@misc{ParaskevopoulouDennisWeithoffetal.2019, author = {Paraskevopoulou, Sofia and Dennis, Alice B. and Weithoff, Guntram and Hartmann, Stefanie and Tiedemann, Ralph}, title = {Within species expressed genetic variability and gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {796}, issn = {1866-8372}, doi = {10.25932/publishup-44105}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-441050}, pages = {23}, year = {2019}, abstract = {Genetic divergence is impacted by many factors, including phylogenetic history, gene flow, genetic drift, and divergent selection. Rotifers are an important component of aquatic ecosystems, and genetic variation is essential to their ongoing adaptive diversification and local adaptation. In addition to coding sequence divergence, variation in gene expression may relate to variable heat tolerance, and can impose ecological barriers within species. Temperature plays a significant role in aquatic ecosystems by affecting species abundance, spatio-temporal distribution, and habitat colonization. Recently described (formerly cryptic) species of the Brachionus calyciflorus complex exhibit different temperature tolerance both in natural and in laboratory studies, and show that B. calyciflorus sensu stricto (s.s.) is a thermotolerant species. Even within B. calyciflorus s.s., there is a tendency for further temperature specializations. Comparison of expressed genes allows us to assess the impact of stressors on both expression and sequence divergence among disparate populations within a single species. Here, we have used RNA-seq to explore expressed genetic diversity in B. calyciflorus s.s. in two mitochondrial DNA lineages with different phylogenetic histories and differences in thermotolerance. We identify a suite of candidate genes that may underlie local adaptation, with a particular focus on the response to sustained high or low temperatures. We do not find adaptive divergence in established candidate genes for thermal adaptation. Rather, we detect divergent selection among our two lineages in genes related to metabolism (lipid metabolism, metabolism of xenobiotics).}, language = {en} } @article{ParaskevopoulouDennisWeithoffetal.2019, author = {Paraskevopoulou, Sofia and Dennis, Alice B. and Weithoff, Guntram and Hartmann, Stefanie and Tiedemann, Ralph}, title = {Within species expressed genetic variability and gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto}, series = {PLoS ONE}, volume = {9}, journal = {PLoS ONE}, number = {14}, publisher = {PLoS ONE}, address = {San Francisco, California}, issn = {1932-6203}, doi = {10.1371/journal.pone.0223134}, pages = {21}, year = {2019}, abstract = {Genetic divergence is impacted by many factors, including phylogenetic history, gene flow, genetic drift, and divergent selection. Rotifers are an important component of aquatic ecosystems, and genetic variation is essential to their ongoing adaptive diversification and local adaptation. In addition to coding sequence divergence, variation in gene expression may relate to variable heat tolerance, and can impose ecological barriers within species. Temperature plays a significant role in aquatic ecosystems by affecting species abundance, spatio-temporal distribution, and habitat colonization. Recently described (formerly cryptic) species of the Brachionus calyciflorus complex exhibit different temperature tolerance both in natural and in laboratory studies, and show that B. calyciflorus sensu stricto (s.s.) is a thermotolerant species. Even within B. calyciflorus s.s., there is a tendency for further temperature specializations. Comparison of expressed genes allows us to assess the impact of stressors on both expression and sequence divergence among disparate populations within a single species. Here, we have used RNA-seq to explore expressed genetic diversity in B. calyciflorus s.s. in two mitochondrial DNA lineages with different phylogenetic histories and differences in thermotolerance. We identify a suite of candidate genes that may underlie local adaptation, with a particular focus on the response to sustained high or low temperatures. We do not find adaptive divergence in established candidate genes for thermal adaptation. Rather, we detect divergent selection among our two lineages in genes related to metabolism (lipid metabolism, metabolism of xenobiotics).}, language = {en} } @article{KaechDennisVorburger2021, author = {Kaech, Heidi and Dennis, Alice B. and Vorburger, Christoph}, title = {Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa}, series = {BMC genomics}, volume = {22}, journal = {BMC genomics}, number = {1}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/s12864-021-07742-8}, pages = {21}, year = {2021}, abstract = {Background Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly. Results We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402. Conclusions Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola.}, language = {en} } @article{ParaskevopoulouDennisWeithoffetal.2020, author = {Paraskevopoulou, Sofia and Dennis, Alice B. and Weithoff, Guntram and Tiedemann, Ralph}, title = {Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers}, series = {Scientific Reports}, volume = {10}, journal = {Scientific Reports}, publisher = {Macmillan Publishers Limited, part of Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-020-70173-0}, pages = {15}, year = {2020}, abstract = {Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species' adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.}, language = {en} } @misc{ParaskevopoulouDennisWeithoffetal.2020, author = {Paraskevopoulou, Sofia and Dennis, Alice B. and Weithoff, Guntram and Tiedemann, Ralph}, title = {Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {1012}, issn = {1866-8372}, doi = {10.25932/publishup-48228}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-482280}, pages = {17}, year = {2020}, abstract = {Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species' adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.}, language = {en} } @misc{KaechMatheHubertDennisetal.2017, author = {K{\"a}ch, Heidi and Math{\´e}-Hubert, Hugo and Dennis, Alice B. and Vorburger, Christoph}, title = {Rapid evolution of symbiont-­mediated resistance compromises biological control of aphids by parasitoids}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {620}, issn = {1866-8372}, doi = {10.25932/publishup-42354}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-423542}, pages = {11}, year = {2017}, abstract = {There is growing interest in biological control as a sustainable and environmentally friendly way to control pest insects. Aphids are among the most detrimental agricultural pests worldwide, and parasitoid wasps are frequently employed for their control. The use of asexual parasitoids may improve the effectiveness of biological control because only females kill hosts and because asexual populations have a higher growth rate than sexuals. However, asexuals may have a reduced capacity to track evolutionary change in their host populations. We used a factorial experiment to compare the ability of sexual and asexual populations of the parasitoid Lysiphlebus fabarum to control caged populations of black bean aphids (Aphis fabae) of high and low clonal diversity. The aphids came from a natural population, and one-­third of the aphid clones harbored Hamiltonella defensa, a heritable bacterial endosymbiont that increases resistance to parasitoids. We followed aphid and parasitoid population dynamics for 3 months but found no evidence that the reproductive mode of parasitoids affected their effectiveness as biocontrol agents, independent of host clonal diversity. Parasitoids failed to control aphids in most cases, because their introduction resulted in strong selection for clones protected by H. defensa. The increasingly resistant aphid populations escaped control by parasitoids, and we even observed parasitoid extinctions in many cages. The rapid evolution of symbiont-­conferred resistance in turn imposed selection on parasitoids. In cages where asexual parasitoids persisted until the end of the experiment, they became dominated by a single genotype able to overcome the protection provided by H. defensa. Thus, there was evidence for parasitoid counteradaptation, but it was generally too slow for parasitoids to regain control over aphid populations. It appears that when pest aphids possess defensive symbionts, the presence of parasitoid genotypes able to overcome symbiont-­conferred resistance is more important for biocontrol success than their reproductive mode.}, language = {en} } @article{KaechMatheHubertDennisetal.2018, author = {K{\"a}ch, Heidi and Mathe-Hubert, Hugo and Dennis, Alice B. and Vorburger, Christoph}, title = {Rapid evolution of symbiont-mediated resistance compromises biological control of aphids by parasitoids}, series = {Evolutionary applications}, volume = {11}, journal = {Evolutionary applications}, number = {2}, publisher = {Wiley}, address = {Hoboken}, issn = {1752-4571}, doi = {10.1111/eva.12532}, pages = {220 -- 230}, year = {2018}, abstract = {There is growing interest in biological control as a sustainable and environmentally friendly way to control pest insects. Aphids are among the most detrimental agricultural pests worldwide, and parasitoid wasps are frequently employed for their control. The use of asexual parasitoids may improve the effectiveness of biological control because only females kill hosts and because asexual populations have a higher growth rate than sexuals. However, asexuals may have a reduced capacity to track evolutionary change in their host populations. We used a factorial experiment to compare the ability of sexual and asexual populations of the parasitoid Lysiphlebus fabarum to control caged populations of black bean aphids (Aphis fabae) of high and low clonal diversity. The aphids came from a natural population, and one-third of the aphid clones harbored Hamiltonella defensa, a heritable bacterial endosymbiont that increases resistance to parasitoids. We followed aphid and parasitoid population dynamics for 3months but found no evidence that the reproductive mode of parasitoids affected their effectiveness as biocontrol agents, independent of host clonal diversity. Parasitoids failed to control aphids in most cases, because their introduction resulted in strong selection for clones protected by H.defensa. The increasingly resistant aphid populations escaped control by parasitoids, and we even observed parasitoid extinctions in many cages. The rapid evolution of symbiont-conferred resistance in turn imposed selection on parasitoids. In cages where asexual parasitoids persisted until the end of the experiment, they became dominated by a single genotype able to overcome the protection provided by H.defensa. Thus, there was evidence for parasitoid counteradaptation, but it was generally too slow for parasitoids to regain control over aphid populations. It appears that when pest aphids possess defensive symbionts, the presence of parasitoid genotypes able to overcome symbiont-conferred resistance is more important for biocontrol success than their reproductive mode.}, language = {en} } @article{TwortDennisParketal.2017, author = {Twort, Victoria G. and Dennis, Alice B. and Park, Duckchul and Lomas, Kathryn F. and Newcomb, Richard D. and Buckley, Thomas R.}, title = {Positive selection and comparative molecular evolution of reproductive proteins from New Zealand tree weta (Orthoptera, Hemideina)}, series = {PLoS one}, volume = {12}, journal = {PLoS one}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0188147}, pages = {144 -- 170}, year = {2017}, abstract = {Animal reproductive proteins, especially those in the seminal fluid, have been shown to have higher levels of divergence than non-reproductive proteins and are often evolving adaptively. Seminal fluid proteins have been implicated in the formation of reproductive barriers between diverging lineages, and hence represent interesting candidates underlying speciation. RNA-seq was used to generate the first male reproductive transcriptome for the New Zealand tree weta species Hemideina thoracica and H. crassidens. We identified 865 putative reproductive associated proteins across both species, encompassing a diverse range of functional classes. Candidate gene sequencing of nine genes across three Hemideina, and two Deinacrida species suggests that H. thoracica has the highest levels of intra-specific genetic diversity. Non-monophyly was observed in the majority of sequenced genes indicating that either gene flow may be occurring between the species, or that reciprocal monophyly at these loci has yet to be attained. Evidence for positive selection was found for one lectin-related reproductive protein, with an overall omega of 7.65 and one site in particular being under strong positive selection. This candidate gene represents the first step in the identification of proteins underlying the evolutionary basis of weta reproduction and speciation.}, language = {en} } @inproceedings{DennisInaebnit2021, author = {Dennis, Alice B. and In{\"a}bnit, Thomas}, title = {Physiological and genomic variation among cryptic species of a marsh snail (Melampus bidentatus)}, series = {Integrative and comparative biology / Society of Integrative and Comparative Biology}, volume = {61}, booktitle = {Integrative and comparative biology / Society of Integrative and Comparative Biology}, publisher = {Oxford University Press}, address = {Oxford}, issn = {1540-7063}, doi = {10.1093/icb/icab001}, pages = {E195 -- E196}, year = {2021}, language = {en} } @article{DennisPatelOliveretal.2017, author = {Dennis, Alice B. and Patel, Vilas and Oliver, Kerry M. and Vorburger, Christoph}, title = {Parasitoid gene expression changes after adaptation to symbiont-protected hosts}, series = {Evolution}, volume = {71}, journal = {Evolution}, publisher = {Wiley}, address = {Hoboken}, issn = {0014-3820}, doi = {10.1111/evo.13333}, pages = {2599 -- 2617}, year = {2017}, abstract = {Reciprocal selection between aphids, their protective endosymbionts, and the parasitoid wasps that prey upon them offers an opportunity to study the basis of their coevolution. We investigated adaptation to symbiont\&\#8208;conferred defense by rearing the parasitoid wasp Lysiphlebus fabarum on aphids (Aphis fabae) possessing different defensive symbiont strains (Hamiltonella defensa). After ten generations of experimental evolution, wasps showed increased abilities to parasitize aphids possessing the H. defensa strain they evolved with, but not aphids possessing the other strain. We show that the two symbiont strains encode different toxins, potentially creating different targets for counter\&\#8208;adaptation. Phenotypic and behavioral comparisons suggest that neither life\&\#8208;history traits nor oviposition behavior differed among evolved parasitoid lineages. In contrast, comparative transcriptomics of adult female wasps identified a suite of differentially expressed genes among lineages, even when reared in a common, symbiont\&\#8208;free, aphid host. In concurrence with the specificity of each parasitoid lineages' infectivity, most differentially expressed parasitoid transcripts were also lineage\&\#8208;specific. These transcripts are enriched with putative venom toxins and contain highly expressed, potentially defensive viral particles. Together, these results suggest that wild populations of L. fabarum employ a complicated offensive arsenal with sufficient genetic variation for wasps to adapt rapidly and specifically to their hosts' microbial defenses.}, language = {en} } @article{MattheyDoretvanderKooiJeffriesetal.2019, author = {Matthey-Doret, Cyril and van der Kooi, Casper J. and Jeffries, Daniel L. and Bast, Jens and Dennis, Alice B. and Vorburger, Christoph and Schwander, Tanja}, title = {Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp}, series = {Genome biology and evolution}, volume = {11}, journal = {Genome biology and evolution}, number = {10}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1759-6653}, doi = {10.1093/gbe/evz219}, pages = {2954 -- 2962}, year = {2019}, abstract = {Sex determination has evolved in a variety of ways and can depend on environmental and genetic signals. A widespread form of genetic sex determination is haplodiploidy, where unfertilized, haploid eggs develop into males and fertilized diploid eggs into females. One of the molecular mechanisms underlying haplodiploidy in Hymenoptera, the large insect order comprising ants, bees, and wasps, is complementary sex determination (CSD). In species with CSD, heterozygosity at one or several loci induces female development. Here, we identify the genomic regions putatively underlying multilocus CSD in the parasitoid wasp Lysiphlebus fabarum using restriction -site associated DNA sequencing. By analyzing segregation patterns at polymorphic sites among 331 diploid males and females, we identify up to four CSD candidate regions, all on different chromosomes. None of the candidate regions feature evidence for homology with the csd gene from the honey bee, the only species in which CSD has been characterized, suggesting that CSD in L. fabarum is regulated via a novel molecular mechanism. Moreover, no homology is shared between the candidate loci, in contrast to the idea that multilocus CSD should emerge from duplications of an ancestral single -locus system. Taken together, our results suggest that the molecular mechanisms underlying CSD in Hymenoptera are not conserved between species, raising the question as to whether CSD may have evolved multiple times independently in the group.}, language = {en} } @article{AutenriethHartmannLahetal.2018, author = {Autenrieth, Marijke and Hartmann, Stefanie and Lah, Ljerka and Roos, Anna and Dennis, Alice B. and Tiedemann, Ralph}, title = {High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12932}, pages = {1469 -- 1481}, year = {2018}, abstract = {The harbour porpoise (Phocoena phocoena) is a highly mobile cetacean found across the Northern hemisphere. It occurs in coastal waters and inhabits basins that vary broadly in salinity, temperature and food availability. These diverse habitats could drive subtle differentiation among populations, but examination of this would be best conducted with a robust reference genome. Here, we report the first harbour porpoise genome, assembled de novo from an individual originating in the Kattegat Sea (Sweden). The genome is one of the most complete cetacean genomes currently available, with a total size of 2.39 Gb and 50\% of the total length found in just 34 scaffolds. Using 122 of the longest scaffolds, we were able to show high levels of synteny with the genome of the domestic cattle (Bos taurus). Our draft annotation comprises 22,154 predicted genes, which we further annotated through matches to the NCBI nucleotide database, GO categorization and motif prediction. Within the predicted genes, we have confirmed the presence of >20 genes or gene families that have been associated with adaptive evolution in other cetaceans. Overall, this genome assembly and draft annotation represent a crucial addition to the genomic resources currently available for the study of porpoises and Phocoenidae evolution, phylogeny and conservation.}, language = {en} } @article{DennisBallesterosRobinetal.2020, author = {Dennis, Alice B. and Ballesteros, Gabriel I. and Robin, St{\´e}phanie and Schrader, Lukas and Bast, Jens and Bergh{\"o}fer, Jan and Beukeboom, Leo W. and Belghazi, Maya and Bretaudeau, Anthony and Buellesbach, Jan and Cash, Elizabeth and Colinet, Dominique and Dumas, Zo{\´e} and Errbii, Mohammed and Falabella, Patrizia and Gatti, Jean-Luc and Geuverink, Elzemiek and Gibson, Joshua D. and Hertaeg, Corinne and Hartmann, Stefanie and Jacquin-Joly, Emmanuelle and Lammers, Mark and Lavandero, Blas I. and Lindenbaum, Ina and Massardier-Galata, Lauriane and Meslin, Camille and Montagn{\´e}, Nicolas and Pak, Nina and Poiri{\´e}, Maryl{\`e}ne and Salvia, Rosanna and Smith, Chris R. and Tagu, Denis and Tares, Sophie and Vogel, Heiko and Schwander, Tanja and Simon, Jean-Christophe and Figueroa, Christian C. and Vorburger, Christoph and Legeai, Fabrice and Gadau, J{\"u}rgen}, title = {Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum}, series = {BMC Genomics}, volume = {21}, journal = {BMC Genomics}, publisher = {BioMed Central}, address = {London}, issn = {1471-2164}, doi = {10.1186/s12864-020-6764-0}, pages = {27}, year = {2020}, abstract = {Background Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. Results We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8\%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. Conclusions These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.}, language = {en} } @misc{DennisBallesterosRobinetal.2020, author = {Dennis, Alice B. and Ballesteros, Gabriel I. and Robin, St{\´e}phanie and Schrader, Lukas and Bast, Jens and Bergh{\"o}fer, Jan and Beukeboom, Leo W. and Belghazi, Maya and Bretaudeau, Anthony and Buellesbach, Jan and Cash, Elizabeth and Colinet, Dominique and Dumas, Zo{\´e} and Errbii, Mohammed and Falabella, Patrizia and Gatti, Jean-Luc and Geuverink, Elzemiek and Gibson, Joshua D. and Hertaeg, Corinne and Hartmann, Stefanie and Jacquin-Joly, Emmanuelle and Lammers, Mark and Lavandero, Blas I. and Lindenbaum, Ina and Massardier-Galata, Lauriane and Meslin, Camille and Montagn{\´e}, Nicolas and Pak, Nina and Poiri{\´e}, Maryl{\`e}ne and Salvia, Rosanna and Smith, Chris R. and Tagu, Denis and Tares, Sophie and Vogel, Heiko and Schwander, Tanja and Simon, Jean-Christophe and Figueroa, Christian C. and Vorburger, Christoph and Legeai, Fabrice and Gadau, J{\"u}rgen}, title = {Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {989}, issn = {1866-8372}, doi = {10.25932/publishup-47612}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476129}, pages = {29}, year = {2020}, abstract = {Background Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. Results We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8\%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. Conclusions These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.}, language = {en} } @misc{ObbardShiRobertsetal.2020, author = {Obbard, Darren J. and Shi, Mang and Roberts, Katherine E. and Longdon, Ben and Dennis, Alice B.}, title = {A new lineage of segmented RNA viruses infecting animals}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1}, issn = {1866-8372}, doi = {10.25932/publishup-51604}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-516040}, pages = {12}, year = {2020}, abstract = {Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.}, language = {en} } @article{ObbardShiRobertsetal.2020, author = {Obbard, Darren J. and Shi, Mang and Roberts, Katherine E. and Longdon, Ben and Dennis, Alice B.}, title = {A new lineage of segmented RNA viruses infecting animals}, series = {Virus Evolution}, volume = {6}, journal = {Virus Evolution}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2057-1577}, doi = {10.1093/ve/vez061}, pages = {1 -- 10}, year = {2020}, abstract = {Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called 'dark' virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose 'dark' virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.}, language = {en} }