scholarly journals Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes

2019 ◽  
Vol 11 (10) ◽  
pp. 2750-2766 ◽  
Author(s):  
Gavin M Douglas ◽  
Morgan G I Langille
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
De Novo ◽  
Antibiotic Resistance Genes ◽  
Gene Families ◽  
Gene Gain ◽  
Loss Of Function ◽  
Shotgun Metagenomics ◽  
Gain And Loss ◽  
Natural Communities

Abstract High-throughput shotgun metagenomics sequencing has enabled the profiling of myriad natural communities. These data are commonly used to identify gene families and pathways that were potentially gained or lost in an environment and which may be involved in microbial adaptation. Despite the widespread interest in these events, there are no established best practices for identifying gene gain and loss in metagenomics data. Horizontal gene transfer (HGT) represents several mechanisms of gene gain that are especially of interest in clinical microbiology due to the rapid spread of antibiotic resistance genes in natural communities. Several additional mechanisms of gene gain and loss, including gene duplication, gene loss-of-function events, and de novo gene birth are also important to consider in the context of metagenomes but have been less studied. This review is largely focused on detecting HGT in prokaryotic metagenomes, but methods for detecting these other mechanisms are first discussed. For this article to be self-contained, we provide a general background on HGT and the different possible signatures of this process. Lastly, we discuss how improved assembly of genomes from metagenomes would be the most straight-forward approach for improving the inference of gene gain and loss events. Several recent technological advances could help improve metagenome assemblies: long-read sequencing, determining the physical proximity of contigs, optical mapping of short sequences along chromosomes, and single-cell metagenomics. The benefits and limitations of these advances are discussed and open questions in this area are highlighted.

scholarly journals Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae

2020 ◽  
Vol 12 (11) ◽  
pp. 2002-2014
Author(s):  
Ling-Ling Yang ◽  
Zhao Jiang ◽  
Yan Li ◽  
En-Tao Wang ◽  
Xiao-Yang Zhi
Keyword(s):  
Nitrogen Fixation ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Symbiotic Nitrogen Fixation ◽  
Gene Families ◽  
Time Span ◽  
Soil Conditions ◽  
Gene Gain ◽  
Nitrogen Fixing ◽  
Pan Genome

Abstract Rhizobia are soil bacteria capable of forming symbiotic nitrogen-fixing nodules associated with leguminous plants. In fast-growing legume-nodulating rhizobia, such as the species in the family Rhizobiaceae, the symbiotic plasmid is the main genetic basis for nitrogen-fixing symbiosis, and is susceptible to horizontal gene transfer. To further understand the symbioses evolution in Rhizobiaceae, we analyzed the pan-genome of this family based on 92 genomes of type/reference strains and reconstructed its phylogeny using a phylogenomics approach. Intriguingly, although the genetic expansion that occurred in chromosomal regions was the main reason for the high proportion of low-frequency flexible gene families in the pan-genome, gene gain events associated with accessory plasmids introduced more genes into the genomes of nitrogen-fixing species. For symbiotic plasmids, although horizontal gene transfer frequently occurred, transfer may be impeded by, such as, the host’s physical isolation and soil conditions, even among phylogenetically close species. During coevolution with leguminous hosts, the plasmid system, including accessory and symbiotic plasmids, may have evolved over a time span, and provided rhizobial species with the ability to adapt to various environmental conditions and helped them achieve nitrogen fixation. These findings provide new insights into the phylogeny of Rhizobiaceae and advance our understanding of the evolution of symbiotic nitrogen fixation.

scholarly journals Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss

2016 ◽  
Vol 33 (7) ◽  
pp. 1843-1857 ◽  
Author(s):  
Seyed Alireza Zamani-Dahaj ◽  
Mohamed Okasha ◽  
Jakub Kosakowski ◽  
Paul G. Higgs
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Gain ◽  
Gain And Loss ◽  
Phylogenetic Models

scholarly journals De Novo Gene Birth, Horizontal Gene Transfer, and Gene Duplication as Sources of New Gene Families Associated with the Origin of Symbiosis in Amanita

2020 ◽  
Vol 12 (11) ◽  
pp. 2168-2182
Author(s):  
Yen-Wen Wang ◽  
Jaqueline Hess ◽  
Jason C Slot ◽  
Anne Pringle
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Duplication ◽  
De Novo ◽  
Gene Families ◽  
Negative Regulator ◽  
Orphan Gene ◽  
Unique Gene ◽  
De Novo Gene ◽  
New Gene

Abstract By introducing novel capacities and functions, new genes and gene families may play a crucial role in ecological transitions. Mechanisms generating new gene families include de novo gene birth, horizontal gene transfer, and neofunctionalization following a duplication event. The ectomycorrhizal (ECM) symbiosis is a ubiquitous mutualism and the association has evolved repeatedly and independently many times among the fungi, but the evolutionary dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first understand if gene families unique to ECM Amanita fungi and absent from closely related asymbiotic species are functionally relevant to the symbiosis, and then to systematically infer their origins. We identified 109 gene families unique to ECM Amanita species. Genes belonging to unique gene families are under strong purifying selection and are upregulated during symbiosis, compared with genes of conserved or orphan gene families. The origins of seven of the unique gene families are strongly supported as either de novo gene birth (two gene families), horizontal gene transfer (four), or gene duplication (one). An additional 34 families appear new because of their selective retention within symbiotic species. Among the 109 unique gene families, the most upregulated gene in symbiotic cultures encodes a 1-aminocyclopropane-1-carboxylate deaminase, an enzyme capable of downregulating the synthesis of the plant hormone ethylene, a common negative regulator of plant-microbial mutualisms.

scholarly journals Origins of major archaeal clades do not correspond to gene acquisitions from bacteria

2015 ◽  
Author(s):  
Mathieu Groussin ◽  
Bastien Boussau ◽  
Gergely Szöllősi ◽  
Laura Eme ◽  
Manolo Gouy ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Recent Article ◽  
Specific Gene ◽  
Gene Gain ◽  
Number Of Genes ◽  
Gain And Loss ◽  
Phylogenetic Models

In a recent article, Nelson-Sathi et al. [NS] report that the origins of Major Archaeal Lineages [MAL] correspond to massive group-specific gene acquisitions via horizontal gene transfer (HGT) from bacteria (Nelson-Sathi et al., 2015, Nature 517(7532):77-80). If correct, this would have fundamental implications for the process of diversification in microbes. However, a re-examination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A re-analysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea.

scholarly journals Identification of a Novel Conjugative Plasmid in Mycobacteria That Requires Both Type IV and Type VII Secretion

mBio ◽  
2014 ◽  
Vol 5 (5) ◽  
Author(s):  
Roy Ummels ◽  
Abdallah M. Abdallah ◽  
Vincent Kuiper ◽  
Anouar Aâjoud ◽  
Marion Sparrius ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Antibiotic Resistance Genes ◽  
Conjugative Plasmid ◽  
Content Type ◽  
Conjugative Plasmids ◽  
Type Vii Secretion ◽  
Type Iv ◽  
Slow Growing

ABSTRACTConjugative plasmids have been identified in a wide variety of different bacteria, ranging from proteobacteria to firmicutes, and conjugation is one of the most efficient routes for horizontal gene transfer. The most widespread mechanism of plasmid conjugation relies on different variants of the type IV secretion pathway. Here, we describe the identification of a novel type of conjugative plasmid that seems to be unique for mycobacteria. Interestingly, while this plasmid is efficiently exchanged between different species of slow-growing mycobacteria, includingMycobacterium tuberculosis, it could not be transferred to any of the fast-growing mycobacteria tested. Genetic analysis of the conjugative plasmid showed the presence of a locus containing homologues of three type IV secretion system components and a relaxase. In addition, a new type VII secretion locus was present. Using transposon insertion mutagenesis, we show that in fact both these secretion systems are essential for conjugation, indicating that this plasmid represents a new class of conjugative plasmids requiring two secretion machineries. This plasmid could form a useful new tool to exchange or introduce DNA in slow-growing mycobacteria.IMPORTANCEConjugative plasmids play an important role in horizontal gene transfer between different bacteria and, as such, in their adaptation and evolution. This effect is most obvious in the spread of antibiotic resistance genes. Thus far, conjugation of natural plasmids has been described only rarely for mycobacterial species. In fact, it is generally accepted thatM. tuberculosisdoes not show any recent sign of horizontal gene transfer. In this study, we describe the identification of a new widespread conjugative plasmid that can also be efficiently transferred toM. tuberculosis. This plasmid therefore poses both a threat and an opportunity. The threat is that, through the acquisition of antibiotic resistance markers, this plasmid could start a rapid spread of antibiotic resistance genes between pathogenic mycobacteria. The opportunity is that we could use this plasmid to generate new tools for the efficient introduction of foreign DNA in slow-growing mycobacteria.

scholarly journals Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects

Genetics ◽  
2020 ◽  
Vol 216 (2) ◽  
pp. 543-558
Author(s):  
Shai Slomka ◽  
Itamar Françoise ◽  
Gil Hornung ◽  
Omer Asraf ◽  
Tammy Biniashvili ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Growth Yield ◽  
Genomic Variation ◽  
Bacterial Populations ◽  
Flagellar Proteins ◽  
Foreign Dna

Tracing evolutionary processes that lead to fixation of genomic variation in wild bacterial populations is a prime challenge in molecular evolution. In particular, the relative contribution of horizontal gene transfer (HGT) vs.de novo mutations during adaptation to a new environment is poorly understood. To gain a better understanding of the dynamics of HGT and its effect on adaptation, we subjected several populations of competent Bacillus subtilis to a serial dilution evolution on a high-salt-containing medium, either with or without foreign DNA from diverse pre-adapted or naturally salt tolerant species. Following 504 generations of evolution, all populations improved growth yield on the medium. Sequencing of evolved populations revealed extensive acquisition of foreign DNA from close Bacillus donors but not from more remote donors. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. In the largest burst, close to 2% of the genome has been replaced by HGT. Acquired segments tend to be clustered in integration hotspots. Other than HGT, genomes also acquired spontaneous mutations. Many of these mutations occurred within, and seem to alter, the sequence of flagellar proteins. Finally, we show that, while some HGT fragments could be neutral, others are adaptive and accelerate evolution.

scholarly journals Mycobacterial Phylogenomics: An Enhanced Method for Gene Turnover Analysis Reveals Uneven Levels of Gene Gain and Loss among Species and Gene Families

2014 ◽  
Vol 6 (6) ◽  
pp. 1454-1465 ◽  
Author(s):  
Pablo Librado ◽  
Filipe G. Vieira ◽  
Alejandro Sánchez-Gracia ◽  
Sergios-Orestis Kolokotronis ◽  
Julio Rozas
Keyword(s):  
Gene Families ◽  
Gene Gain ◽  
Gain And Loss
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