scholarly journals Endogenous virophages populate the genomes of a marine heterotrophic flagellate

2020 ◽  
Author(s):  
Thomas Hackl ◽  
Sarah Duponchel ◽  
Karina Barenhoff ◽  
Alexa Weinmann ◽  
Matthias G. Fischer
Keyword(s):  
Gc Content ◽  
Nuclear Genome ◽  
Host Population ◽  
Heterotrophic Flagellate ◽  
Dna Viruses ◽  
Integration Sites ◽  
Dynamic Genome ◽  
Microbial System ◽  
Population Survival ◽  
Endogenous Viral Elements

AbstractEndogenous viral elements (EVEs) are frequently found in eukaryotic genomes, yet their integration dynamics and biological functions remain largely unknown. Unlike most other eukaryotic DNA viruses, the virophage mavirus integrates efficiently into the nuclear genome of its host, the marine heterotrophic flagellate Cafeteria burkhardae. Mavirus EVEs can reactivate upon superinfection with the lytic giant virus CroV and may act as an adaptive antiviral defense system, because mavirus increases host population survival during a coinfection with CroV. However, the prevalence of endogenous virophages in natural flagellate populations has not been explored. Here we report dozens of endogenous mavirus-like elements (EMALEs) in the nuclear genomes of four C. burkhardae strains. EMALEs were typically 20 kilobase pairs long and constituted 0.7% to 1.8% of each host genome. We analyzed 33 fully assembled EMALEs that fell into two main clusters and eight types based on GC-content, nucleotide similarity, and coding potential. Inter-strain comparison showed conservation of some EMALE insertion loci, whereas the majority of integration sites were unique to a given host strain. We also describe a group of tyrosine recombinase retrotransposons, some of which exhibited a strong preference for integration into EMALEs and represent yet another layer of parasitism in this microbial system. Our findings show that virophages are common, diverse, and dynamic genome components of the marine protist C. burkhardae, which implies important eco-evolutionary roles for these enigmatic viruses.

scholarly journals Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 358
Author(s):  
Joan Pedrola-Monfort ◽  
David Lázaro-Gimeno ◽  
Carlos G. Boluda ◽  
Laia Pedrola ◽  
Alfonso Garmendia ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Evolutionary Biology ◽  
Repetitive Sequences ◽  
Gc Content ◽  
Nuclear Genome ◽  
Nuclear Ribosomal Dna ◽  
Sequence Evolution ◽  
Evolutionary Trends ◽  
Genome Length ◽  
Evolutionary Patterns

Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three genetic compartments, particularly during the transition from water to land. To clarify the evolutionary trends in the mitochondrial genome of Archaeplastida, we analyzed the sequences from 37 complete genomes. Therefore, we utilized mitochondrial, plastidial and nuclear ribosomal DNA molecular markers on 100 species of Streptophyta for each subunit. Hierarchical models of sequence evolution were fitted to test the heterogeneity in the base composition. The best resulting phylogenies were used for reconstructing the ancestral Guanine-Cytosine (GC) content and equilibrium GC frequency (GC*) using non-homogeneous and non-stationary models fitted with a maximum likelihood approach. The mitochondrial genome length was strongly related to repetitive sequences across Archaeplastida evolution; however, the length seemed not to be linked to the other studied variables, as different lineages showed diverse evolutionary patterns. In contrast, Streptophyta exhibited a powerful positive relationship between the GC content, non-coding DNA, and repetitive sequences, while the evolution of Chlorophyta reflected a strong positive linear relationship between the genome length and the number of genes.

scholarly journals Inside environmental Clostridium perfringens genomes: antibiotic resistance genes, virulence factors and genomic features

2020 ◽  
Vol 18 (4) ◽  
pp. 477-493
Author(s):  
Johannes Cornelius Jacobus Fourie ◽  
Cornelius Carlos Bezuidenhout ◽  
Tomasz Janusz Sanko ◽  
Charlotte Mienie ◽  
Rasheed Adeleke
Keyword(s):  
Antibiotic Resistance ◽  
Clostridium Perfringens ◽  
Resistance Genes ◽  
Gc Content ◽  
Antibiotic Resistance Genes ◽  
Open Reading Frames ◽  
Health Security ◽  
Genes Encoding ◽  
Integration Sites ◽  
Potential Pathogenicity

Abstract Until recently, research has focused on Clostridium perfringens in clinical settings without considering environmental isolates. In this study, environmental genomes were used to investigate possible antibiotic resistance and the presence of virulence traits in C. perfringens strains from raw surface water. In silico assembly of three C. perfringens strains, DNA generated almost complete genomes setting their length ranging from 3.4 to 3.6 Mbp with GC content of 28.18%. An average of 3,175 open reading frames was identified, with the majority associated with carbohydrate and protein metabolisms. The genomes harboured several antibiotic resistance genes for glycopeptides, macrolide–lincosamide–streptogramin B, β-lactam, trimethoprim, tetracycline and aminoglycosides and also the presence of several genes encoding for polypeptides and multidrug resistance efflux pumps and 35 virulence genes. Some of these encode for haemolysins, sialidase, hyaluronidase, collagenase, perfringolysin O and phospholipase C. All three genomes contained sequences indicating phage, antibiotic resistance and pathogenic islands integration sites. A genomic comparison of these three strains confirmed high similarity and shared core genes with clinical C. perfringens strains, highlighting their health security risks. This study provides a genomic insight into the potential pathogenicity of C. perfringens present in the environment and emphasises the importance of monitoring this niche in the future.

scholarly journals Evidence for densovirus integrations into tapeworm genomes

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Michaela Herz ◽  
Klaus Brehm
Keyword(s):  
Genetic Manipulation ◽  
Taenia Solium ◽  
Gene Clusters ◽  
Hymenolepis Diminuta ◽  
Stem Cell Population ◽  
Dna Viruses ◽  
Integration Sites ◽  
Bioinformatic Approaches ◽  
Underlying Mechanisms ◽  
Pirna Pathway

Abstract Background Tapeworms lack a canonical piRNA-pathway, raising the question of how they can silence existing mobile genetic elements (MGE). Investigation towards the underlying mechanisms requires information on tapeworm transposons which is, however, presently scarce. Methods The presence of densovirus-related sequences in tapeworm genomes was studied by bioinformatic approaches. Available RNA-Seq datasets were mapped against the Echinococcus multilocularis genome to calculate expression levels of densovirus-related genes. Transcription of densovirus loci was further analyzed by sequencing and RT-qPCR. Results We herein provide evidence for the presence of densovirus-related elements in a variety of tapeworm genomes. In the high-quality genome of E. multilocularis we identified more than 20 individual densovirus integration loci which contain the information for non-structural and structural virus proteins. The majority of densovirus loci are present as head-to-tail concatemers in isolated repeat containing regions of the genome. In some cases, unique densovirus loci have integrated close to histone gene clusters. We show that some of the densovirus loci of E. multilocularis are actively transcribed, whereas the majority are transcriptionally silent. RT-qPCR data further indicate that densovirus expression mainly occurs in the E. multilocularis stem cell population, which probably forms the germline of this organism. Sequences similar to the non-structural densovirus genes present in E. multilocularis were also identified in the genomes of E. canadensis, E. granulosus, Hydatigera taeniaeformis, Hymenolepis diminuta, Hymenolepis microstoma, Hymenolepis nana, Taenia asiatica, Taenia multiceps, Taenia saginata and Taenia solium. Conclusions Our data indicate that densovirus integration has occurred in many tapeworm species. This is the first report on widespread integration of DNA viruses into cestode genomes. Since only few densovirus integration sites were transcriptionally active in E. multilocularis, our data are relevant for future studies into gene silencing mechanisms in tapeworms. Furthermore, they indicate that densovirus-based vectors might be suitable tools for genetic manipulation of cestodes.

scholarly journals Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

2014 ◽  
Vol 89 (2) ◽  
pp. 1278-1285 ◽  
Author(s):  
Jinglie Zhou ◽  
Dawei Sun ◽  
Alyson Childers ◽  
Timothy R. McDermott ◽  
Yongjie Wang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Open Reading Frames ◽  
Lake Ecosystem ◽  
Photic Zone ◽  
Yellowstone Lake ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Unique Distribution

ABSTRACTVirophages are a unique group of circular double-stranded DNA viruses that are considered parasites of giant DNA viruses, which in turn are known to infect eukaryotic hosts. In this study, the genomes of three novel Yellowstone Lake virophages (YSLVs)—YSLV5, YSLV6, and YSLV7—were identified from Yellowstone Lake through metagenomic analyses. The relative abundance of these three novel virophages and previously identified Yellowstone Lake virophages YSLV1 to -4 were determined in different locations of the lake, revealing that most of the sampled locations in the lake, including both mesophilic and thermophilic habitats, had multiple virophage genotypes. This likely reflects the diverse habitats or diversity of the eukaryotic hosts and their associated giant viruses that serve as putative hosts for these virophages. YSLV5 has a 29,767-bp genome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a close evolutionary relationship with YSLV1 to -4, whereas YSLV5 and YSLV7 are distantly related to the others, and YSLV7 represents the fourth novel virophage lineage. In addition, the genome of YSLV5 has a G+C content of 51.1% that is much higher than all other known virophages, indicating a unique host range for YSLV5. These results suggest that virophages are abundant and have diverse genotypes that likely mirror diverse giant viral and eukaryotic hosts within the Yellowstone Lake ecosystem.IMPORTANCEThis study discovered novel virophages present within the Yellowstone Lake ecosystem using a conserved major capsid protein as a phylogenetic anchor for assembly of sequence reads from Yellowstone Lake metagenomic samples. The three novel virophage genomes (YSLV5 to -7) were completed by identifying specific environmental samples containing these respective virophages, and closing gaps by targeted PCR and sequencing. Most of the YSLV genotypes were associated primarily with photic-zone and nonhydrothermal samples; however, YSLV5 had a unique distribution with an occurrence in vent samples similar to that in photic-zone samples and with a higher GC content that suggests a distinct host and habitat compared to other YSLVs. In addition, genome content and phylogenetic analyses indicate that YSLV5 and YSLV7 are distinct from known virophages and that additional as-yet-uncharacterized virophages are likely present within the Yellowstone Lake ecosystem.

scholarly journals A first insight into the genome of Prototheca wickerhamii, a major causative agent of human protothecosis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zofia Bakuła ◽  
Paweł Siedlecki ◽  
Robert Gromadka ◽  
Jan Gawor ◽  
Agnieszka Gromadka ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Fungal Pathogens ◽  
Opportunistic Infections ◽  
Gc Content ◽  
Nuclear Genome ◽  
Sequencing Analysis ◽  
Emerging Pathogens ◽  
Interaction Database ◽  
Host Interaction ◽  
Prototheca Wickerhamii

Abstract Background Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. The Prototheca algae are emerging pathogens, whose incidence has increased importantly over the past two decades. Prototheca wickerhamii is a major human pathogen, responsible for at least 115 cases worldwide. Although the algae are receiving more attention nowadays, there is still a substantial knowledge gap regarding their biology, and pathogenicity in particular. Here we report, for the first time, the complete nuclear genome, organelle genomes, and transcriptome of the P. wickerhamii type strain ATCC 16529. Results The assembled genome size was of 16.7 Mbp, making it the smallest and most compact genome sequenced so far among the protothecans. Key features of the genome included a high overall GC content (64.5%), a high number (6081) and proportion (45.9%) of protein-coding genes, and a low repetitive sequence content (2.2%). The vast majority (90.6%) of the predicted genes were confirmed with the corresponding transcripts upon RNA-sequencing analysis. Most (93.2%) of the genes had their putative function assigned when searched against the InterProScan database. A fourth (23.3%) of the genes were annotated with an enzymatic activity possibly associated with the adaptation to the human host environment. The P. wickerhamii genome encoded a wide array of possible virulence factors, including those already identified in two model opportunistic fungal pathogens, i.e. Candida albicans and Trichophyton rubrum, and thought to be involved in invasion of the host or elicitation of the adaptive stress response. Approximately 6% of the P. wickerhamii genes matched a Pathogen-Host Interaction Database entry and had a previously experimentally proven role in the disease development. Furthermore, genes coding for proteins (e.g. ATPase, malate dehydrogenase) hitherto considered as potential virulence factors of Prototheca spp. were demonstrated in the P. wickerhamii genome. Conclusions Overall, this study is the first to describe the genetic make-up of P. wickerhamii and discovers proteins possibly involved in the development of protothecosis.

scholarly journals Modeling the Potential Impact of Host Population Survival on the Evolution of M. tuberculosis Latency

PLoS ONE ◽  
2014 ◽  
Vol 9 (8) ◽  
pp. e105721 ◽  
Author(s):  
Nibiao Zheng ◽  
Christopher C. Whalen ◽  
Andreas Handel
Keyword(s):  
Host Population ◽  
Population Survival ◽  
Potential Impact

scholarly journals Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses

2015 ◽  
Vol 112 (38) ◽  
pp. E5318-E5326 ◽  
Author(s):  
Guillaume Blanc ◽  
Lucie Gallot-Lavallée ◽  
Florian Maumus
Keyword(s):  
Host Cell ◽  
Nuclear Genome ◽  
Eukaryotic Cell ◽  
Dna Viruses ◽  
Unicellular Eukaryotes ◽  
Indirect Control ◽  
Double Stranded Dna ◽  
Cell Mortality ◽  
Giant Viruses ◽  
Nucleocytoplasmic Large Dna Viruses

Virophages are recently discovered double-stranded DNA virus satellites that prey on giant viruses (nucleocytoplasmic large DNA viruses; NCLDVs), which are themselves parasites of unicellular eukaryotes. This coupled parasitism can result in the indirect control of eukaryotic cell mortality by virophages. However, the details of such tripartite relationships remain largely unexplored. We have discovered ∼300 predicted genes of putative virophage origin in the nuclear genome of the unicellular alga Bigelowiella natans. Physical clustering of these genes indicates that virophage genomes are integrated into the B. natans genome. Virophage inserts show high levels of similarity and synteny between each other, indicating that they are closely related. Virophage genes are transcribed not only in the sequenced B. natans strain but also in other Bigelowiella isolates, suggesting that transcriptionally active virophage inserts are widespread in Bigelowiella populations. Evidence that B. natans is also a host to NCLDV members is provided by the identification of NCLDV inserts in its genome. These putative large DNA viruses may be infected by B. natans virophages. We also identify four repeated elements sharing structural and genetic similarities with transpovirons—a class of mobile elements first discovered in giant viruses—that were probably independently inserted in the B. natans genome. We argue that endogenized provirophages may be beneficial to both the virophage and B. natans by (i) increasing the chances for the virophage to coinfect the host cell with an NCLDV prey and (ii) defending the host cell against fatal NCLDV infections.

scholarly journals Identification of Two Virus Integration Sites in the Brown Alga Feldmannia Chromosome

2007 ◽  
Vol 82 (3) ◽  
pp. 1407-1413 ◽  
Author(s):  
Russel H. Meints ◽  
Richard G. Ivey ◽  
Amy M. Lee ◽  
Tae-Jin Choi
Keyword(s):  
Vegetative Cells ◽  
Stem Loop ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Virus Particles ◽  
Double Stranded Dna ◽  
Stem Loop Structure ◽  
Integration Sites ◽  
Virus Integration ◽  
Cg Dinucleotide

ABSTRACT Two similar, large double-stranded DNA viruses, Feldmannia species virus 158 (FsV-158) and FsV-178, replicate only in the unilocular reproductive cells (sporangia) of a brown filamentous alga in the genus Feldmannia. Virus particles are not present in vegetative cells but they are produced in the sporangia formed on vegetative filaments that have been transferred newly into culture. Thus, we proposed that these viruses exist in the vegetative cells in a latent form (R. G. Ivey, E. C. Henry, A. M. Lee, L. Klepper, S. K. Krueger, and R. H. Meints, Virology 220:267-273, 1996). In this article we present evidence that the two FsV genomes are integrated into the host genome during vegetative growth. The FsV genome integration sites were identified by cloning the regions where the FsV genome is linked to the host DNA. FsV-158 and FsV-178 are integrated into two distinct locations in the algal genome. In contrast, the integration sites in the two viral genomes are identical. Notably, the integration sites in the host and viruses contain GC and CG dinucleotide sequences, respectively, from which the GC sequences are recovered at both host-virus junctions. The splice sites in the two FsV genomes are predicted to form a stem-loop structure with the CG dinucleotide in the loop portion.

scholarly journals Does the Zinc Finger Antiviral Protein (ZAP) Shape the Evolution of Herpesvirus Genomes?

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1857
Author(s):  
Yao-Tang Lin ◽  
Long-Fung Chau ◽  
Hannah Coutts ◽  
Matin Mahmoudi ◽  
Vayalena Drampa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Zinc Finger ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Antiviral Protein ◽  
Dna Viruses ◽  
Cpg Dinucleotides ◽  
Host Restriction ◽  
Counter Measures ◽  
Cpg Dinucleotide

An evolutionary arms race occurs between viruses and hosts. Hosts have developed an array of antiviral mechanisms aimed at inhibiting replication and spread of viruses, reducing their fitness, and ultimately minimising pathogenic effects. In turn, viruses have evolved sophisticated counter-measures that mediate evasion of host defence mechanisms. A key aspect of host defences is the ability to differentiate between self and non-self. Previous studies have demonstrated significant suppression of CpG and UpA dinucleotide frequencies in the coding regions of RNA and small DNA viruses. Artificially increasing these dinucleotide frequencies results in a substantial attenuation of virus replication, suggesting dinucleotide bias could facilitate recognition of non-self RNA. The interferon-inducible gene, zinc finger antiviral protein (ZAP) is the host factor responsible for sensing CpG dinucleotides in viral RNA and restricting RNA viruses through direct binding and degradation of the target RNA. Herpesviruses are large DNA viruses that comprise three subfamilies, alpha, beta and gamma, which display divergent CpG dinucleotide patterns within their genomes. ZAP has recently been shown to act as a host restriction factor against human cytomegalovirus (HCMV), a beta-herpesvirus, which in turn evades ZAP detection by suppressing CpG levels in the major immediate-early transcript IE1, one of the first genes expressed by the virus. While suppression of CpG dinucleotides allows evasion of ZAP targeting, synonymous changes in nucleotide composition that cause genome biases, such as low GC content, can cause inefficient gene expression, especially in unspliced transcripts. To maintain compact genomes, the majority of herpesvirus transcripts are unspliced. Here we discuss how the conflicting pressures of ZAP evasion, the need to maintain compact genomes through the use of unspliced transcripts and maintaining efficient gene expression may have shaped the evolution of herpesvirus genomes, leading to characteristic CpG dinucleotide patterns.

scholarly journals An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses

2021 ◽  
Author(s):  
Sifan Ye ◽  
Congyu Lu ◽  
Ye Qiu ◽  
Heping Zheng ◽  
Xingyi Ge ◽  
...  
Keyword(s):  
Gc Content ◽  
Tissue Tropism ◽  
Virus Species ◽  
Interacting Proteins ◽  
Random Forest Algorithm ◽  
Dna Viruses ◽  
Human Virus ◽  
Age Dependent ◽  
Human Viruses ◽  
Viral Receptors

Viruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed. This study curated an atlas of human viruses from public databases and literatures, and built the Human Virus Database (HVD) available at http://computationalbiology.cn/humanVirusBase/#/. The HVD contains 1,131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue range of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue range of DNA viruses was predicted using a random-forest algorithm with a medium performance. Overall, the study not only provides a valuable resource for further studies of human viruses, but also deepens our understanding towards the diversity and tissue tropism of human viruses.

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