ArticleScientific reports2018
Comparative analyses of whole-genome protein sequences from multiple organisms.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Complete mitochondrial genome characterization of the haemosporidian parasiteCurrent research in parasitology & vector-borne diseases · 2026Article
- The Gut Microbiota of Peruvian Children Under the Age of Two During the Complementary Feeding Period.International journal of environmental research and public health · 2025Article
- Use of Field pathogenomics approach for Puccinia striiformis f. sp. tritici race identification and phylogenomic delineation in North India.World journal of microbiology & biotechnology · 2025Article
- From gut to liver: unveiling the differences of intestinal microbiota in NAFL and NASH patients.Frontiers in microbiology · 2024Article
- Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota.PloS one · 2023Article
- Characteristic alterations of gut microbiota in uncontrolled gout.Journal of microbiology (Seoul, Korea) · 2022Article
- A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders.Applied microbiology and biotechnology · 2022Article
- Potential autotrophic carbon-fixer and Fe(II)-oxidizerFrontiers in microbiology · 2022Article
- Differences in the Composition of Gut Microbiota between Patients with Parkinson's Disease and Healthy Controls: A Cohort Study.Journal of clinical medicine · 2021Article
- Article
- Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the FamilyFrontiers in microbiology · 2021Article
- Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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