Prediction of horizontal gene transfers in eukaryotes: approaches and challenges

2009 ◽  
Vol 37 (4) ◽  
pp. 792-795 ◽  
Author(s):  
John W. Whitaker ◽  
Glenn A. McConkey ◽  
David R. Westhead
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Present Review ◽  
Bacterial Evolution ◽  
Eukaryotic Evolution ◽  
Metabolic Evolution ◽  
Eukaryotic Genomes

HGT (horizontal gene transfer) is recognized as an important force in bacterial evolution. Now that many eukaryotic genomes have been sequenced, it has become possible to carry out studies of HGT in eukaryotes. The present review compares the different approaches that exist for identifying HGT genes and assess them in the context of studying eukaryotic evolution. The metabolic evolution resource metaTIGER is then described, with discussion of its application in identification of HGT in eukaryotes.

Horizontal gene transfer in eukaryotic evolution

2008 ◽  
Vol 9 (8) ◽  
pp. 605-618 ◽  
Author(s):  
Patrick J. Keeling ◽  
Jeffrey D. Palmer
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Eukaryotic Evolution

scholarly journals SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes

2013 ◽  
Vol 30 (8) ◽  
pp. 1081-1086 ◽  
Author(s):  
K. S. Jaron ◽  
J. C. Moravec ◽  
N. Martinkova
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Eukaryotic Genomes

scholarly journals Beyond horizontal gene transfer: the role of plasmids in bacterial evolution

2021 ◽  
Author(s):  
Jerónimo Rodríguez-Beltrán ◽  
Javier DelaFuente ◽  
Ricardo León-Sampedro ◽  
R. Craig MacLean ◽  
Álvaro San Millán
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Evolution

scholarly journals Widespread Horizontal Gene Transfer from Circular Single-stranded DNA Viruses to Eukaryotic Genomes

2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Huiquan Liu ◽  
Yanping Fu ◽  
Bo Li ◽  
Xiao Yu ◽  
Jiatao Xie ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Eukaryotic Genomes

scholarly journals Parasitism-evoked horizontal gene transfer between plants as a novel trigger for specialized metabolism evolution

2021 ◽  
Author(s):  
Eiichiro Ono ◽  
Kohki Shimizu ◽  
Jun Murata ◽  
Akira Shiraishi ◽  
Ryusuke Yokoyama ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Host Plants ◽  
Molecular Mechanisms ◽  
Sequence Similarity ◽  
Metabolic Evolution ◽  
Apparent Lack ◽  
Cuscuta Campestris ◽  
Genomic Studies ◽  
Biological Impacts

Abstract Recent genomic studies of parasitic plants have revealed that there are numerous footprints indicative of horizontal gene transfer (HGT) to the parasites from their host plants. However, the molecular mechanisms and biological impacts of this phenomenon have remained largely unknown. Here, we made the striking observation that two parasitic dodders, Cuscuta campestris and C. australis, have functional homologues of Si_CYP81Q1, which encodes piperitol/sesamin synthase (PSS) in the phylogenetically remote plant Sesamum indicum (sesame). The apparent lack of sequence similarity between the regions flanking PSS in Sesamum and Cuscuta spp. suggests the occurrence of HGT tightly associated with the PSS gene. Upon parasitism, C. campestris induced expression of the host Si_CYP81Q1 at the parasitic interface and mature and intron-retained Si_CYP81Q1 mRNA was transferred to C. campestris, suggesting that CYP81Q1 was translocated via RNA-mediated HGT. Thus, parasitism-evoked HGT might have had an unexpected role in the metabolic evolution of plants.

scholarly journals Horizontal Gene Transfers from Bacteria toEntamoebaComplex: A Strategy for Dating Events along Species Divergence

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Miguel Romero ◽  
R. Cerritos ◽  
Cecilia Ximenez
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Entamoeba Histolytica ◽  
Lateral Gene Transfer ◽  
Adaptive Radiation ◽  
Fossil Record ◽  
Evolutionary History ◽  
Divergence Time ◽  
Eukaryotic Evolution ◽  
History Of

Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasiteEntamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genusEntamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of someEntamoebaspecies was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence betweenE. histolyticaandE. nuttalliiprobably occurred 5.93 million years ago (Mya); this lineage diverged fromE. dispar9.97 Mya, while the ancestor of the latter separated fromE. invadens68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of theEntamoebagenus.

scholarly journals Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution

2004 ◽  
Vol 186 (19) ◽  
pp. 6575-6585 ◽  
Author(s):  
Pavel S. Novichkov ◽  
Marina V. Omelchenko ◽  
Mikhail S. Gelfand ◽  
Andrei A. Mironov ◽  
Yuri I. Wolf ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Orthologous Gene ◽  
Statistical Technique ◽  
Bacterial Evolution ◽  
Gene Sets ◽  
Genome Wide ◽  
Straight Line ◽  
Genome Scale ◽  
Bacterial Lineages

ABSTRACT We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. The approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. Under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straight line. A statistical technique to identify significant deviations from the clock-like behavior is described. For several hundred analyzed orthologous sets representing three well-defined bacterial lineages, the α-Proteobacteria, the γ-Proteobacteria, and the Bacillus-Clostridium group, the clock-like null hypothesis could not be rejected for ∼70% of the sets, whereas the rest showed substantial anomalies. Subsequent detailed phylogenetic analysis of the genes with the strongest deviations indicated that over one-half of these genes probably underwent a distinct form of horizontal gene transfer, xenologous gene displacement, in which a gene is displaced by an ortholog from a different lineage. The remaining deviations from the clock-like model could be explained by lineage-specific acceleration of evolution. The results indicate that although xenologous gene displacement is a major force in bacterial evolution, a significant majority of orthologous gene sets in three major bacterial lineages evolved in accordance with the clock-like model. The approach described here allows rapid detection of deviations from this mode of evolution on the genome scale.

scholarly journals The proficiency of the original host species determines community-level plasmid dynamics

2020 ◽  
Author(s):  
Anastasia Kottara ◽  
James P.J. Hall ◽  
Michael A. Brockhurst
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Host Species ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Community Level ◽  
Mercury Resistance ◽  
Bacterial Evolution ◽  
Selection For ◽  
Selective Environment

ABSTRACTPlasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: Whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency affects plasmid persistence in communities. Here, we test this using multispecies bacterial soil communities comprising species varying in their proficiency to host a large conjugative mercury resistance plasmid. Plasmids reached higher community-level abundance where beneficial and when introduced to the community in a more proficient host species. Proficient plasmid host species were also better able to disseminate the plasmid to a wider diversity of host species. These findings suggest that the dynamics of plasmids in natural bacterial communities depend not only upon the plasmid’s attributes and the selective environment, but also upon the proficiency of their host species.

scholarly journals Specificity and selective advantage of an exclusion system in the integrative and conjugative element ICEBs1 of Bacillus subtilis

2021 ◽  
Author(s):  
Kathleen P. Davis ◽  
Alan D. Grossman
Keyword(s):  
Bacillus Subtilis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Cell Envelope ◽  
Donor Cell ◽  
High Specificity ◽  
Host Cells ◽  
Cell Contact ◽  
Bacterial Evolution ◽  
Potential Donor

AbstractIntegrative and conjugative elements (ICEs) are mobile genetic elements capable of transferring their own and other DNA. They contribute to the spread of antibiotic resistances and other important traits for bacterial evolution. Exclusion is a mechanism used by many conjugative plasmids and a few ICEs to prevent their host cell from acquiring a second copy of the cognate element. ICEBs1 of Bacillus subtilis has an exclusion mechanism whereby the exclusion protein YddJ in a potential recipient inhibits the activity of the ICEBs1-encoded conjugation machinery in a potential donor. The target of YddJ-mediated exclusion is the conjugation protein ConG (a VirB6 homolog). Here we defined the regions of YddJ and ConG that confer exclusion specificity and determined the importance of exclusion to host cells. Using chimeras that had parts of ConG from ICEBs1 and the closely related ICEBat1 we identified a putative extracellular loop of ConG that conferred specificity for exclusion by the cognate YddJ. Using chimeras of YddJ from ICEBs1 and ICEBat1 we identified two regions in YddJ needed for exclusion specificity. We also found that YddJ-mediated exclusion reduced death of donor cells following conjugation into recipients. Donor death was dependent on the ability of transconjugants to themselves become donors and was reduced under osmo-protective conditions, indicating that death was likely due to alterations in the donor cell envelope caused by excessive conjugation. We postulate that elements that can have high frequencies of transfer likely evolved exclusion mechanisms to protect the host cells from excessive death.ImportanceHorizontal gene transfer is a driving force in bacterial evolution, responsible for the spread of many traits, including antibiotic and heavy metal resistances. Conjugation, one type of horizontal gene transfer, involves DNA transfer from donor to recipient cells through conjugation machinery and direct cell-cell contact. Exclusion mechanisms allow conjugative elements to prevent their host from acquiring additional copies of the element, and are highly specific enabling hosts to acquire heterologous elements. We defined regions of the exclusion protein and its target in the conjugation machinery that convey high specificity of exclusion. We found that exclusion protects donors from cell death during periods of high transfer. This is likely important for the element to enter new populations of cells.

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