scholarly journals Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile “Ferrovum”

2016 ◽  
Vol 7 ◽  
Author(s):  
Sophie R. Ullrich ◽  
Carolina González ◽  
Anja Poehlein ◽  
Judith S. Tischler ◽  
Rolf Daniel ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution ◽  
Gene Loss

Archaeal integrases and mechanisms of gene capture

2004 ◽  
Vol 32 (2) ◽  
pp. 222-226 ◽  
Author(s):  
Q. She ◽  
B. Shen ◽  
L. Chen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution ◽  
Trna Genes ◽  
Gene Fragment ◽  
Integrase Gene ◽  
Site Specific ◽  
Conjugative Plasmids ◽  
Site Specific Integration ◽  
Target Sites

Archaeal integrases facilitate the formation of two distinctive types of integrated element within archaeal chromosomes: the SSV type and pNOB8 type. The former carries a smaller N-terminal and a larger C-terminal integrase gene fragment, and the latter an intact integrase gene. All integrated elements overlap tRNA genes that were target sites for integration. It has been demonstrated that SSV (Sulfolobus spindle virus) viruses, carrying an SSV-type integrase gene, and conjugative plasmids, carrying a pNOB8-type integrase, are integrative elements. Two mechanisms have been proposed for stably maintaining an integrated element within archaeal chromosomes. There is also evidence for changes having occurred in the captured integrated elements present in archaeal genomes. Thus we infer that site-specific integration constitutes an important mechanism for horizontal gene transfer and genome evolution.

scholarly journals Horizontal gene transfer and genome evolution in Methanosarcina

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Sofya K. Garushyants ◽  
Marat D. Kazanov ◽  
Mikhail S. Gelfand
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution

scholarly journals Shared transcriptional control and disparate gain and loss of aphid parasitism genes and loci acquired via horizontal gene transfer

2018 ◽  
Author(s):  
Peter Thorpe ◽  
Carmen M. Escudero-Martinez ◽  
Peter J. A. Cock ◽  
D. Laetsch ◽  
Sebastian Eves-van den Akker ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Duplication ◽  
Host Range ◽  
Genome Evolution ◽  
Transcriptional Control ◽  
Control Mechanism ◽  
Aphid Species ◽  
Gain And Loss ◽  
Genome Assemblies

AbstractBackgroundAphids are a diverse group of taxa that contain hundreds of agronomically important species, which vary in their host range and pathogenicity. However, the genome evolution underlying agriculturally important aphid traits is not well understood.ResultsWe generated highly-contiguous draft genome assemblies for two aphid species: the narrow host range Myzus cerasi, and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these genome assemblies, and those of three related species (Acyrthosiphon pisum, D. noxia and M. persicae), we show that aphid genomes consistently encode similar gene numbers, and in the case of A. pisum, fewer and larger genes than previously reported. We compare gene content, gene duplication, synteny, horizontal gene transfer events, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites.Aphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth, and are characterized by disparate gain and loss of genes acquired by horizontal gene transfer (HGT). Such HGT events account for approximately 1% of loci, and contribute to the protein-coding content of aphid species analysed. Putative effector repertoires, originating from duplicated loci, putative HGT events and other loci, have an unusual genomic organisation and evolutionary history. We identify a highly conserved effector-pair that is tightly genetically-linked in all aphid species. In R. padi, this effector pair is tightly transcriptionally-linked, and shares a transcriptional control mechanism with a subset of approximately 50 other putative effectors distributed across the genome.ConclusionsThis study extends our current knowledge on the evolution of aphid genomes and reveals evidence for a shared control mechanism, which underlies effector expression, and ultimately plant parasitism.

Horizontal Gene Transfer in Microbial Genome Evolution

2002 ◽  
Vol 61 (4) ◽  
pp. 489-495 ◽  
Author(s):  
Ravi Jain ◽  
Maria C. Rivera ◽  
Jonathan E. Moore ◽  
James A. Lake
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution ◽  
Microbial Genome

scholarly journals Horizontal gene transfer barrier shapes the evolution of prokaryotic pangenomes

2020 ◽  
Author(s):  
Itamar Sela ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Evolution ◽  
Genome Size ◽  
Bacterial Genomes ◽  
Prokaryotic Genomes ◽  
Simplifying Assumptions ◽  
Specific Shape ◽  
Foreign Genes ◽  
The Cost

AbstractThe genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. To elucidate the evolutionary factors that define the specific shape of this distribution, we investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genomes intersections for 33 groups of closely related bacterial genomes. The combined analysis of genome intersections and gene commonality shows that at least one of the two simplifying assumptions that are usually adopted for modeling the evolution of the U-shaped distribution, those of infinitely many genes and constant genome size, is invalid. The violation of both these assumptions stems from the horizontal gene transfer barrier, i.e. the cost of accommodation of foreign genes by prokaryotes.

scholarly journals Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

2017 ◽  
Vol 83 (7) ◽  
Author(s):  
Xian Zhang ◽  
Xueduan Liu ◽  
Yili Liang ◽  
Xue Guo ◽  
Yunhua Xiao ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Adaptive Evolution ◽  
Gene Loss ◽  
Environmental Changes ◽  
Driving Forces ◽  
Critical Force ◽  
Phylogenomic Analysis ◽  
Content Type ◽  
Microbial Genomes

ABSTRACT Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillus thermosulfidooxidans. Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains. IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.

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