Phylogenetic analysis, genome evolution and the rate of gene gain in the Herpesviridae

2007 ◽  
Vol 43 (3) ◽  
pp. 1066-1075 ◽  
Author(s):  
Nan Wang ◽  
Pierre F. Baldi ◽  
Brandon S. Gaut
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Evolution ◽  
Gene Gain

scholarly journals The First Evidence of a Host-to-Parasite Mitochondrial Gene Transfer in Orobanchaceae

2017 ◽  
Vol 59 (1) ◽  
pp. 13-22 ◽  
Author(s):  
Dagmara Kwolek ◽  
Magdalena Denysenko-Bennett ◽  
Grzegorz Góralski ◽  
Magdalena Cygan ◽  
Patryk Mizia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Mitochondrial Genome ◽  
Genome Evolution ◽  
Horizontal Transfer ◽  
Mitochondrial Gene ◽  
Genetic Material ◽  
Parasitic Plants ◽  
Mitochondrial Genes ◽  
Mitochondrial Genome Evolution

AbstractSeveral parasitic plants are known to have acquired mitochondrial genes via a horizontal transfer from their hosts. However, mitochondrial gene transfer in this direction has not yet been found in the parasite-rich family Orobanchaceae. Based on a phylogenetic analysis of the mitochondrialatp6gene in selected species ofOrobanches.l., we provide evidence of a host-to-parasite transfer of this gene inO. coerulescens, which is a Eurasiatic species that parasitisesArtemisia(Asteraceae). We did not find the originalOrobanche atp6gene in this species, which suggests that it has been replaced by a gene that was acquired from Asteraceae. In addition, our data suggest the occurrence of a second HGT event in theatp6sequence – from Asteraceae toPhelipanche. Our results support the view that the transfer of genetic material from hosts to parasites influences the mitochondrial genome evolution in the latter.

scholarly journals Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jaime Iranzo ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin ◽  
Itamar Sela
Keyword(s):  
Homologous Recombination ◽  
Genome Evolution ◽  
Phylogenetic Trees ◽  
Sequence Divergence ◽  
Gene Gain ◽  
Sequence Evolution ◽  
Gene Trees ◽  
Branch Lengths ◽  
Gain And Loss ◽  
Recombination Gene

AbstractBacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation.

scholarly journals Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations

2019 ◽  
Author(s):  
Jaime Iranzo ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin ◽  
Itamar Sela
Keyword(s):  
Homologous Recombination ◽  
Genome Evolution ◽  
Phylogenetic Trees ◽  
Prokaryotic Genome ◽  
Sequence Divergence ◽  
Mechanistic Explanation ◽  
Gene Gain ◽  
Sequence Evolution ◽  
Gene Trees ◽  
Gain And Loss

AbstractEvolution of bacterial and archaeal genomes is a highly dynamic process that involves extensive gain and loss of genes. Therefore, phylogenetic trees of prokaryotes can be constructed both by the traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we found that the terminal branches of gene trees were systematically compressed compared to those of genome trees. Thus, sequence evolution seems to be significantly delayed with respect to genome evolution by gene gain and loss. The extent of this delay widely differs among bacterial and archaeal lineages. We develop and explore mathematical models demonstrating that the delay of sequence divergence can be explained by sequence homogenization that is caused by homologous recombination. Once evolving genomes become isolated by barriers that impede homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. This model of prokaryotic genome evolution gives a mechanistic explanation of our previous finding that archaeal genomes contain a class of genes that turn over rapidly, before significant sequence divergence occurs, and provides a framework for correcting phylogenetic trees, to make them consistent with the dynamics of gene turnover.

Poxvirus genome evolution by gene gain and loss

2005 ◽  
Vol 35 (1) ◽  
pp. 186-195 ◽  
Author(s):  
Austin L. Hughes ◽  
Robert Friedman
Keyword(s):  
Genome Evolution ◽  
Gene Gain ◽  
Poxvirus Genome ◽  
Gain And Loss

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

Nature ◽  
2003 ◽  
Vol 422 (6930) ◽  
pp. 433-438 ◽  
Author(s):  
John E. Bowers ◽  
Brad A. Chapman ◽  
Junkang Rong ◽  
Andrew H. Paterson
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Evolution ◽  
Duplication Events ◽  
Chromosomal Duplication ◽  
Angiosperm Genome

scholarly journals Genome Rearrangement ShapesProchlorococcusEcological Adaptation

2018 ◽  
Vol 84 (17) ◽  
Author(s):  
Wei Yan ◽  
Shuzhen Wei ◽  
Qiong Wang ◽  
Xilin Xiao ◽  
Qinglu Zeng ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Genome Rearrangement ◽  
Marine Ecosystems ◽  
Biogeochemical Cycles ◽  
Ecological Niches ◽  
Gene Gain ◽  
Low Light ◽  
Free Living ◽  
Content Type ◽  
Photosynthetic Microorganism

ABSTRACTProchlorococcusis the most abundant and smallest known free-living photosynthetic microorganism and is a key player in marine ecosystems and biogeochemical cycles.Prochlorococcuscan be broadly divided into high-light-adapted (HL) and low-light-adapted (LL) clades. In this study, we isolated two low-light-adapted clade I (LLI) strains from the western Pacific Ocean and obtained their genomic data. We reconstructedProchlorococcusevolution based on genome rearrangement. Our results showed that genome rearrangement might have played an important role inProchlorococcusevolution. We also found that theProchlorococcusclades with streamlined genomes maintained relatively high synteny throughout most of their genomes, and several regions served as rearrangement hotspots. Backbone analysis showed that different clades shared a conserved backbone but also had clade-specific regions, and the genes in these regions were associated with ecological adaptations.IMPORTANCEProchlorococcus, the most abundant and smallest known free-living photosynthetic microorganism, plays a key role in marine ecosystems and biogeochemical cycles.Prochlorococcusgenome evolution is a fundamental issue related to howProchlorococcusclades adapted to different ecological niches. Recent studies revealed that the gene gain and loss is crucial to the clade differentiation. The significance of our research is that we interpreted theProchlorococcusgenome evolution from the perspective of genome structure and associated the genome rearrangement with theProchlorococcusclade differentiation and subsequent ecological adaptation.

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