestor. Branching patterns of the members of each phylum of Bacteria and Archaea are largely consistent with previous reports. The topologies are largely consistent with those reconstructed by other methods. These results strongly suggest that this approach has sufficient taxonomic resolution and reliability to infer phylogeny, from phylum to strain, of a wide range of organisms.
format	article
author	Makio Yokono Soichirou Satoh Ayumi Tanaka
author_facet	Makio Yokono Soichirou Satoh Ayumi Tanaka
author_sort	Makio Yokono
title	Comparative analyses of whole-genome protein sequences from multiple organisms
title_short	Comparative analyses of whole-genome protein sequences from multiple organisms
title_full	Comparative analyses of whole-genome protein sequences from multiple organisms
title_fullStr	Comparative analyses of whole-genome protein sequences from multiple organisms
title_full_unstemmed	Comparative analyses of whole-genome protein sequences from multiple organisms
title_sort	comparative analyses of whole-genome protein sequences from multiple organisms
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/16656572c4ac44f09059ab5223ee6e71
work_keys_str_mv	AT makioyokono comparativeanalysesofwholegenomeproteinsequencesfrommultipleorganisms AT soichirousatoh comparativeanalysesofwholegenomeproteinsequencesfrommultipleorganisms AT ayumitanaka comparativeanalysesofwholegenomeproteinsequencesfrommultipleorganisms
_version_	1718393902500675584

Comparative analyses of whole-genome protein sequences from multiple organisms

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