scholarly journals Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps

2019 ◽  
Author(s):  
Fabrice Legeai ◽  
Bernardo F. Santos ◽  
Stéphanie Robin ◽  
Anthony Bretaudeau ◽  
Rebecca B. Dikow ◽  
...  
Keyword(s):  
Particle Production ◽  
Biological Properties ◽  
Gene Content ◽  
Wasp Species ◽  
Virulence Proteins ◽  
Endogenous Viruses ◽  
Genomic Environment ◽  
Hyposoter Didymator ◽  
Conserved Gene ◽  
Genomic Regions

AbstractPolydnaviruses (PDVs) are mutualistic endogenous viruses associated with some lineages of parasitoid wasps that allow successful development of the wasps within their hosts. PDVs include two taxa resulting from independent virus acquisitions in braconid (bracoviruses) and ichneumonid wasps (ichnoviruses). PDV genomes are fully incorporated into the wasp genomes and comprise (1) virulence genes located on proviral segments that are packaged into the viral particle, and (2) genes involved in the production of the viral particles, which are not encapsidated. Whereas the genomic organization of bracoviruses within the wasp genome is relatively well known, the architecture of endogenous ichnoviruses remains poorly understood. We sequenced the genome of two ichnovirus-carrying wasp species, Hyposoter didymator and Campoletis sonorensis. Complete assemblies with long scaffold sizes allowed identification of the integrated ichnovirus, highlighting an extreme dispersion within the wasp genomes of the viral loci, i.e. isolated proviral segments and clusters of replication genes. Comparing the two wasp species, proviral segments harbor distinct gene content and variable genomic environment, whereas viral machinery clusters show conserved gene content and order, and can be inserted in collinear wasp genomic regions. This distinct architecture is consistent with the biological properties of the two viral elements: proviral segments producing virulence proteins allowing parasitism success are fine-tuned to the host physiology, while an ancestral viral architecture was likely maintained for the genes involved in virus particle production. Finding a distinct genomic architecture of ichnoviruses and bracoviruses highlights different evolutionary trajectories leading to virus domestication in the two wasp lineages.

scholarly journals Cotesia congregata Bracovirus Circles Encoding PTP and Ankyrin Genes Integrate into the DNA of Parasitized Manduca sexta Hemocytes

2018 ◽  
Vol 92 (15) ◽  
Author(s):  
Germain Chevignon ◽  
Georges Periquet ◽  
Gabor Gyapay ◽  
Nathalie Vega-Czarny ◽  
Karine Musset ◽  
...  
Keyword(s):  
Manduca Sexta ◽  
High Throughput Sequencing ◽  
Particle Production ◽  
Parasitoid Wasp ◽  
Gene Families ◽  
Parasitoid Wasps ◽  
Content Type ◽  
Virulence Proteins ◽  
Cotesia Congregata ◽  
Dividing Cells

ABSTRACT Polydnaviruses (PDVs) are essential for the parasitism success of tens of thousands of species of parasitoid wasps. PDVs are present in wasp genomes as proviruses, which serve as the template for the production of double-stranded circular viral DNA carrying virulence genes that are injected into lepidopteran hosts. PDV circles do not contain genes coding for particle production, thereby impeding viral replication in caterpillar hosts during parasitism. Here, we investigated the fate of PDV circles of Cotesia congregata bracovirus during parasitism of the tobacco hornworm, Manduca sexta, by the wasp Cotesia congregata. Sequences sharing similarities with host integration motifs (HIMs) of Microplitis demolitor bracovirus (MdBV) circles involved in integration into DNA could be identified in 12 CcBV circles, which encode PTP and VANK gene families involved in host immune disruption. A PCR approach performed on a subset of these circles indicated that they persisted in parasitized M. sexta hemocytes as linear forms, possibly integrated in host DNA. Furthermore, by using a primer extension capture method based on these HIMs and high-throughput sequencing, we could show that 8 out of 9 circles tested were integrated in M. sexta hemocyte genomic DNA and that integration had occurred specifically using the HIM, indicating that an HIM-mediated specific mechanism was involved in their integration. Investigation of BV circle insertion sites at the genome scale revealed that certain genomic regions appeared to be enriched in BV insertions, but no specific M. sexta target site could be identified. IMPORTANCE The identification of a specific and efficient integration mechanism shared by several bracovirus species opens the question of its role in braconid parasitoid wasp parasitism success. Indeed, results obtained here show massive integration of bracovirus DNA in somatic immune cells at each parasitism event of a caterpillar host. Given that bracoviruses do not replicate in infected cells, integration of viral sequences in host DNA might allow the production of PTP and VANK virulence proteins within newly dividing cells of caterpillar hosts that continue to develop during parasitism. Furthermore, this integration process could serve as a basis to understand how PDVs mediate the recently identified gene flux between parasitoid wasps and Lepidoptera and the frequency of these horizontal transfer events in nature.

scholarly journals The Jekyll and Hyde Symbiont: Could Wolbachia Be a Nutritional Mutualist?

2019 ◽  
Vol 202 (4) ◽  
Author(s):  
Irene L. G. Newton ◽  
Danny W. Rice
Keyword(s):  
Large Scale ◽  
Gene Content ◽  
Scale Analysis ◽  
Content Type ◽  
Wolbachia Pipientis ◽  
Beneficial Role ◽  
Intracellular Symbiont ◽  
Large Scale Analysis ◽  
Conserved Gene

ABSTRACT The most common intracellular symbiont on the planet—Wolbachia pipientis—is infamous largely for the reproductive manipulations induced in its host. However, more recent evidence suggests that this bacterium may also serve as a nutritional mutualist in certain host backgrounds and for certain metabolites. We performed a large-scale analysis of conserved gene content across all sequenced Wolbachia genomes to infer potential nutrients made by these symbionts. We review and critically evaluate the prior research supporting a beneficial role for Wolbachia and suggest future experiments to test hypotheses of metabolic provisioning.

scholarly journals Recent advances in understanding mitochondrial genome diversity

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 270 ◽  
Author(s):  
Rafael Zardoya
Keyword(s):  
Mitochondrial Genome ◽  
High Throughput Sequencing ◽  
Gene Content ◽  
Mitochondrial Genomes ◽  
Genetic Codes ◽  
Evolutionary Trajectories ◽  
Gene Structures ◽  
Mitochondrial Genome Diversity ◽  
Conserved Gene ◽  
Self Splicing

Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.

scholarly journals Gene composition as a potential barrier to large recombinations in the bacterial pathogen Klebsiella pneumoniae

2018 ◽  
Author(s):  
Francesco Comandatore ◽  
Davide Sassera ◽  
Sion C. Bayliss ◽  
Erika Scaltriti ◽  
Stefano Gaiarsa ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Recombination Event ◽  
Bacterial Species ◽  
Bacterial Pathogen ◽  
Genomic Region ◽  
Gene Content ◽  
Entire Genome ◽  
Clonal Group ◽  
Recent Emergence ◽  
Genomic Regions

AbstractKlebsiella pneumoniae (Kp) is one of the most important nosocomial pathogens world-wide, being responsible for frequent hospital outbreaks and causing sepsis and multi-organ infections with a high mortality rate and frequent hospital outbreaks. The most prevalent and widely disseminated lineage of K. pneumoniae is clonal group 258 (CG258), which includes the highly resistant “high-risk” genotypes ST258 and ST11. Recent studies revealed that very large recombination events have occurred during the recent emergence of Kp lineages. A striking example is provided by ST258, which has undergone a recombination event that replaced over 1 Mb of the genome with DNA from an unrelated Kp donor. Although several examples of this phenomenon have been documented in Kp and other bacterial species, the significance of these very large recombination events for the emergence of either hyper-virulent or resistant clones remains unclear. Here we present an analysis of 834 Kp genomes that provides data on the frequency of these very large recombination events (defined as those involving >100Kb), their distribution within the genome, and the dynamics of gene flow within the Kp population. We note that very large recombination events occur frequently, and in multiple lineages, and that the majority of recombinational exchanges are clustered within two overlapping genomic regions, which result to be involved by recombination events with different frequencies. Our results also indicate that certain non-CG258 lineages are more likely to act as donors to CG258 recipients than others. Furthermore, comparison of gene content in CG258 and non-CG258 strains agrees with this pattern, suggesting that the success of a large recombination depends on gene composition in the exchanged genomic portion.Author SummaryKlebsiella pneumoniae (Kp) is an opportunistic bacterial pathogen, a major cause of deadly infections and outbreaks in hospitals worldwide. This bacterium is able to exchange large genomic portions (up to a fourth of the entire genome) within a single recombination event. Indeed, the most epidemiologically important Kp clone, is actually a hybrid which emerged after a > 1Mb recombination event. In this work, we investigated how recombinations affected the evolution of the most studied Kp Clonal Group, CG258. We found that large recombinations occurred frequently during Kp evolution, and occurred preferentially in a well-delimited genomic region. Furthermore, we found that four epidemiologically important clones emerged after large recombinations. We identified the donors of several large recombinations: despite many Kp lineages acted as donors during CG258 evolution, two of them have been involved more frequently. We hypothesize that the observed pattern of donors-recipients in recombinations, and the presence of a large recombinogenic region in Kp genome, could be related to gene composition. Indeed, genomic analyses showed a pattern compatible with this hypothesis, suggesting that gene content can represent a main factor in the success of a large recombination.

scholarly journals Independent Evolution of Sex Chromosomes in Eublepharid Geckos, a Lineage with Environmental and Genotypic Sex Determination

2020 ◽  
Author(s):  
Eleonora Pensabene ◽  
Lukáš Kratochvíl ◽  
Michail Rovatsos
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Gene Content ◽  
Gene Copy ◽  
Specific Gene ◽  
Evolution Of Sex ◽  
Copy Numbers ◽  
Genotypic Sex Determination ◽  
The Difference ◽  
Genomic Regions

Geckos demonstrate a remarkable variability in sex determination systems, but our limited knowledge prohibits accurate conclusions on the evolution of sex determination in this group. Eyelid geckos (Eublepharidae) are of particular interest, as they encompass species with both environmental and genotypic sex determination. We identified for the first time the X-specific gene content in the Yucatán banded gecko, Coleonyx elegans, possessing X1X1X2X2/X1X2Y multiple sex chromosomes by comparative genome coverage analysis between sexes. The X-specific gene content of Coleonyx elegans was revealed to be partially homologous to genomic regions linked to the chicken autosomes 1, 6 and 11. A qPCR-based test was applied to validate a subset of X-specific genes by comparing the difference in gene copy numbers between sexes, and to explore the homology of sex chromosomes across 11 eublepharid, two phyllodactylid and one sphaerodactylid species. Homologous sex chromosomes are shared between Coleonyx elegans and Coleonyx mitratus, two species diverged approximately 34 million years ago, but not with other tested species. As far as we know, the X-specific gene content of Coleonyx elegans / Coleonyx mitratus was never involved in the sex chromosomes of other gecko lineages, indicating that the sex chromosomes in this clade of eublepharid geckos evolved independently.

scholarly journals Pseudogenization, genome streamlining and specific gene repertoire landmark the genomes ofCarnobacterium maltaromaticumisolated from diseased sharks

2019 ◽  
Author(s):  
Laura Martinez Steele ◽  
Christopher G Lowe ◽  
Mark S Okihiro ◽  
Jesse G. Dillon ◽  
Renaud Berlemont
Keyword(s):  
Specific Gene ◽  
Shark Species ◽  
Gene Repertoire ◽  
Genomic Signatures ◽  
Thresher Shark ◽  
Independent Life ◽  
Conserved Gene ◽  
Genomic Regions ◽  
High Degree

AbstractCarnobacterium maltaromaticumis a well-known pathogen of bony fish. More recently,C. maltaromaticumhave been isolated from the brain and inner ear of disorientated and stranded common thresher (Alopias vulpinus) and salmon shark (Lamna ditropis). While thresher shark strandings are recent, salmon sharks have been stranding for decades, suggesting a long-term association betweenC. maltaromaticumand sharks. Interestingly, some strains ofC. maltaromaticumare used by the food industry for their probiotic and antimicrobial activity. Here, we sequenced the genome of 9C. maltaromaticumstrains (SK-isolates) from diseased common thresher and salmon sharks and compared them to otherC. maltaromaticumstrains in order to identify the genomic signatures that differentiate the disease-associated from the innocuousC. maltaromaticumisolates. SK strains formed a monophyletic clade, with a conserved gene repertoire, and shared a high degree of pseudogenization even though isolates were from different shark species, locations, and across years. In addition, these strains displayed few virulence associated genes and unique genomic regions, some resulting from horizontal gene transfer. The association of diseased sharks and SK strains suggests their role as potential pathogens. Although the high degree of pseudogenization suggests a transition to a host-adapted lifestyle, a set of conserved functional genes highlights the need of essential functions required for a host-independent life style. Globally, this work identifies specific genomic signatures ofC. maltaromaticumstrains isolated from infected sharks, provides the framework to elucidate the role of SK strains in the development of the disease in sharks, and further investigate the dissemination of SK strains in populations of wild fish.

scholarly journals Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

2020 ◽  
Author(s):  
Jérémy Gauthier ◽  
Hélène Boulain ◽  
Joke J.F.A. van Vugt ◽  
Lyam Baudry ◽  
Emma Persyn ◽  
...  
Keyword(s):  
Particle Production ◽  
Parasitic Wasp ◽  
Viral Gene Expression ◽  
Parasitoid Wasp ◽  
Viral Gene ◽  
Parasitoid Wasps ◽  
Genomic Comparison ◽  
Immune Genes ◽  
Endogenous Viruses ◽  
First Time

AbstractMost endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.

scholarly journals Unbiased optical mapping of telomere-integrated endogenous human herpesvirus 6

2020 ◽  
Vol 117 (49) ◽  
pp. 31410-31416 ◽  
Author(s):  
Darren J. Wight ◽  
Giulia Aimola ◽  
Amr Aswad ◽  
Chi-Yu Jill Lai ◽  
Christian Bahamon ◽  
...  
Keyword(s):  
Optical Mapping ◽  
Human Herpesvirus ◽  
Low Complexity ◽  
Virus Genome ◽  
Sequencing Technologies ◽  
Site Mapping ◽  
Endogenous Viruses ◽  
High Resolution Map ◽  
Mapping Technology ◽  
Genomic Regions

Next-generation sequencing technologies allowed sequencing of thousands of genomes. However, there are genomic regions that remain difficult to characterize, including telomeres, centromeres, and other low-complexity regions, as well as transposable elements and endogenous viruses. Human herpesvirus 6A and 6B (HHV-6A and HHV-6B) are closely related viruses that infect most humans and can integrate their genomes into the telomeres of infected cells. Integration also occurs in germ cells, meaning that the virus can be inherited and result in individuals harboring the virus in every cell of their body. The integrated virus can reactivate and cause disease in humans. While it is well established that the virus resides in the telomere region, the integration locus is poorly defined due to the low sequence complexity (TTAGGG)n of telomeres that cannot be easily resolved through sequencing. We therefore employed genome imaging of the integrated HHV-6A and HHV-6B genomes using whole-genome optical site mapping technology. Using this technology, we identified which chromosome arm harbors the virus genome and obtained a high-resolution map of the integration loci of multiple patients. Surprisingly, this revealed long telomere sequences at the virus−subtelomere junction that were previously missed using PCR-based approaches. Contrary to what was previously thought, our technique revealed that the telomere lengths of chromosomes harboring the integrated virus genome were comparable to the other chromosomes. Taken together, our data shed light on the genetic structure of the HHV-6A and HHV-6B integration locus, demonstrating the utility of optical mapping for the analysis of genomic regions that are difficult to sequence.

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