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

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 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

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.

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 Prey range and genome evolution ofHalobacteriovorax marinuspredatory bacteria from an estuary

2017 ◽  
Author(s):  
Brett G. Enos ◽  
Molly K. Anthony ◽  
Joseph A. DeGiorgis ◽  
Laura E. Williams
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Codon Usage ◽  
Genome Evolution ◽  
Genome Analysis ◽  
Regulation Of Gene Expression ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Predatory Bacteria ◽  
The Impact

AbstractBackgroundHalobacteriovoraxare saltwater-adapted predatory bacteria that attack Gram-negative bacteria and therefore may play an important role in shaping microbial communities. To understand the impact ofHalobacteriovoraxon ecosystems and develop them as biocontrol agents, it is important to characterize variation in predation phenotypes such as prey range and investigate the forces impactingHalobacteriovoraxgenome evolution across different phylogenetic distances.ResultsWe isolatedH. marinusBE01 from an estuary in Rhode Island usingVibriofrom the same site as prey. Small, fast-moving attack phase BE01 cells attach to and invade prey cells, consistent with the intraperiplasmic predation strategy ofH. marinustype strain SJ. BE01 is a prey generalist, forming plaques onVibriostrains from the estuary as well asPseudomonasfrom soil andE. coli. Genome analysis revealed that BE01 is very closely related to SJ, with extremely high conservation of gene order and amino acid sequences. Despite this similarity, we identified two regions of gene content difference that likely resulted from horizontal gene transfer. Analysis of modal codon usage frequencies supports the hypothesis that these regions were acquired from bacteria with different codon usage biases compared toHalobacteriovorax. In BE01, one of these regions includes genes associated with mobile genetic elements, such as a transposase not found in SJ and degraded remnants of an integrase occurring as a full-length gene in SJ. The corresponding region in SJ included unique mobile genetic element genes, such as a site-specific recombinase and bacteriophage-related genes not found in BE01. Acquired functions in BE01 include thedndoperon, which encodes a pathway for DNA modification that may protect DNA from nucleases, and a suite of genes involved in membrane synthesis and regulation of gene expression that was likely acquired from anotherHalobacteriovoraxlineage.ConclusionsOur results support previous observations thatHalobacteriovoraxprey on a broad range of Gram-negative bacteria. Genome analysis suggests strong selective pressure to maintain the genome in theH. marinuslineage represented by BE01 and SJ, although our results also provide further evidence that horizontal gene transfer plays an important role in genome evolution in predatory bacteria.

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