Genome phylogeny based on gene content

@article{Snel1999GenomePB,
  title={Genome phylogeny based on gene content},
  author={Berend Snel and Peer Bork and Martijn A. Huynen},
  journal={Nature Genetics},
  year={1999},
  volume={21},
  pages={108-110}
}
Species phylogenies derived from comparisons of single genes are rarely consistent with each other, due to horizontal gene transfer, unrecognized paralogy and highly variable rates of evolution. The advent of completely sequenced genomes allows the construction of a phylogeny that is less sensitive to such inconsistencies and more representative of whole-genomes than are single-gene trees. Here, we present a distance-based phylogeny constructed on the basis of gene content, rather than on… 

Figures, Tables, and Topics from this paper

Phylogenetic tree inference from local gene content
TLDR
A practical approach for measuring local gene conservation in two genomes is developed, which appears to be substantially resistant to the observed instances of gene loss and horizontal transfer, two evolutionary forces which can cause systematic biases in the genome-based phylogenies.
GO4genome: A Prokaryotic Phylogeny Based on Genome Organization
TLDR
GO4genome is a new paradigm, which is based on a detailed analysis of gene function and the location of the respective genes, and uses gene ontology enabling a comparison of function independent of evolutionary relationship.
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history.
TLDR
An attempt to use a supertree method to build the phylogenetic tree of 45 organisms, with special focus on bacterial phylogeny, by performing a phylogenetic study of congruence of tree topologies, which allows the identification of a core of genes supporting similar species phylogeny.
A Distance Measure for Genome Phylogenetic Analysis
TLDR
An information theoretic measure of genetic distances between genomes based on the biological compression algorithm expert model is presented and it is demonstrated that this distance measure can be applied to reconstruct the consensus phylogenetic tree of a number of Plasmodium parasites from their genomes.
Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology.
TLDR
The poor performance of gene family content-based phylogenetic analysis in the case of prokaryotes appears to reflect high levels of homoplasy resulting not only from horizontal gene transfer but also, more importantly, from extensive parallel loss of gene families in certain bacteria genomes.
Prokaryotic Phylogenies Inferred from Whole-Genome Sequence and Annotation Data
TLDR
Simulation results show that CGCPhy achieves high average accuracy and has a low standard deviation on different datasets, so it has an applicative potential for phylogenetic analysis.
Bacterial molecular phylogeny using supertree approach.
TLDR
A new method based on supertree construction is used, which permits to cumulate in one supertree the information and statistical support of hundreds of trees from orthologous gene families and to build the phylogeny of 33 prokaryotes and four eukaryotes with completely sequenced genomes, which demonstrates that a phylogenY of proKaryotic species is conceivable and challenges the hypothesis of a thermophilic origin of bacteria and present-day life.
Baculovirus Phylogeny Based on Genome Rearrangements
TLDR
A gene rearrangement-based approach to study Baculovirus phylogeny results in phylogenetic relationships that are largely consistent with conventional gene-based approaches, with some differences that provide insight into the rearrangements of BacULoviridae genomes.
Whole-genome prokaryotic clustering based on gene lengths
TLDR
A novel method of taxonomic analysis, constructed on the basis of gene content and lengths of orthologous genes of 66 completely sequenced genomes of unicellular organisms using Clusters of Orthologous Groups (COGs).
Phylogenetic analyses of phylum Actinobacteria based on whole genome sequences.
TLDR
The present investigation clearly revealed that the consensus approach is a useful tool for phylogenetic inference and theTaxonomic affiliations must be based on this approach and there is a need for taxonomic amendments of the orders Frankiales and Micrococcales.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 39 REFERENCES
Measuring genome evolution.
  • M. Huynen, P. Bork
  • Biology, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
A hierarchy of rates at which genomes have changed during evolution is established and it is shown that some genomes are more highly organized than others: they show a higher degree of the clustering of genes that have orthologs in other genomes.
The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny.
TLDR
It is found that a combined data set of EF-Tu and EF-G sequences favors placement of the eukaryotes within the Archaea, as the sister group to the Crenarchaeota.
A genomic perspective on protein families.
TLDR
Comparison of proteins encoded in seven complete genomes from five major phylogenetic lineages and elucidation of consistent patterns of sequence similarities allowed the delineation of 720 clusters of orthologous groups (COGs), which comprise a framework for functional and evolutionary genome analysis.
Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.
TLDR
The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced and a functional classification to a large number of ORFs is tentatively assigned and the biochemical and physiological properties of this bacterium are deduced.
Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics
The complete 1,751,377-bp sequence of the genome of the thermophilic archaeon Methanobacterium thermoautotrophicum deltaH has been determined by a whole-genome shotgun sequencing approach. A total of
Differential genome analysis applied to the species‐specific features of Helicobacter pylori
TLDR
It is hypothesized that a family of outer membrane proteins is critical for the ability of H. pylori to colonize host cells in highly acidic environments.
Comparative analysis of the genomes of the bacteria Mycoplasma pneumoniae and Mycoplasma genitalium.
TLDR
The sequenced genomes of the two closely related bacteria MyCoplasma genitalium and Mycoplasma pneumoniae were compared with emphasis on genome organization and coding capacity and it is explained the different organization of the segments by translocation via homologous recombination.
The winds of (evolutionary) change: breathing new life into microbiology.
TLDR
The split between the Archaea and the Bacteria is now recognized as the primary phylogenetic division and that the Eucarya have branched from the same side of the tree as the archaea.
Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions.
  • T. Kaneko, S. Sato, +21 authors S. Tabata
  • Medicine, Biology
    DNA research : an international journal for rapid publication of reports on genes and genomes
  • 1996
The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously
Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions (supplement).
  • T. Kaneko, S. Sato, +21 authors S. Tabata
  • Biology, Medicine
    DNA research : an international journal for rapid publication of reports on genes and genomes
  • 1996
The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously
...
1
2
3
4
...