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Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
TLDR
It is shown that in the unicellular eukaryote Paramecium tetraurelia, a ciliate, most of the nearly 40,000 genes arose through at least three successive whole-genome duplications. Expand
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria
TLDR
The analysis indicates that single-copy orthologous genes are resistant to horizontal transfer, even in ancient bacterial groups subject to high rates of LGT, thus establishing a foundation for reconstructing the evolutionary transitions that underlie diversity in genome content and organization. Expand
Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli.
TLDR
By identifying sequences unique to monophyletic groups at increasing phylogenetic depths, this work can make direct comparisons of the characteristics of ORFans of different ages in the Escherichia coli genome, and establish their functional status and evolutionary rates. Expand
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
TLDR
The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses. Expand
Evolutionary Origins of Genomic Repertoires in Bacteria
TLDR
An exhaustive analysis of gene phylogenies for all gene families in a widely sampled group, the γ-Proteobacteria, shows that, although these bacterial genomes display striking differences in gene repertoires, most gene families having representatives in several species have congruent histories. Expand
The source of laterally transferred genes in bacterial genomes
TLDR
It is shown that contrary to what is often supposed, these genes fit the description of recently described genes in lambdoid phages, named 'morons', and should not be cited as evidence for genetic exchange between distantly related bacteria. Expand
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. Expand
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations.
TLDR
New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism. Expand
Genome-scale coestimation of species and gene trees.
TLDR
A new probabilistic model is presented to jointly infer rooted species and gene trees for dozens of genomes and thousands of gene families and yields a more accurate picture of ancestral genomes than the trees available in the authoritative database Ensembl. Expand
Models, algorithms and programs for phylogeny reconciliation
TLDR
Reconciliations between gene and species trees are reviewed, which are rigorous approaches for identifying duplications, transfers and losses that mark the evolution of a gene family. Expand
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