Genomic Parasites: Coevolution between host and parasites
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BMC Evolutionary Biology | Abstract | The expression and evolution of virulence in multiple infections: the role of specificity, relative virulence and relative dose

Multiple infections of the same host by different strains of the same microparasite species are believed to play a crucial role during the evolution of parasite virulence.
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Background

Multiple infections of the same host by different strains of the same microparasite species are believed to play a crucial role during the evolution of parasite virulence. We investigated the role of specificity, relative virulence and relative dose in determining the competitive outcome of multiple infections in the Daphnia magna-Pasteuria ramosa host-parasite system.

Results

We found that infections by P. ramosa clones (single genotype) were less virulent and produced more spores than infections by P. ramosa isolates (possibly containing multiple genotypes). We also found that two similarly virulent isolates of P. ramosa differed considerably in their within-host competitiveness and their effects on host offspring production when faced with coinfecting P. ramosa isolates and clones. Although the relative virulence of a P. ramosa isolate/clone appears to be a good indicator of its competitiveness during multiple infections, the relative dose may alter the competitive outcome. Moreover, spore counts on day 20 post-infection indicate that the competitive outcome is largely decided early in the parasite's growth phase, possibly mediated by direct interference or apparent competition.

Conclusions

Our results emphasize the importance of epidemiology as well as of various parasite traits in determining the outcome of within-host competition. Incorporating realistic epidemiological and ecological conditions when testing theoretical models of multiple infections, as well as using a wider range of host and parasite genotypes, will enable us to better understand the course of virulence evolution.

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Outbreak of Zika virus infection, Chiapas State, Mexico, 2015, and first confirmed transmission by Aedes aegypti mosquitoes in the Americas

Outbreak of Zika virus infection, Chiapas State, Mexico, 2015, and first confirmed transmission by Aedes aegypti mosquitoes in the Americas | Genomic Parasites: Coevolution between host and parasites | Scoop.it
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Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

Transposable Elements  versus  the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Author Summary Transposable elements (TEs) are enigmatic genetic units that have played important roles in the evolution of eukaryotic genomes. Since their discovery in the 1950s, they have gained increasing attention and are known today as active genome modelers in multiple species. Although these elements have been widely studied in plants, much less is known about their occurrence and impact on the fungal kingdom. Using a diverse set of basidiomycete and ascomycete fungi, we quantified and characterized a huge diversity of DNA and RNA transposable elements, and we identified species that had 0.02 to 29.8% of their genomes occupied by transposable elements. In addition, using our basidiomycete model Pleurotus ostreatus , we demonstrated how TE insertions produced detrimental effects on the expression of upstream and downstream genes, which were downregulated compared with the control groups. This silencing mechanism was present in the basidiomycetes tested but exhibited a patchy distribution in ascomycetes, and might be related to specific genome defense mechanisms that control transposon proliferation. This finding reveals the broader impact of transposable elements in fungi. In addition to their importance as long-term evolutionary forces, they play major roles in the more dynamic transcriptome regulation of certain species.
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Identification of Bari Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer

Identification of  Bari  Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Bari elements are members of the Tc1-mariner superfamily of DNA transposons, originally discovered in Drosophila melanogaster, and subsequently identified in silico in 11 sequenced Drosophila genomes and as experimentally isolated in four non-sequenced Drosophila species. Bari-like elements have been also studied for their mobility both in vivo and in vitro. We analyzed 23 Drosophila genomes and carried out a detailed characterization of the Bari elements identified, including those from the heterochromatic Bari1 cluster in D. melanogaster. We have annotated 401 copies of Bari elements classified either as putatively autonomous or inactive according to the structure of the terminal sequences and the presence of a complete transposase-coding region. Analyses of the integration sites revealed that Bari transposase prefers AT-rich sequences in which the TA target is cleaved and duplicated. Furthermore evaluation of transposon’s co-occurrence near the integration sites of Bari elements showed a non-random distribution of other transposable elements. We also unveil the existence of a putatively autonomous Bari1 variant characterized by two identical long Terminal Inverted Repeats, in D. rhopaloa. In addition, we detected MITEs related to Bari transposons in 9 species. Phylogenetic analyses based on transposase gene and the terminal sequences confirmed that Bari-like elements are distributed into three subfamilies. A few inconsistencies in Bari phylogenetic tree with respect to the Drosophila species tree could be explained by the occurrence of horizontal transfer events as also suggested by the results of dS analyses. This study further clarifies the Bari transposon’s evolutionary dynamics and increases our understanding on the Tc1-mariner elements’ biology.
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Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes. - PubMed - NCBI

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes. - PubMed - NCBI | Genomic Parasites: Coevolution between host and parasites | Scoop.it
BMC Genomics. 2016 May 10;17(1):344. doi: 10.1186/s12864-016-2648-8.
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Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes : Nature Communications : Nature Publishing Group

Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes : Nature Communications : Nature Publishing Group | Genomic Parasites: Coevolution between host and parasites | Scoop.it
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DeNovo: virus-host sequence-based protein–protein interaction prediction

Motivation: Can we predict protein–protein interactions (PPIs) of a novel virus with its host? Three major problems arise: the lack of known PPIs for that virus to learn from, the cost of learning about its proteins and the sequence dissimilarity among viral families that makes most methods inapplicable or inefficient. We develop DeNovo, a sequence-based negative sampling and machine learning framework that learns from PPIs of different viruses to predict for a novel one, exploiting the shared host proteins. We tested DeNovo on PPIs from different domains to assess generalization.


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Transposable element targeting by piRNAs in Laurasiatherians with distinct transposable element histories

Transposable element targeting by piRNAs in Laurasiatherians with distinct transposable element histories | Genomic Parasites: Coevolution between host and parasites | Scoop.it
PIWI proteins and PIWI interacting RNAs (piRNAs) are part of a cellular pathway that has evolved to protect genomes against the proliferation of transposable elements (TEs). PIWIs and piRNAs assemble into complexes that are involved in epigenetic and post-transcriptional repression of TEs. Most of our understanding of the mechanisms of piRNA mediated TE silencing come from fruit fly and mouse models. However, even in these well studied animals it is unclear how piRNA responses relate to variable TE expression and whether the strength of the piRNA response affects TE content over time. Here, we assessed the evolutionary interactions between TE and piRNAs in a statistical framework using three non-model laurasiatherian mammals as a study system: dog, horse and a vesper bat. These three species diverged approximately 80 million years ago and have distinct genomic TE contents. By comparing species with distinct TE landscapes, we aimed to identify clear relationships among TE content, expression and piRNAs. We found that the TE subfamilies that are the most transcribed appear to elicit the strongest “ping-pong” response. This was most evident among LINEs, but the relationships between expression and ping-pong piRNA expression (PPE) were more complex among SINEs. SINE transcripts were equally abundant in the dog and horse yet new SINE insertions were relatively rare in the horse genome, where we identified a stronger piRNA response. Our analyses suggest that the piRNA response can have a strong impact on the TE composition of a genome. However, our results also suggest that the presence of a robust piRNA response is apparently not sufficient to stop TE mobilization and accumulation.
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West Nile virus evolution differs by species of mosquito carrier

West Nile virus evolution differs by species of mosquito carrier | Genomic Parasites: Coevolution between host and parasites | Scoop.it
A new study on how the West Nile virus evolves in four species of mosquitos shows that viruses accumulate mutations in their insect carriers that reduce how well they reproduce when passed on to a bird host. Viruses carried by one of the tropical species were best able to maintain their reproductive fitness and thus spread. The study could help in the prediction of future viral outbreaks.

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MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets

MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets | Genomic Parasites: Coevolution between host and parasites | Scoop.it
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Recurrent gene duplication diversifies genome defense repertoire in Drosophila

Recurrent gene duplication diversifies genome defense repertoire in Drosophila | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Transposable elements (TEs) comprise large fractions of many eukaryotic genomes and imperil host genome integrity. The host genome combats these challenges by encoding proteins that silence TE activity. Both the introduction of new TEs via horizontal transfer and TE sequence evolution requires constant innovation of host-encoded TE silencing machinery to keep pace with TEs. One form of host innovation is the adaptation of existing, single-copy host genes. Indeed, host suppressors of TE replication often harbor signatures of positive selection. Such signatures are especially evident in genes encoding the piRNA (piwi-associated RNAs) pathway of gene silencing e.g., the female germline-restricted TE silencer, HP1D/Rhino. Host genomes can also innovate via gene duplication and divergence. However, the importance of gene family expansions, contractions, and gene turnover to host genome defense has been largely unexplored. Here, we functionally characterize Oxpecker, a young, tandem duplicate gene of HP1D/rhino. We demonstrate that Oxpecker supports female fertility in Drosophila melanogaster and silences several transposable element families that are incompletely silenced by HP1D/Rhino in the female germline. We further show that, like Oxpecker, at least ten additional, structurally diverse, HP1D/rhino-derived daughter and “granddaughter” genes emerged during a short 15 million year period of Drosophila evolution. These young paralogs are transcribed primarily in germline tissues, where the genetic conflict between host genomes and TEs plays out. Our findings suggest that gene family expansion is an underappreciated yet potent evolutionary mechanism of genome defense diversification.
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Regulatory evolution of innate immunity through co-option of endogenous retroviruses

Regulatory evolution of innate immunity through co-option of endogenous retroviruses | Genomic Parasites: Coevolution between host and parasites | Scoop.it
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Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Author Summary Animal genomes contain ancient pathogens known as endogenous retroviruses (ERVs). Though the widespread abundance of ERVs is due to their ability to self replicate, some ERVs are known to have become important to host processes including placentation, and in the case of HERV-H, the functioning of human stem cells. In our study we place the insertion and deletion activity of primate ERV families in direct quantitative comparison. In particular, we show that ERV deletion is an age dependent process, so that as an ERV ages it becomes less likely to be deleted at any given instant. We also find that ERVs from the HERV-H family are unusually slowly deleted, an interesting result that suggests that the exaptation of HERV-H may have involved internal regions of the virus and not just its terminal promoters. Assuming the behaviour of primate ERVs is not unusual, our study suggests that future bioinformatics screening for ERVs with slow deletion dynamics could help identify large-scale exaptations in distant species. Furthermore, as we demonstrate that ERVs are deleted rapidly, we think that such screening could be performed using ratios of conserved to deleted elements and could therefore be applied to single genomes.
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Determinants of Arbovirus Vertical Transmission in Mosquitoes

Determinants of Arbovirus Vertical Transmission in Mosquitoes | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Vertical transmission (VT) and horizontal transmission (HT) of pathogens refer to parental and non-parental chains of host-to-host transmission. Combining HT with VT enlarges considerably the range of ecological conditions in which a pathogen can persist, but the factors governing the relative frequency of each transmission mode are poorly understood for pathogens with mixed-mode transmission. Elucidating these factors is particularly important for understanding the epidemiology of arthropod-borne viruses (arboviruses) of public health significance. Arboviruses are primarily maintained by HT between arthropod vectors and vertebrate hosts in nature, but are occasionally transmitted vertically in the vector population from an infected female to her offspring, which is a proposed maintenance mechanism during adverse conditions for HT. Here, we review over a century of published primary literature on natural and experimental VT, which we previously assembled into large databases, to identify biological factors associated with the efficiency of arbovirus VT in mosquito vectors. Using a robust statistical framework, we highlight a suite of environmental, taxonomic, and physiological predictors of arbovirus VT. These novel insights contribute to refine our understanding of strategies employed by arboviruses to persist in the environment and cause substantial public health concern. They also provide hypotheses on the biological processes underlying the relative VT frequency for pathogens with mixed-mode transmission that can be tested empirically.
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P53 and the defenses against genome instability caused by transposons and repetitive elements - Levine - 2016 - BioEssays - Wiley Online Library

P53 and the defenses against genome instability caused by transposons and repetitive elements - Levine - 2016 - BioEssays - Wiley Online Library | Genomic Parasites: Coevolution between host and parasites | Scoop.it
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Wolbachia from Drosophila incompta: just a hitchhiker shared by Drosophila in the New and Old World? - Wallau - 2016 - Insect Molecular Biology - Wiley Online Library

Wolbachia from Drosophila incompta: just a hitchhiker shared by Drosophila in the New and Old World? - Wallau - 2016 - Insect Molecular Biology - Wiley Online Library | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Gabriel Wallau's insight:
Finally is out our paper which supports our view of Wolbachia HT risks (See figure 5B and C) proposed in this letter http://science.sciencemag.org/content/351/6279/1273.2.abstract
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Adaptation to Global Change: A Transposable Element–Epigenetics Perspective: Trends in Ecology & Evolution

Adaptation to Global Change: A Transposable Element–Epigenetics Perspective: Trends in Ecology & Evolution | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Understanding how organisms cope with global change is a major scientific challenge. The molecular pathways underlying rapid adaptive phenotypic responses to global change remain poorly understood. Here, we highlight the relevance of two environment-sensitive molecular elements: transposable elements (TEs) and epigenetic components (ECs). We first outline the sensitivity of these elements to global change stressors and review how they interact with each other. We then propose an integrative molecular engine coupling TEs and ECs and allowing organisms to fine-tune phenotypes in a real-time fashion, adjust the production of phenotypic and genetic variation, and produce heritable phenotypes with different levels of transmission fidelity. We finally discuss the implications of this molecular engine in the context of global change.
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MGEScan: a Galaxy based system for identifying retrotransposons in genomes

MGEScan: a Galaxy based system for identifying retrotransposons in genomes | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Summary: MGEScan-LTR and MGEScan-nonLTR are successfully used programs for identifying long terminal repeats (LTR) and non-LTR retrotransposons in eukaryotic genome sequences. However, these programs are not supported by easy-to-use interfaces nor well suited for data visualization in general data formats. Here, we present MGEScan, a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters. MGEScan and Galaxy empower researchers to identify transposable elements in a graphi-cal user interface with ready-to-use workflows. MGEScan also visualizes the custom annotation tracks for mobile genetic elements in public genome browsers. A maximum speedup of 3.26× is attained for execution time using concurrent processing and MPI on four virtual cores. MGEScan provides four operational modes: as a command line tool, as a Galaxy Toolshed, on a Galaxy-based web server, and on a virtual cluster on the Amazon cloud.
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Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci

Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci | Genomic Parasites: Coevolution between host and parasites | Scoop.it
LINE-1 (L1) retrotransposons represent approximately one sixth of the human genome, but only the human-specific L1HS-Ta subfamily acts as an endogenous mutagen in modern humans, reshaping both somatic and germline genomes. Due to their high levels of sequence identity and the existence of many polymorphic insertions absent from the reference genome, the transcriptional activation of individual genomic L1HS-Ta copies remains poorly understood. Here we comprehensively mapped fixed and polymorphic L1HS-Ta copies in 12 commonly-used somatic cell lines, and identified transcriptional and epigenetic signatures allowing the unambiguous identification of active L1HS-Ta copies in their genomic context. Strikingly, only a very restricted subset of L1HS-Ta loci - some being polymorphic among individuals - significantly contributes to the bulk of L1 expression, and these loci are differentially regulated among distinct cell lines. Thus, our data support a local model of L1 transcriptional activation in somatic cells, governed by individual-, locus-, and cell-type-specific determinants.
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Mobile DNA

Mobile DNA | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Background
The revolutionary concept of “jumping genes” was conceived by McClintock in the late 1940s while studying the Activator/Dissociation (Ac/Ds) system in maize. Transposable elements (TEs) represent the most abundant component of many eukaryotic genomes. Mobile elements are a driving force of eukaryotic genome evolution. McClintock’s Ac, the autonomous element of the Ac/Ds system, together with hobo from Drosophila and Tam3 from snapdragon define an ancient and diverse DNA transposon superfamily named hAT. Other members of the hAT superfamily include the insect element Hermes and Tol2 from medaka. In recent years, genetic tools derived from the ‘cut’ and ‘paste’ Tol2 DNA transposon have been widely used for genomic manipulation in zebrafish, mammals and in cells in vitro.

Results
We report the purification of a functional recombinant Tol2 protein from E.coli. We demonstrate here that following microinjection using a zebrafish embryo test system, purified Tol2 transposase protein readily catalyzes gene transfer in both somatic and germline tissues in vivo. We show that purified Tol2 transposase can promote both in vitro cutting and pasting in a defined system lacking other cellular factors. Notably, our analysis of Tol2 transposition in vitro reveals that the target site preference observed for Tol2 in complex host genomes is maintained using a simpler target plasmid test system, indicating that the primary sequence might encode intrinsic cues for transposon integration.

Conclusions
This active Tol2 protein is an important new tool for diverse applications including gene discovery and molecular medicine, as well as for the biochemical analysis of transposition and regulation of hAT transposon/genome interactions. The measurable but comparatively modest insertion site selection bias noted for Tol2 is largely determined by the primary sequence encoded in the target sequence as assessed through studying Tol2 protein-mediated transposition in a cell-free system.
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Horizontal transfer - imperative mission of acellular life forms, Acytota

Horizontal transfer - imperative mission of acellular life forms, Acytota | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Acytota is a kingdom of life covering satellites, plasmids, transposable elements, viroids and viruses, all outside the conventional tree of life but satisfying most life definitions. This review focuses on some aspects of Acytota, their “genomes” and life styles, the dominance of transposable elements and their evolutionary influence on other life forms in order to vindicate the Acytota as a life kingdom no more polyphyletic than other kingdoms and its members no more parasitic than other life forms.
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Phylogenetically resolving epidemiologic linkage

Phylogenetically resolving epidemiologic linkage | Genomic Parasites: Coevolution between host and parasites | Scoop.it
Phylogenetic inference of who infected whom has great value in epidemiological investigations because it should provide an objective test of an explicit hypothesis about how transmission(s) occurred. Until now, however, there has not been a systematic evaluation of which phylogeny to expect from different transmission histories, and thus the interpretation of what an observed phylogeny actually means has remained somewhat elusive. Here, we show that certain types of phylogenies associate with different transmission histories, which may make it possible to exclude possible intermediary links or identify cases where a common source was likely but not sampled. Our systematic classification and evaluation of expected topologies should make future interpretation of phylogenetic results in epidemiological investigations more objective and informative.
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