Indirect identification of horizontal gene transfer

AbstractSeveral implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question “how much information about all HGT events is contained in LDT graphs” with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.

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Horizontally transferred genes in the ctenophore Mnemiopsis leidyi encode enzymes and are expressed during early development

10.7287/peerj.preprints.3462v1 ◽

2017 ◽

Author(s):

Alexandra M Hernandez ◽

Joseph F Ryan

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Early Development ◽

Genetic Information ◽

Mnemiopsis Leidyi ◽

Uncharacterized Protein ◽

Phylogenetic Incongruence ◽

Wide Range ◽

Growing Body

Horizontal gene transfer has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that horizontal gene transfer (HGT) between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) appear to perform enzymatic activities in M. leidyi, supporting previous observations that enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during early development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

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Role of Horizontal Gene Transfer in the Development of Multidrug Resistance in Haemophilus influenzae

mSphere ◽

10.1128/msphere.00969-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 3

Author(s):

Kristin Hegstad ◽

Haima Mylvaganam ◽

Jessin Janice ◽

Ellen Josefsen ◽

Audun Sivertsen ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Haemophilus Influenzae ◽

Resistance Genes ◽

Mobile Genetic Elements ◽

Beta Lactam ◽

Content Type ◽

Genetic Elements ◽

Wide Range ◽

Chromosomal Genes

ABSTRACT Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. Resistance to extended-spectrum cephalosporins in H. influenzae is rare in Europe. In this study, we defined acquired resistance gene loci and ftsI mutations in multidrug-resistant (MDR) and/or PBP3-mediated beta-lactam-resistant (rPBP3) H. influenzae strains, intending to understand the mode of spread of antibiotic resistance determinants in this species. Horizontal transfer of mobile genetic elements and transformation with resistance-conferring ftsI alleles were contributory. We found one small plasmid and three novel integrative conjugative elements (ICEs) which carry different combinations of resistance genes. Demonstration of transfer and/or ICE circular forms showed that the ICEs are functional. Two extensively MDR genetically unrelated H. influenzae strains (F and G) from the same geographical region shared an identical novel MDR ICE (Tn6686) harboring blaTEM-1, catA2-like, and tet(B). The first Nordic case of MDR H. influenzae septicemia, strain 0, originating from the same geographical area as these strains, had a similar resistance pattern but contained another ICE [Tn6687 with blaTEM-1, catP and tet(B)] with an overall structure quite similar to that of Tn6686. Comparison of the complete ftsI genes among rPBP3 strains revealed that the entire gene or certain regions of it are identical in genetically unrelated strains, indicating horizontal gene transfer. Our findings illustrate that H. influenzae is capable of acquiring resistance against a wide range of commonly used antibiotics through horizontal gene transfer, in terms of conjugative transfer of ICEs and transformation of chromosomal genes. IMPORTANCE Haemophilus influenzae colonizes the respiratory tract in humans and causes both invasive and noninvasive infections. As a threat to treatment, resistance against critically important antibiotics is on the rise in H. influenzae. Identifying mechanisms for horizontal acquisition of resistance genes is important to understand how multidrug resistance develops. The present study explores the antimicrobial resistance genes and their context in beta-lactam-resistant H. influenzae with coresistance to up to four non-beta-lactam groups. The results reveal that this organism is capable of acquiring resistance to a wide range of commonly used antibiotics through conjugative transfer of mobile genetic elements and transformation of chromosomal genes, resulting in mosaic genes with a broader resistance spectrum. Strains with chromosomally mediated resistance to extended-spectrum cephalosporins, co-trimoxazole, and quinolones combined with mobile genetic elements carrying genes mediating resistance to ampicillin, tetracyclines, and chloramphenicol have been reported, and further dissemination of such strains represents a particular concern.

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

Journal of Parasitology Research ◽

10.1155/2016/3241027 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 2

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.

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A Metric on the Space of Partly Reduced Phylogenetic Networks

BioMed Research International ◽

10.1155/2016/7534258 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Juan Wang

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Polynomial Time ◽

Phylogenetic Trees ◽

Special Kind ◽

Population Level ◽

Phylogenetic Networks

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, such as recombination between genes, hybridization between lineages, and horizontal gene transfer. The researchers have designed several measures for computing the dissimilarity between two phylogenetic networks, and each measure has been proven to be a metric on a special kind of phylogenetic networks. However, none of the existing measures is a metric on the space of partly reduced phylogenetic networks. In this paper, we provide a metric,de-distance, on the space of partly reduced phylogenetic networks, which is polynomial-time computable.

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The ECF sigma factor PvdS regulates the type I-F CRISPR-Cas system in Pseudomonas aeruginosa

10.1101/2020.01.31.929752 ◽

2020 ◽

Cited By ~ 2

Author(s):

Stephen Dela Ahator ◽

Wang Jianhe ◽

Lian-Hui Zhang

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Sigma Factor ◽

Regulatory System ◽

Stress Factors ◽

Iron Limitation ◽

Transport Systems ◽

Type I ◽

Ecf Sigma Factor ◽

Wide Range

AbstractDuring infection, successful colonization of bacteria requires a fine-tuned supply of iron acquired via iron transport systems. However, the transport systems serve as phage attachment sites and entry portals for foreign nucleic acid. Most bacteria possess the CRISPR-Cas system, which targets and destroys foreign nucleic acids and prevents deleterious effects of horizontal gene transfer. To understand the regulation of the CRISPR-Cas system, we performed genome-wide random transposon mutagenesis which led to the identification of the Extracytoplasmic Function (ECF) Sigma factor, PvdS as a regulator of the Type I-F CRISPR-Cas system in P. aeruginosa. We show that under iron-depleted conditions PvdS induces the expression of the type I-F CRISPR-Cas system. This regulatory mechanism involves direct interaction of PvdS with specific binding sites in the promoter region of cas1. Furthermore, activation of the CRISPR-Cas system under iron-depleted conditions increases horizontal gene transfer (HGT) interference and adaptation. The PvdS activation of the CRISPR-Cas system under iron limitation highlights the versatility of the P. aeruginosa in multitasking its regulatory machinery to integrate multiple stress factors.ImportanceP. aeruginosa infects a wide range of host organisms and adapts to various environmental stress factors such as iron limitation due to its elaborate regulatory system. P aeruginosa possesses the type I-F CRISPR-Cas system as a defense mechanism against phages infection and HGT. This work highlights the ability of P. aeruginosa to multitask its iron regulatory system to control the CRISPR-Cas system under a physiologically relevant stress factor such as iron limitation where the bacteria are vulnerable to phage infection. It also adds to the knowledge of the regulation of the CRISPR-Cas system in bacteria and presents a possible target that could prevent the emergence of phage resistance via the CRISPR-Cas system during the development of phage therapy.

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Horizontally transferred genes in the ctenophore Mnemiopsis leidyi

10.7287/peerj.preprints.3462 ◽

2018 ◽

Author(s):

Alexandra M Hernandez ◽

Joseph F Ryan

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genetic Information ◽

Mnemiopsis Leidyi ◽

Uncharacterized Protein ◽

Phylogenetic Incongruence ◽

Wide Range ◽

Growing Body ◽

Genes Encoding

Horizontal gene transfer has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that horizontal gene transfer (HGT) between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

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Horizontally transferred genes in the ctenophore Mnemiopsis leidyi

10.7287/peerj.preprints.3462v3 ◽

2018 ◽

Author(s):

Alexandra M Hernandez ◽

Joseph F Ryan

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genetic Information ◽

Mnemiopsis Leidyi ◽

Uncharacterized Protein ◽

Phylogenetic Incongruence ◽

Wide Range ◽

Growing Body ◽

Genes Encoding

Horizontal gene transfer has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that horizontal gene transfer (HGT) between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

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Analysis of Ten Brucella Genomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle

Journal of Bacteriology ◽

10.1128/jb.01767-08 ◽

2009 ◽

Vol 191 (11) ◽

pp. 3569-3579 ◽

Cited By ~ 72

Author(s):

Alice R. Wattam ◽

Kelly P. Williams ◽

Eric E. Snyder ◽

Nalvo F. Almeida ◽

Maulik Shukla ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Brucella Melitensis ◽

Large Fraction ◽

Bacterial Pathogen ◽

Detailed Comparison ◽

Phylogenomic Analysis ◽

Host Preferences ◽

Type Iv ◽

Wide Range

ABSTRACT The facultative intracellular bacterial pathogen Brucella infects a wide range of warm-blooded land and marine vertebrates and causes brucellosis. Currently, there are nine recognized Brucella species based on host preferences and phenotypic differences. The availability of 10 different genomes consisting of two chromosomes and representing six of the species allowed for a detailed comparison among themselves and relatives in the order Rhizobiales. Phylogenomic analysis of ortholog families shows limited divergence but distinct radiations, producing four clades as follows: Brucella abortus-Brucella melitensis, Brucella suis-Brucella canis, Brucella ovis, and Brucella ceti. In addition, Brucella phylogeny does not appear to reflect the phylogeny of Brucella species' preferred hosts. About 4.6% of protein-coding genes seem to be pseudogenes, which is a relatively large fraction. Only B. suis 1330 appears to have an intact β-ketoadipate pathway, responsible for utilization of plant-derived compounds. In contrast, this pathway in the other species is highly pseudogenized and consistent with the “domino theory” of gene death. There are distinct shared anomalous regions (SARs) found in both chromosomes as the result of horizontal gene transfer unique to Brucella and not shared with its closest relative Ochrobactrum, a soil bacterium, suggesting their acquisition occurred in spite of a predominantly intracellular lifestyle. In particular, SAR 2-5 appears to have been acquired by Brucella after it became intracellular. The SARs contain many genes, including those involved in O-polysaccharide synthesis and type IV secretion, which if mutated or absent significantly affect the ability of Brucella to survive intracellularly in the infected host.

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Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-02-19-0039-r ◽

2019 ◽

Vol 32 (9) ◽

pp. 1110-1120 ◽

Cited By ~ 1

Author(s):

Masaru Bamba ◽

Seishiro Aoki ◽

Tadashi Kajita ◽

Hiroaki Setoguchi ◽

Yasuyuki Watano ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Lotus Japonicus ◽

Population Expansion ◽

Housekeeping Genes ◽

Natural Environments ◽

Symbiotic Genes ◽

Nodule Bacteria ◽

Wide Range

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.

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Horizontally transferred genes in the ctenophore Mnemiopsis leidyi

PeerJ ◽

10.7717/peerj.5067 ◽

2018 ◽

Vol 6 ◽

pp. e5067 ◽

Cited By ~ 2

Author(s):

Alexandra M. Hernandez ◽

Joseph F. Ryan

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genetic Information ◽

Mnemiopsis Leidyi ◽

Uncharacterized Protein ◽

Phylogenetic Incongruence ◽

Wide Range ◽

Growing Body ◽

Genes Encoding

Horizontal gene transfer (HGT) has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that HGT between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) are homologous to characterized enzymes, supporting previous observations that genes encoding enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

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