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Cheng F, Dennis AB, Baumann O, Kirschbaum F, Abdelilah-Seyfried S, Tiedemann R. Gene and Allele-Specific Expression Underlying the Electric Signal Divergence in African Weakly Electric Fish. Mol Biol Evol 2024; 41:msae021. [PMID: 38410843 PMCID: PMC10897887 DOI: 10.1093/molbev/msae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/15/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
In the African weakly electric fish genus Campylomormyrus, electric organ discharge signals are strikingly different in shape and duration among closely related species, contribute to prezygotic isolation, and may have triggered an adaptive radiation. We performed mRNA sequencing on electric organs and skeletal muscles (from which the electric organs derive) from 3 species with short (0.4 ms), medium (5 ms), and long (40 ms) electric organ discharges and 2 different cross-species hybrids. We identified 1,444 upregulated genes in electric organ shared by all 5 species/hybrid cohorts, rendering them candidate genes for electric organ-specific properties in Campylomormyrus. We further identified several candidate genes, including KCNJ2 and KLF5, and their upregulation may contribute to increased electric organ discharge duration. Hybrids between a short (Campylomormyrus compressirostris) and a long (Campylomormyrus rhynchophorus) discharging species exhibit electric organ discharges of intermediate duration and showed imbalanced expression of KCNJ2 alleles, pointing toward a cis-regulatory difference at this locus, relative to electric organ discharge duration. KLF5 is a transcription factor potentially balancing potassium channel gene expression, a crucial process for the formation of an electric organ discharge. Unraveling the genetic basis of the species-specific modulation of the electric organ discharge in Campylomormyrus is crucial for understanding the adaptive radiation of this emerging model taxon of ecological (perhaps even sympatric) speciation.
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Affiliation(s)
- Feng Cheng
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alice B Dennis
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Laboratory of Adaptive Evolution and Genomics, Research Unit of Environmental and Evolutionary Biology, Institute of Life, Earth & Environment, University of Namur, Namur, Belgium
| | - Otto Baumann
- Department of Animal Physiology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Frank Kirschbaum
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Crop and Animal Science, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Salim Abdelilah-Seyfried
- Department of Animal Physiology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Cheng F, Dennis AB, Osuoha JI, Canitz J, Kirschbaum F, Tiedemann R. A new genome assembly of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha. BMC Genomics 2023; 24:129. [PMID: 36941548 PMCID: PMC10029256 DOI: 10.1186/s12864-023-09196-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/20/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus Campylomormyrus is mostly endemic to the Congo Basin. Campylomormyrus serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome assembly and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorpha fish in general and of electric fish in particular. RESULTS A high-quality weakly electric fish (C. compressirostris) genome was produced from a single individual with a genome size of 862 Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of Paramormyrops kingsleyae and Scleropages formosus. A Computational Analysis of gene Family Evolution (CAFE5) comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (Cyprinus carpio and Oncorhynchus mykiss). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of C. compressirostris. CONCLUSIONS We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appear to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among Campylomormyrus species.
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Affiliation(s)
- Feng Cheng
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alice B Dennis
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Laboratory of Adaptive Evolution and Genomics, Research Unit of Environmental and Evolutionary Biology, Institute of Life, Earth & Environnment, University of Namur, Namur, Belgium
| | - Josephine Ijeoma Osuoha
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Julia Canitz
- Senckenberg German Entomological Institute, Müncheberg, Germany
| | - Frank Kirschbaum
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Department of Crop and Animal Science, Faculty of Life Sciences, Humboldt University, Berlin, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Paul SC, Singh P, Dennis AB, Müller C. Intergenerational Effects of Early Life Starvation on Life-History, Consumption, and Transcriptome of a Holometabolous Insect. Am Nat 2022; 199:E229-E243. [DOI: 10.1086/719397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kaech H, Dennis AB, Vorburger C. Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa. BMC Genomics 2021; 22:449. [PMID: 34134631 PMCID: PMC8207614 DOI: 10.1186/s12864-021-07742-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/20/2021] [Indexed: 11/10/2022] Open
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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07742-8.
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Affiliation(s)
- Heidi Kaech
- Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland. .,D-USYS, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
| | - Alice B Dennis
- Institute of Biochemistry and Biology, University Potsdam, Potsdam, Germany
| | - Christoph Vorburger
- Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,D-USYS, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa CC, Vorburger C, Legeai F, Gadau J. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 2020; 21:376. [PMID: 32471448 PMCID: PMC7257214 DOI: 10.1186/s12864-020-6764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
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.
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Affiliation(s)
- Alice B Dennis
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland.
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Jens Bast
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
- Institute of Zoology, Universität zu Köln, 50674, Köln, Germany
| | - Jan Berghöfer
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, Marseille, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jan Buellesbach
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Elizabeth Cash
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Zoé Dumas
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Corinne Hertaeg
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Department of Environmental Systems Sciences, D-USYS, ETH Zürich, Zürich, Switzerland
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Mark Lammers
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Blas I Lavandero
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ina Lindenbaum
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nina Pak
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Chris R Smith
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
| | - Sophie Tares
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.
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Matthey-Doret C, van der Kooi CJ, Jeffries DL, Bast J, Dennis AB, Vorburger C, Schwander T. Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp. Genome Biol Evol 2020; 11:2954-2962. [PMID: 31596478 PMCID: PMC6821247 DOI: 10.1093/gbe/evz219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/22/2022] Open
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.
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Affiliation(s)
- Cyril Matthey-Doret
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Casper J van der Kooi
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, the Netherlands
| | - Daniel L Jeffries
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Jens Bast
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Alice B Dennis
- Institute of Integrative Biology, ETH Zürich, Switzerland.,Department of Aquatic Ecology, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland.,Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Germany
| | - Christoph Vorburger
- Institute of Integrative Biology, ETH Zürich, Switzerland.,Department of Aquatic Ecology, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Tanja Schwander
- Department of Ecology and Evolution, University of Lausanne, Switzerland
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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.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Mang Shi
- Charles Perkins Center, The University of Sydney, NSW 2006, Australia
| | - Katherine E Roberts
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Ben Longdon
- Biosciences, College of Life & Environmental Sciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK
| | - Alice B Dennis
- Department of Evolutionary Biology & Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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Lüthi MN, Vorburger C, Dennis AB. A Novel RNA Virus in the Parasitoid Wasp Lysiphlebus fabarum: Genomic Structure, Prevalence, and Transmission. Viruses 2020; 12:E59. [PMID: 31947801 PMCID: PMC7019493 DOI: 10.3390/v12010059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
We report on a novel RNA virus infecting the wasp Lysiphlebus fabarum, a parasitoid of aphids. This virus, tentatively named "Lysiphlebus fabarum virus" (LysV), was discovered in transcriptome sequences of wasps from an experimental evolution study in which the parasitoids were allowed to adapt to aphid hosts (Aphis fabae) with or without resistance-conferring endosymbionts. Based on phylogenetic analyses of the viral RNA-dependent RNA polymerase (RdRp), LysV belongs to the Iflaviridae family in the order of the Picornavirales, with the closest known relatives all being parasitoid wasp-infecting viruses. We developed an endpoint PCR and a more sensitive qPCR assay to screen for LysV in field samples and laboratory lines. These screens verified the occurrence of LysV in wild parasitoids and identified the likely wild-source population for lab infections in Western Switzerland. Three viral haplotypes could be distinguished in wild populations, of which two were found in the laboratory. Both vertical and horizontal transmission of LysV were demonstrated experimentally, and repeated sampling of laboratory populations suggests that the virus can form persistent infections without obvious symptoms in infected wasps.
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Affiliation(s)
- Martina N. Lüthi
- Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland; (C.V.); (A.B.D.)
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Christoph Vorburger
- Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland; (C.V.); (A.B.D.)
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Alice B. Dennis
- Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland; (C.V.); (A.B.D.)
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
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Paraskevopoulou S, Dennis AB, Weithoff G, Hartmann S, Tiedemann R. Within species expressed genetic variability and gene expression response to different temperatures in the rotifer Brachionus calyciflorus sensu stricto. PLoS One 2019; 14:e0223134. [PMID: 31568501 PMCID: PMC6768451 DOI: 10.1371/journal.pone.0223134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/14/2019] [Indexed: 01/14/2023] Open
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).
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Affiliation(s)
- Sofia Paraskevopoulou
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Unit of Ecology and Ecosystem Modelling, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- * E-mail:
| | - Alice B. Dennis
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Guntram Weithoff
- Unit of Ecology and Ecosystem Modelling, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Stefanie Hartmann
- Unit of Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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10
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Autenrieth M, Hartmann S, Lah L, Roos A, Dennis AB, Tiedemann R. High-quality whole-genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena). Mol Ecol Resour 2018; 18:1469-1481. [PMID: 30035363 DOI: 10.1111/1755-0998.12932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 11/27/2022]
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.
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Affiliation(s)
- Marijke Autenrieth
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Ljerka Lah
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Anna Roos
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Alice B Dennis
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Institute of Biochemistry and Biology, Evolutionary Biology/Systematic Zoology, University of Potsdam, Potsdam, Germany
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11
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Kelly AL, Gough T, Isreb M, Dhumal R, Jones JW, Nicholson S, Dennis AB, Paradkar A. In-process rheometry as a PAT tool for hot melt extrusion. Drug Dev Ind Pharm 2017; 44:670-676. [PMID: 29161918 DOI: 10.1080/03639045.2017.1408641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Real time measurement of melt rheology has been investigated as a Process Analytical Technology (PAT) to monitor hot melt extrusion of an Active Pharmaceutical Ingredient (API) in a polymer matrix. A developmental API was melt mixed with a commercial copolymer using a heated twin screw extruder at different API loadings and set temperatures. The extruder was equipped with an instrumented rheological slit die which incorporated three pressure transducers flush mounted to the die surface. Pressure drop measurements within the die at a range of extrusion throughputs were used to calculate rheological parameters, such as shear viscosity and exit pressure, related to shear and elastic melt flow properties, respectively. Results showed that the melt exhibited shear thinning behavior whereby viscosity decreased with increasing flow rate. Increase in drug loading and set extrusion temperature resulted in a reduction in melt viscosity. Shear viscosity and exit pressure measurements were found to be sensitive to API loading. These findings suggest that this technique could be used as a simple tool to measure material attributes in-line, to build better overall process understanding for hot melt extrusion.
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Affiliation(s)
- A L Kelly
- a Centre for Pharmaceutical Engineering Science , University of Bradford , Bradford , UK
| | - T Gough
- a Centre for Pharmaceutical Engineering Science , University of Bradford , Bradford , UK
| | - M Isreb
- a Centre for Pharmaceutical Engineering Science , University of Bradford , Bradford , UK
| | - R Dhumal
- a Centre for Pharmaceutical Engineering Science , University of Bradford , Bradford , UK
| | - J W Jones
- b Bristol-Myers Squibb Research and Development , Moreton , UK
| | - S Nicholson
- b Bristol-Myers Squibb Research and Development , Moreton , UK
| | - A B Dennis
- b Bristol-Myers Squibb Research and Development , Moreton , UK
| | - A Paradkar
- a Centre for Pharmaceutical Engineering Science , University of Bradford , Bradford , UK
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12
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Twort VG, Dennis AB, Park D, Lomas KF, Newcomb RD, Buckley TR. Positive selection and comparative molecular evolution of reproductive proteins from New Zealand tree weta (Orthoptera, Hemideina). PLoS One 2017; 12:e0188147. [PMID: 29131842 PMCID: PMC5683631 DOI: 10.1371/journal.pone.0188147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/01/2017] [Indexed: 11/18/2022] Open
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 intraspecific 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.
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Affiliation(s)
- Victoria G. Twort
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
- * E-mail:
| | | | | | | | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, New Zealand
| | - Thomas R. Buckley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Landcare Research, Auckland, New Zealand
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13
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Dennis AB, Patel V, Oliver KM, Vorburger C. Parasitoid gene expression changes after adaptation to symbiont-protected hosts. Evolution 2017; 71:2599-2617. [DOI: 10.1111/evo.13333] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Alice B. Dennis
- Institute of Integrative Biology; ETH Zürich; Zürich Switzerland
- EAWAG; Swiss Federal Institute of Aquatic Science and Technology; Dübendorf Switzerland
- Current address: Unit of Evolutionary Biology and Systematic Zoology, Institute of Biochemistry and Biology; University of Potsdam; Potsdam Germany
| | - Vilas Patel
- Department of Entomology; University of Georgia; Athens Georgia 30602
| | - Kerry M. Oliver
- Department of Entomology; University of Georgia; Athens Georgia 30602
| | - Christoph Vorburger
- Institute of Integrative Biology; ETH Zürich; Zürich Switzerland
- EAWAG; Swiss Federal Institute of Aquatic Science and Technology; Dübendorf Switzerland
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14
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Käch H, Mathé-Hubert H, Dennis AB, Vorburger C. Rapid evolution of symbiont-mediated resistance compromises biological control of aphids by parasitoids. Evol Appl 2017; 11:220-230. [PMID: 29387157 PMCID: PMC5775498 DOI: 10.1111/eva.12532] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022] Open
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.
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Affiliation(s)
- Heidi Käch
- Aquatic Ecology Eawag Dübendorf Switzerland.,Institute of Integrative Biology ETH Zürich Zürich Switzerland
| | | | - Alice B Dennis
- Institute for Biochemistry & Biology University of Potsdam Potsdam Germany
| | - Christoph Vorburger
- Aquatic Ecology Eawag Dübendorf Switzerland.,Institute of Integrative Biology ETH Zürich Zürich Switzerland
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15
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MacMillan HA, Knee JM, Dennis AB, Udaka H, Marshall KE, Merritt TJS, Sinclair BJ. Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome. Sci Rep 2016; 6:28999. [PMID: 27357258 PMCID: PMC4928047 DOI: 10.1038/srep28999] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/07/2016] [Indexed: 01/05/2023] Open
Abstract
Cold tolerance is a key determinant of insect distribution and abundance, and thermal acclimation can strongly influence organismal stress tolerance phenotypes, particularly in small ectotherms like Drosophila. However, there is limited understanding of the molecular and biochemical mechanisms that confer such impressive plasticity. Here, we use high-throughput mRNA sequencing (RNA-seq) and liquid chromatography – mass spectrometry (LC-MS) to compare the transcriptomes and metabolomes of D. melanogaster acclimated as adults to warm (rearing) (21.5 °C) or cold conditions (6 °C). Cold acclimation improved cold tolerance and led to extensive biological reorganization: almost one third of the transcriptome and nearly half of the metabolome were differentially regulated. There was overlap in the metabolic pathways identified via transcriptomics and metabolomics, with proline and glutathione metabolism being the most strongly-supported metabolic pathways associated with increased cold tolerance. We discuss several new targets in the study of insect cold tolerance (e.g. dopamine signaling and Na+-driven transport), but many previously identified candidate genes and pathways (e.g. heat shock proteins, Ca2+ signaling, and ROS detoxification) were also identified in the present study, and our results are thus consistent with and extend the current understanding of the mechanisms of insect chilling tolerance.
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Affiliation(s)
- Heath A MacMillan
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Jose M Knee
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Alice B Dennis
- Landcare Research, Auckland, New Zealand.,Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
| | - Hiroko Udaka
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Katie E Marshall
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Thomas J S Merritt
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Brent J Sinclair
- Department of Biology, University of Western Ontario, London, ON, Canada
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16
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Wu C, Crowhurst RN, Dennis AB, Twort VG, Liu S, Newcomb RD, Ross HA, Buckley TR. De Novo Transcriptome Analysis of the Common New Zealand Stick Insect Clitarchus hookeri (Phasmatodea) Reveals Genes Involved in Olfaction, Digestion and Sexual Reproduction. PLoS One 2016; 11:e0157783. [PMID: 27336743 PMCID: PMC4919086 DOI: 10.1371/journal.pone.0157783] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/03/2016] [Indexed: 11/21/2022] Open
Abstract
Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female olfactory gene repertoire revealed ten odorant binding proteins with three recently duplicated, 12 chemosensory proteins, 16 odorant receptors, and 17 ionotropic receptors. The majority of these olfactory genes were over-expressed in female antennae and have the inferred function of odorant reception. Others that were predominantly expressed in male terminalia (n = 3) and female midgut (n = 1) suggest they have a role in sexual reproduction and digestion, respectively. Over-represented transcripts in the midgut were enriched with digestive enzyme gene families. Clitarchus hookeri is likely to harbour nine members of an endogenous cellulase family (glycoside hydrolase family 9), two of which appear to be specific to the C. hookeri lineage. All of these cellulase sequences fall into four main phasmid clades and show gene duplication events occurred early in the diversification of Phasmatodea. In addition, C. hookeri genome is likely to express γ-proteobacteria pectinase transcripts that have recently been shown to be the result of horizontal transfer. We also predicted 711 male terminalia-enriched transcripts that are candidate accessory gland proteins, 28 of which were annotated to have molecular functions of peptidase activity and peptidase inhibitor activity, two groups being widely reported to regulate female reproduction through proteolytic cascades. Our study has yielded new insights into the genetic basis of odour detection, nutrient digestion, and male sexual traits in stick insects. The C. hookeri reference transcriptome, together with identified gene families, provides a comprehensive resource for studying the evolution of sensory perception, digestive systems, and reproductive success in phasmids.
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Affiliation(s)
- Chen Wu
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- * E-mail:
| | - Ross N. Crowhurst
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Alice B. Dennis
- Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Victoria G. Twort
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Shanlin Liu
- China National GeneBank, BGI-Shenzhen, Shen Zhen, China
| | - Richard D. Newcomb
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- New Zealand Institute for Plant & Food Research Ltd, Auckland, New Zealand
| | - Howard A. Ross
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Thomas R. Buckley
- Landcare Research, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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17
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Dunning LT, Dennis AB, Sinclair BJ, Newcomb RD, Buckley TR. Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus). Mol Ecol 2014; 23:2712-26. [DOI: 10.1111/mec.12767] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 04/10/2014] [Accepted: 04/16/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Luke T. Dunning
- Landcare Research; Private Bag 92170 Auckland New Zealand
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
| | - Alice B. Dennis
- Landcare Research; Private Bag 92170 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
| | - Brent J. Sinclair
- Department of Biology; The University of Western Ontario; London ON Canada N6G 1L3
| | - Richard D. Newcomb
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
- The New Zealand Institute of Plant & Food Research Limited; Private Bag 92169 Auckland New Zealand
| | - Thomas R. Buckley
- Landcare Research; Private Bag 92170 Auckland New Zealand
- School of Biological Sciences; The University of Auckland; Private Bag 92019 Auckland New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Palmerston North New Zealand
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18
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Dunning LT, Dennis AB, Thomson G, Sinclair BJ, Newcomb RD, Buckley TR. Positive selection in glycolysis among Australasian stick insects. BMC Evol Biol 2013; 13:215. [PMID: 24079656 PMCID: PMC3850572 DOI: 10.1186/1471-2148-13-215] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/23/2013] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The glycolytic pathway is central to cellular energy production. Selection on individual enzymes within glycolysis, particularly phosphoglucose isomerase (Pgi), has been associated with metabolic performance in numerous organisms. Nonetheless, how whole energy-producing pathways evolve to allow organisms to thrive in different environments and adopt new lifestyles remains little explored. The Lanceocercata radiation of Australasian stick insects includes transitions from tropical to temperate climates, lowland to alpine habitats, and winged to wingless forms. This permits a broad investigation to determine which steps within glycolysis and what sites within enzymes are the targets of positive selection. To address these questions we obtained transcript sequences from seven core glycolysis enzymes, including two Pgi paralogues, from 29 Lanceocercata species. RESULTS Using maximum likelihood methods a signature of positive selection was inferred in two core glycolysis enzymes. Pgi and Glyceraldehyde 3-phosphate dehydrogenase (Gaphd) genes both encode enzymes linking glycolysis to the pentose phosphate pathway. Positive selection among Pgi paralogues and orthologues predominately targets amino acids with residues exposed to the protein's surface, where changes in physical properties may alter enzyme performance. CONCLUSION Our results suggest that, for Lancerocercata stick insects, adaptation to new stressful lifestyles requires a balance between maintaining cellular energy production, efficiently exploiting different energy storage pools and compensating for stress-induced oxidative damage.
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Affiliation(s)
- Luke T Dunning
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
- Imperial College London, Silwood Park Campus, Buckhurst Road, SL5 7PY, Ascot, Berks, UK
| | - Alice B Dennis
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
| | - Geoffrey Thomson
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Brent J Sinclair
- Department of Biology, The University of Western Ontario, London, ON, Canada N6G 1L3
| | - Richard D Newcomb
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
- The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
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19
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Dunning LT, Dennis AB, Park D, Sinclair BJ, Newcomb RD, Buckley TR. Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 2013; 8:24-31. [DOI: 10.1016/j.cbd.2012.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 10/19/2012] [Accepted: 10/20/2012] [Indexed: 12/22/2022]
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20
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Hellberg ME, Dennis AB, Arbour-Reily P, Aagaard JE, Swanson WJ. The Tegula tango: a coevolutionary dance of interacting, positively selected sperm and egg proteins. Evolution 2012; 66:1681-94. [PMID: 22671539 DOI: 10.1111/j.1558-5646.2011.01530.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reproductive proteins commonly show signs of rapid divergence driven by positive selection. The mechanisms driving these changes have remained ambiguous in part because interacting male and female proteins have rarely been examined. We isolate an egg protein the vitelline envelope receptor for lysin (VERL) from Tegula, a genus of free-spawning marine snails. Like VERL from abalone, Tegula VERL is a major component of the VE surrounding the egg, includes a conserved zona pellucida (ZP) domain at its C-terminus, and possesses a unique, negatively charged domain of about 150 amino acids implicated in interactions with the positively charged lysin. Unlike for abalone VERL, where this unique VERL domain occurs in a tandem array of 22 repeats, Tegula VERL has just one such domain. Interspecific comparisons show that both lysin and the VERL domain diverge via positive selection, whereas the ZP domain evolves neutrally. Rates of nonsynonymous substitution are correlated between lysin and the VERL domain, consistent with sexual antagonism, although lineage-specific effects, perhaps owing to different ecologies, may alter the relative evolutionary rates of sperm- and egg-borne proteins.
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Affiliation(s)
- Michael E Hellberg
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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21
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Dennis AB, Farr S, Kellaway IW, Taylor G, Davidson R. Gamma Scintigraphic Evaluation and Simultaneous Plasma Analysis of Rapid Release Ketoprofen Semi-Solid Matrix Capsules. J Pharm Pharmacol 2011. [DOI: 10.1111/j.2042-7158.1990.tb14522.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- AB Dennis
- Bristol-Myers Squibb, International Development Laboratories, Moreton, Merseyside, UK
| | - S Farr
- Welsh School of pharmacy, University of Wales, Cardiff, UK
| | - IW Kellaway
- Welsh School of pharmacy, University of Wales, Cardiff, UK
| | - G Taylor
- Welsh School of pharmacy, University of Wales, Cardiff, UK
| | - R Davidson
- Pfizer Central Research, Sandwich, Kent, UK
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Robin AL, Siegel PT, Moye AW, Gilroy M, Dennis AB, Sikand A. A controlled comparison of family versus individual therapy for adolescents with anorexia nervosa. J Am Acad Child Adolesc Psychiatry 1999; 38:1482-9. [PMID: 10596247 DOI: 10.1097/00004583-199912000-00008] [Citation(s) in RCA: 272] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To compare the effectiveness of behavioral family systems therapy (BFST) with that of ego-oriented individual therapy (EOIT) as treatments for adolescents with anorexia nervosa. METHOD Thirty-seven adolescents meeting DSM-III-R criteria for anorexia nervosa were randomly assigned to receive BFST or EOIT, in addition to a common medical and dietary regimen. In BFST, the family was seen conjointly, the parents were placed in control of the adolescent's eating, distorted beliefs were targeted through cognitive restructuring, and strategic/behavioral interventions were used to change family interactions. In EOIT, the adolescent was seen individually, with an emphasis on building ego strength and uncovering the dynamics blocking eating; parents were seen collaterally. Measures administered before, after, and at 1-year follow-up tapped body mass index, menstruation, eating attitudes, ego functioning, depression, and family interactions. RESULTS BFST produced greater weight gain and higher rates of resumption of menstruation than EOIT. Both treatments produced comparably large improvements in eating attitudes, depression, and eating-related family conflict, but very few changes occurred on ego functioning. CONCLUSIONS BFST and EOIT proved to be effective treatments for adolescents with anorexia nervosa, but BFST produced a faster return to health.
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Affiliation(s)
- A L Robin
- Wayne State University, Detroit, USA.
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Abstract
Anorexia nervosa and bulimia nervosa are expressed differently in children and adolescents than in adults. Consequently, diagnostic procedures and multidisciplinary treatments need to be tailored to the unique developmental, medical, nutritional, and psychological needs of children and adolescents with eating disorders. This paper reviews current research outlining the differences between child, adolescent, and adult eating disorders. Research is then reviewed concerning the effectiveness of hospitalization, partial hospitalization, individual dynamic therapy, cognitive-behavioral therapy, interpersonal therapy, family therapy, and medication for treating anorexia nervosa, bulimia nervosa, and related eating disorders in children and adolescents. Specific recommendations are made for practitioners to tailor these treatments to their eating-disordered child and adolescent patients, following a stepped-care, decision-tree model of intervention that takes into account the effectiveness, cost, and intrusiveness of the interventions.
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Abstract
This study investigates the treatment impressions and termination experiences of faculty clinicians treating individuals with borderline personality disorder. Thirty-nine clinicians (28 psychiatrists and 11 psychologists) completed the Treatment of Borderlines Survey. Results indicated that individual psychotherapy was perceived to be the most valuable treatment modality, that the majority of respondents work towards character change but do not expect "normal," the most common reported reasons for patient termination were "patient does not see the purpose of treatment" and "patient terminates through acting-out behaviors," and a slight majority reported that they had "cured" at least some of their borderline patients. The most common concerns experienced during the termination process included regression, acting-out, and self-destructive behavior. There were very few differences in the perceptions and treatment experiences between psychiatrists and psychologists. These results provide empirical support for claims made in the clinical literature on treating borderline patients.
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Affiliation(s)
- R A Sansone
- Department of Psychiatry, Wright State University School of Medicine, Dayton, OH
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Tobin DL, Johnson C, Steinberg S, Staats M, Dennis AB. Multifactorial assessment of bulimia nervosa. J Abnorm Psychol 1991. [PMID: 2005266 DOI: 10.1037//0021-843x.100.1.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We investigated a multifactorial approach to the assessment of bulimia nervosa by means of hierarchical factor analysis. Two hundred forty-five bulimia nervosa patients and 68 patients with either anorexia nervosa or eating disorders not otherwise specified were administered a self-report battery that was organized into 21 dimensions relevant to eating disorder patients. When dimensions from this battery were subjected to hierarchical factor analysis, support for bulimia nervosa as a unique diagnostic category was obtained. However, the emergence of 3 secondary factors and 6 primary factors suggests that bulimia nervosa can also be described more complexly. The emergence of a multifactorial model of bulimia nervosa that incorporates several existing undimensional models suggests the potential for both divergent and complicated clinical presentation in bulimia nervosa patients.
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Affiliation(s)
- D L Tobin
- Department of Psychiatry, University of Chicago, Illinois 60640
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Abstract
We investigated a multifactorial approach to the assessment of bulimia nervosa by means of hierarchical factor analysis. Two hundred forty-five bulimia nervosa patients and 68 patients with either anorexia nervosa or eating disorders not otherwise specified were administered a self-report battery that was organized into 21 dimensions relevant to eating disorder patients. When dimensions from this battery were subjected to hierarchical factor analysis, support for bulimia nervosa as a unique diagnostic category was obtained. However, the emergence of 3 secondary factors and 6 primary factors suggests that bulimia nervosa can also be described more complexly. The emergence of a multifactorial model of bulimia nervosa that incorporates several existing undimensional models suggests the potential for both divergent and complicated clinical presentation in bulimia nervosa patients.
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Affiliation(s)
- D L Tobin
- Department of Psychiatry, University of Chicago, Illinois 60640
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