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Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes

https://doi.org/10.1101/731091
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s002390010224openalex-snapshot
Defining the Core of Nontransferable Prokaryotic Genes: The Euryarchaeal Core
inferredcites →https://doi.org/10.1007/s00253-018-9120-4openalex-snapshot
Extracellular DNA in natural environments: features, relevance and applications
inferredcites →https://doi.org/10.1016/0025-5564(81)90043-2openalex-snapshot
Comparison of phylogenetic trees
inferredcites →https://doi.org/10.1016/j.margen.2015.08.007openalex-snapshot
Origin, dynamics, and implications of extracellular DNA pools in marine sediments
inferredcites →https://doi.org/10.1038/297197a0openalex-snapshot
Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences
inferredcites →https://doi.org/10.1038/30234openalex-snapshot
Gene transfer to the nucleus and the evolution of chloroplasts
inferredcites →https://doi.org/10.1038/90129openalex-snapshot
Universal trees based on large combined protein sequence data sets
inferredcites →https://doi.org/10.1038/nature14447openalex-snapshot
Complex archaea that bridge the gap between prokaryotes and eukaryotes
inferredcites →https://doi.org/10.1038/nature21031openalex-snapshot
Asgard archaea illuminate the origin of eukaryotic cellular complexity
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.48openalex-snapshot
A new view of the tree of life
inferredcites →https://doi.org/10.1038/s41559-017-0126openalex-snapshot
Contentious relationships in phylogenomic studies can be driven by a handful of genes
inferredcites →https://doi.org/10.1038/s41559-020-1239-xopenalex-snapshot
Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria
inferredcites →https://doi.org/10.1038/s41586-018-0548-6openalex-snapshot
Genomes of Asgard archaea encode profilins that regulate actin
inferredcites →https://doi.org/10.1038/s41598-017-05590-9openalex-snapshot
Climate oscillations reflected within the microbiome of Arabian Sea sediments
inferredcites →https://doi.org/10.1073/pnas.1209119109openalex-snapshot
Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea
inferredcites →https://doi.org/10.1080/10635150701472164openalex-snapshot
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
inferredcites →https://doi.org/10.1080/10635159950173825openalex-snapshot
Invariable Sites Models and Their Use in Phylogeny Reconstruction
inferredcites →https://doi.org/10.1093/bioinformatics/bti720openalex-snapshot
A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
inferredcites →https://doi.org/10.1093/molbev/msh018openalex-snapshot
Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks
inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a004122openalex-snapshot
Archaeal Phylogeny Based on Ribosomal Proteins
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040126openalex-snapshot
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates.
inferredcites →https://doi.org/10.1093/sysbio/49.2.225openalex-snapshot
Invariable Sites Models and Their Use in Phylogeny Reconstruction
inferredcites →https://doi.org/10.1093/sysbio/syu085openalex-snapshot
Practical Performance of Tree Comparison Metrics
inferredcites →https://doi.org/10.1099/00207713-50-4-1655openalex-snapshot
Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis.
inferredcites →https://doi.org/10.1101/726976openalex-snapshot
Isolation of an archaeon at the prokaryote-eukaryote interface
inferredcites →https://doi.org/10.1101/gr.187002openalex-snapshot
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
inferredcites →https://doi.org/10.1126/sciadv.aaw4108openalex-snapshot
Archaea dominate oxic subseafloor communities over multimillion-year time scales
inferredcites →https://doi.org/10.1126/science.1117475openalex-snapshot
Extracellular DNA Plays a Key Role in Deep-Sea Ecosystem Functioning
inferredcites →https://doi.org/10.1128/aem.62.11.4147-4154.1996openalex-snapshot
Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria
inferredcites →https://doi.org/10.1128/mmbr.00008-17openalex-snapshot
The Physiology of Phagocytosis in the Context of Mitochondrial Origin
inferredcites →https://doi.org/10.1186/1471-2148-10-210openalex-snapshot
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
inferredcites →https://doi.org/10.1371/journal.pgen.1006810openalex-snapshot
Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes
inferredcites →https://doi.org/10.1371/journal.pgen.1007080openalex-snapshot
Asgard archaea are the closest prokaryotic relatives of eukaryotes
inferredcites →https://doi.org/10.1371/journal.pgen.1007215openalex-snapshot
Asgard archaea do not close the debate about the universal tree of life topology
inferredcites →https://doi.org/10.2307/1218253openalex-snapshot
ON THE COMPARISON OF TWO CLASSIFICATIONS OF THE SAME SET OF ELEMENTS
inferredcites →https://doi.org/10.4319/lo.2002.47.3.0899openalex-snapshot
Quantification, base composition, and fate of extracellular DNA in marine sediments

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/gbe/evab085openalex-snapshot
The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3%
inferred← citeshttps://doi.org/10.1101/2019.12.17.879148openalex-snapshot
Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses
inferred← citeshttps://doi.org/10.1101/gr.258640.119openalex-snapshot
Accurate and complete genomes from metagenomes
inferred← citeshttps://doi.org/10.1186/s12866-020-1707-0openalex-snapshot
Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea
inferred← citeshttps://doi.org/10.1186/s13059-019-1923-9openalex-snapshot
Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
inferred← citeshttps://doi.org/10.21203/rs.3.rs-16808/v1openalex-snapshot
A hot spring Asgard archaeon sheds light on the origin of eukaryotic endosomal system.
inferred← citeshttps://doi.org/10.70675/0b6a9095z5dfaz4dd3zbc18z8dabe66a4e67openalex-snapshot
Recherche de séquences environnementales inconnues d’intérêt médical/biologique par l’utilisation de grands réseaux de similarité de séquences
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