scholarly journals Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes

2021 ◽  
Vol 118 (4) ◽  
pp. e2009974118
Author(s):  
Richard G. Dorrell ◽  
Adrien Villain ◽  
Benoît Perez-Lamarque ◽  
Guillemette Audren de Kerdrel ◽  
Giselle McCallum ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Large Scale ◽  
Single Gene ◽  
Gene Trees ◽  
Reference Tree ◽  
In Silico Modeling ◽  
Genes Encoding ◽  
Eukaryotic Genomes ◽  
Algal Evolution

Horizontal gene transfer (HGT) is an important source of novelty in eukaryotic genomes. This is particularly true for the ochrophytes, a diverse and important group of algae. Previous studies have shown that ochrophytes possess a mosaic of genes derived from bacteria and eukaryotic algae, acquired through chloroplast endosymbiosis and from HGTs, although understanding of the time points and mechanisms underpinning these transfers has been restricted by the depth of taxonomic sampling possible. We harness an expanded set of ochrophyte sequence libraries, alongside automated and manual phylogenetic annotation, in silico modeling, and experimental techniques, to assess the frequency and functions of HGT across this lineage. Through manual annotation of thousands of single-gene trees, we identify continuous bacterial HGT as the predominant source of recently arrived genes in the model diatom Phaeodactylum tricornutum. Using a large-scale automated dataset, a multigene ochrophyte reference tree, and mathematical reconciliation of gene trees, we note a probable elevation of bacterial HGTs at foundational points in diatom evolution, following their divergence from other ochrophytes. Finally, we demonstrate that throughout ochrophyte evolutionary history, bacterial HGTs have been enriched in genes encoding secreted proteins. Our study provides insights into the sources and frequency of HGTs, and functional contributions that HGT has made to algal evolution.

scholarly journals Systematic Detection of Large-Scale Multi-Gene Horizontal Transfer in Prokaryotes

2021 ◽  
Author(s):  
Lina Kloub ◽  
Sean Gosselin ◽  
Matthew Fullmer ◽  
Joerg Graf ◽  
J Peter Gogarten ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Large Scale ◽  
Single Gene ◽  
Gene Families ◽  
Microbial Evolution ◽  
Phylogenetic Distance ◽  
Secretion Systems ◽  
Type Iii Secretion Systems ◽  
A Genome ◽  
Conserved Gene

Abstract Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multi-gene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale dataset of over 22000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multi-gene transfer. Among other insights, we find that (i) the observed relative frequency of HMGT increases as divergence between genomes increases, (ii) HMGTs often have conserved gene functions, and (iii) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.

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.

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 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 Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

2009 ◽  
Vol 364 (1527) ◽  
pp. 2229-2239 ◽  
Author(s):  
Gregory P. Fournier ◽  
Jinling Huang ◽  
J. Peter Gogarten
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Gene Trees ◽  
Individual Gene ◽  
Evolution Of Life ◽  
Domains Of Life ◽  
Life On Earth ◽  
Simple Tree

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

Antimicrobial resistance: its emergence and transmission

2008 ◽  
Vol 9 (2) ◽  
pp. 115-126 ◽  
Author(s):  
Patrick Boerlin ◽  
Richard J. Reid-Smith
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Dna Sequencing ◽  
Large Scale ◽  
Mutant Selection ◽  
The Past ◽  
New Concepts ◽  
Selection Window ◽  
Integrative Conjugative Elements

AbstractNew concepts have emerged in the past few years that help us to better understand the emergence and spread of antimicrobial resistance (AMR). These include, among others, the discovery of the mutator state and the concept of mutant selection window for resistances emerging primarily through mutations in existing genes. Our understanding of horizontal gene transfer has also evolved significantly in the past few years, and important new mechanisms of AMR transfer have been discovered, including, among others, integrative conjugative elements and ISCR(insertionsequences withcommonregions) elements. Simultaneously, large-scale studies have helped us to start comprehending the immense and yet untapped reservoir of both AMR genes and mobile genetic elements present in the environment. Finally, new PCR- and DNA sequencing-based techniques are being developed that will allow us to better understand the epidemiology of classical vectors of AMR genes, such as plasmids, and to monitor them in a more global and systematic way.

scholarly journals Novel 4-Chlorophenol Degradation Gene Cluster and Degradation Route via Hydroxyquinol in Arthrobacter chlorophenolicus A6

2005 ◽  
Vol 71 (11) ◽  
pp. 6538-6544 ◽  
Author(s):  
Karolina Nordin ◽  
Maria Unell ◽  
Janet K. Jansson
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Cluster ◽  
Microbial Degradation ◽  
Codon Bias ◽  
Sequence Similarity ◽  
Open Reading Frames ◽  
Genes Encoding ◽  
Arthrobacter Chlorophenolicus ◽  
Reading Frames

ABSTRACT Arthrobacter chlorophenolicus A6, a previously described 4-chlorophenol-degrading strain, was found to degrade 4-chlorophenol via hydroxyquinol, which is a novel route for aerobic microbial degradation of this compound. In addition, 10 open reading frames exhibiting sequence similarity to genes encoding enzymes involved in chlorophenol degradation were cloned and designated part of a chlorophenol degradation gene cluster (cph genes). Several of the open reading frames appeared to encode enzymes with similar functions; these open reading frames included two genes, cphA-I and cphA-II, which were shown to encode functional hydroxyquinol 1,2-dioxygenases. Disruption of the cphA-I gene yielded a mutant that exhibited negligible growth on 4-chlorophenol, thereby linking the cph gene cluster to functional catabolism of 4-chlorophenol in A. chlorophenolicus A6. The presence of a resolvase pseudogene in the cph gene cluster together with analyses of the G+C content and codon bias of flanking genes suggested that horizontal gene transfer was involved in assembly of the gene cluster during evolution of the ability of the strain to grow on 4-chlorophenol.

scholarly journals Extensive Phenotypic Changes Associated with Large-scale Horizontal Gene Transfer

2013 ◽  
Author(s):  
Kevin Dougherty ◽  
Brian A Smith ◽  
Autum F Moore ◽  
Shannon Maitland ◽  
Chris Fanger ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Large Scale ◽  
Pseudomonas Stutzeri ◽  
Transfer Event ◽  
Small Plasmid ◽  
Phenotypic Changes ◽  
Evolutionary Trajectories ◽  
Evolutionary Consequences

Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e. changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmid and phage, little is known about how size of the acquired region affects the magnitude or number of such costs. Here we describe an amazing breadth of phenotypic changes which occur after a large-scale horizontal transfer event (~1Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.

scholarly journals A Comprehensive Classification of Coronaviruses and Inferred Cross-Host Transmissions

2020 ◽  
Author(s):  
Yiran Fu ◽  
Marco Pistolozzi ◽  
Xiaofeng Yang ◽  
Zhanglin Lin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Classification Scheme ◽  
Gene Trees ◽  
Robust Classification ◽  
Protein Clusters ◽  
Comprehensive Classification

AbstractIn this work, we present a unified and robust classification scheme for coronaviruses based on concatenated protein clusters. This subsequently allowed us to infer the apparent “horizontal gene transfer” events via reconciliation with the corresponding gene trees, which we argue can serve as a marker for cross-host transmissions. The cases of SARS-CoV, MERS-CoV, and SARS-CoV-2 are discussed. Our study provides a possible technical route to understand how coronaviruses evolve and are transmitted to humans.

scholarly journals Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes

2019 ◽  
Vol 116 (12) ◽  
pp. 5613-5622 ◽  
Author(s):  
David S. Milner ◽  
Victoria Attah ◽  
Emily Cook ◽  
Finlay Maguire ◽  
Fiona R. Savory ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Fitness Landscape ◽  
Single Gene ◽  
Transporter Gene ◽  
Metabolic Potential ◽  
Gene Acquisition ◽  
A Genome ◽  
Complex Polymers ◽  
Encoding Genes

Many microbes acquire metabolites in a “feeding” process where complex polymers are broken down in the environment to their subunits. The subsequent uptake of soluble metabolites by a cell, sometimes called osmotrophy, is facilitated by transporter proteins. As such, the diversification of osmotrophic microorganisms is closely tied to the diversification of transporter functions. Horizontal gene transfer (HGT) has been suggested to produce genetic variation that can lead to adaptation, allowing lineages to acquire traits and expand niche ranges. Transporter genes often encode single-gene phenotypes and tend to have low protein–protein interaction complexity and, as such, are potential candidates for HGT. Here we test the idea that HGT has underpinned the expansion of metabolic potential and substrate utilization via transfer of transporter-encoding genes. Using phylogenomics, we identify seven cases of transporter-gene HGT between fungal phyla, and investigate compatibility, localization, function, and fitness consequences when these genes are expressed inSaccharomyces cerevisiae. Using this approach, we demonstrate that the transporters identified can alter how fungi utilize a range of metabolites, including peptides, polyols, and sugars. We then show, for one model gene, that transporter gene acquisition by HGT can significantly alter the fitness landscape ofS. cerevisiae. We therefore provide evidence that transporter HGT occurs between fungi, alters how fungi can acquire metabolites, and can drive gain in fitness. We propose a “transporter-gene acquisition ratchet,” where transporter repertoires are continually augmented by duplication, HGT, and differential loss, collectively acting to overwrite, fine-tune, and diversify the complement of transporters present in a genome.

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