Phylogenomics of 10,575 genomes reveals evolutionary proximity …
Dec 2, 2019 · The tree contains 10,575 evenly distributed bacterial and archaeal genomes, with topology reconstructed using ASTRAL based on individual trees of 381 globally sampled marker genes, and branch...
A standardized bacterial taxonomy based on genome phylogeny ...
Aug 27, 2018 · Sequence-based phylogenetic trees provide a framework for the development of a taxonomy that takes into account both evolutionary relationships and differing rates of evolution.
A rooted phylogeny resolves early bacterial evolution | Science
May 7, 2021 · A rooted bacterial tree is necessary to understand early evolution, but the position of the root is contested. Here, we model the evolution of 11,272 gene families to identify the root, extent of horizontal gene transfer (HGT), and the nature …
Bacterial phyla - Wikipedia
Phylogenetic tree showing the diversity of Bacteria, Archaea, and Eukaryota. [1] . Major lineages are assigned arbitrary colours and named, with well-characterized lineage names, in italics. Lineages lacking an isolated representative are highlighted …
A new view of the tree of life | Nature Microbiology
Apr 11, 2016 · The tree includes 92 named bacterial phyla, 26 archaeal phyla and all five of the Eukaryotic supergroups. Major lineages are assigned arbitrary colours and named, with well-characterized...
Towards a balanced view of the bacterial tree of life
Oct 17, 2017 · To identify SSU rRNA gene sequences of mitochondrial, plastid, archaeal, and eukaryotic origin, a phylogenetic tree was constructed with FastTree2 (version 2.1.9 SSE3, OpenMP) and query sequences on long branches affiliated with Rickettsiales, Cyanobacteria, and Archaea or located between Bacteria and the archaeal outgroup were removed from the ...
Phylogenetic trees of closely related bacterial species and …
Apr 20, 2023 · 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.
Living Trees: High-Quality Reproducible and Reusable …
Nov 12, 2019 · phylogenetic tree, bacteria evolution, high-resolution tree construction. Issue Section: METHODS. Associate Editor: Nicole Perna. Introduction. Phylogenetic analysis is central to understanding evolution, biodiversity, and ecology.
RATIONALE: We reconstructed and rooted the bacterial tree by applying a hierarchical phylo-genomic approach that explicitly uses informa-tion from gene duplications and losses within a genome as well as gene transfers between genomes. This approach allowed us to root the tree without including an archaeal outgroup.
A Systematic Approach to Bacterial Phylogeny Using Order Level …
We present a systematic approach for constructing a phylogenetic tree based on simultaneously clustering the complete proteomes of 360 bacterial species. From the homologous clusters, we identify 49 protein sequences shared by 99% of the organisms to build a tree.