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Sarumi OA, Hahn M, Heider D. NeuralBeds: Neural embeddings for efficient DNA data compression and optimized similarity search. Comput Struct Biotechnol J 2024; 23:732-741. [PMID: 38298179 PMCID: PMC10828564 DOI: 10.1016/j.csbj.2023.12.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024] Open
Abstract
The availability of high throughput sequencing tools coupled with the declining costs in the production of DNA sequences has led to the generation of enormous amounts of omics data curated in several databases such as NCBI and EMBL. Identification of similar DNA sequences from these databases is one of the fundamental tasks in bioinformatics. It is essential for discovering homologous sequences in organisms, phylogenetic studies of evolutionary relationships among several biological entities, or detection of pathogens. Improving DNA similarity search is of outmost importance because of the increased complexity of the evergrowing repositories of sequences. Therefore, instead of using the conventional approach of comparing raw sequences, e.g., in fasta format, a numerical representation of the sequences can be used to calculate their similarities and optimize the search process. In this study, we analyzed different approaches for numerical embeddings, including Chaos Game Representation, hashing, and neural networks, and compared them with classical approaches such as principal component analysis. It turned out that neural networks generate embeddings that are able to capture the similarity between DNA sequences as a distance measure and outperform the other approaches on DNA similarity search, significantly.
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Affiliation(s)
- Oluwafemi A. Sarumi
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg, D-35043, Germany
- Institute of Computer Science, Heinrich-Heine-University Duesseldorf, Graf-Adolf-Str. 63, Duesseldorf, D-40215, Germany
| | - Maximilian Hahn
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg, D-35043, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Hans-Meerwein-Str. 6, Marburg, D-35043, Germany
- Institute of Computer Science, Heinrich-Heine-University Duesseldorf, Graf-Adolf-Str. 63, Duesseldorf, D-40215, Germany
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2
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Gracias S, Chazal M, Decombe A, Unterfinger Y, Sogues A, Pruvost L, Robert V, Lacour SA, Lemasson M, Sourisseau M, Li Z, Richardson J, Pellegrini S, Decroly E, Caval V, Jouvenet N. Tick-borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2. EMBO Rep 2023; 24:e57424. [PMID: 37860832 PMCID: PMC10702846 DOI: 10.15252/embr.202357424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
The mechanisms utilized by different flaviviruses to evade antiviral functions of interferons are varied and incompletely understood. Using virological approaches, biochemical assays, and mass spectrometry analyses, we report here that the NS5 protein of tick-borne encephalitis virus (TBEV) and Louping Ill virus (LIV), two related tick-borne flaviviruses, antagonize JAK-STAT signaling through interactions with the tyrosine kinase 2 (TYK2). Co-immunoprecipitation (co-IP) experiments, yeast gap-repair assays, computational protein-protein docking and functional studies identify a stretch of 10 residues of the RNA dependent RNA polymerase domain of tick-borne flavivirus NS5, but not mosquito-borne NS5, that is critical for interactions with the TYK2 kinase domain. Additional co-IP assays performed with several TYK2 orthologs reveal that the interaction is conserved across mammalian species. In vitro kinase assays show that TBEV and LIV NS5 reduce the catalytic activity of TYK2. Our results thus illustrate a novel mechanism by which viruses suppress the interferon response.
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Affiliation(s)
- Ségolène Gracias
- Virus Sensing and Signaling Unit, CNRS UMR3569, Institut PasteurUniversité de Paris CitéParisFrance
| | - Maxime Chazal
- Virus Sensing and Signaling Unit, CNRS UMR3569, Institut PasteurUniversité de Paris CitéParisFrance
| | - Alice Decombe
- AFMB UMR 7257, CNRSAix Marseille UniversitéMarseilleFrance
| | - Yves Unterfinger
- UMR1161 Virologie Laboratoire de Santé Animale, Anses, INRAE, Ecole Nationale Vétérinaire d'AlfortUniversité Paris‐EstMaisons‐AlfortFrance
| | - Adrià Sogues
- Structural and Molecular MicrobiologyVIB‐VUB, Center for Structural BiologyBrusselsBelgium
| | - Lauryne Pruvost
- Virus Sensing and Signaling Unit, CNRS UMR3569, Institut PasteurUniversité de Paris CitéParisFrance
| | | | - Sandrine A Lacour
- UMR1161 Virologie Laboratoire de Santé Animale, Anses, INRAE, Ecole Nationale Vétérinaire d'AlfortUniversité Paris‐EstMaisons‐AlfortFrance
| | - Manon Lemasson
- UMR1161 Virologie Laboratoire de Santé Animale, Anses, INRAE, Ecole Nationale Vétérinaire d'AlfortUniversité Paris‐EstMaisons‐AlfortFrance
- Phagos Pépinière Genopole EntrepriseEvry‐CourcouronnesFrance
| | - Marion Sourisseau
- UMR1161 Virologie Laboratoire de Santé Animale, Anses, INRAE, Ecole Nationale Vétérinaire d'AlfortUniversité Paris‐EstMaisons‐AlfortFrance
| | - Zhi Li
- Unit of Cytokine Signaling, INSERM U122Institut PasteurParisFrance
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut PasteurUniversité de Paris CitéParisFrance
| | - Jennifer Richardson
- UMR1161 Virologie Laboratoire de Santé Animale, Anses, INRAE, Ecole Nationale Vétérinaire d'AlfortUniversité Paris‐EstMaisons‐AlfortFrance
| | | | | | - Vincent Caval
- Virus Sensing and Signaling Unit, CNRS UMR3569, Institut PasteurUniversité de Paris CitéParisFrance
| | - Nolwenn Jouvenet
- Virus Sensing and Signaling Unit, CNRS UMR3569, Institut PasteurUniversité de Paris CitéParisFrance
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3
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Lu X, Simma EA, Spanoghe P, Van Leeuwen T, Dermauw W. Recombinant expression and characterization of GSTd3 from a resistant population of Anopheles arabiensis and comparison of DDTase activity with GSTe2. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 192:105397. [PMID: 37105620 DOI: 10.1016/j.pestbp.2023.105397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/15/2023] [Accepted: 03/19/2023] [Indexed: 06/19/2023]
Abstract
The development of insecticide resistance in malaria vectors is a challenge for the global effort to control and eradicate malaria. Glutathione S-transferases (GSTs) are multifunctional enzymes involved in the detoxification of many classes of insecticides. For mosquitoes, it is known that overexpression of an epsilon GST, GSTe2, confers resistance towards DDT and pyrethroids. In addition to GSTe2, consistent overexpression of a delta class GST, GSTd3, has been observed in insecticide resistant populations of different malaria vector species. However, the functional role of GSTd3 towards DDT resistance has not yet been investigated. Here, we recombinantly expressed both GSTe2 and GSTd3 from Anopheles arabiensis and compared their metabolic activities against DDT. Both AaGSTd3 and AaGSTe2 exhibited CDNB-conjugating and glutathione peroxidase activity and DDT metabolism was observed for both GSTs. However, the DDT dehydrochlorinase activity exhibited by AaGSTe2 was much higher than for AaGSTd3, and AaGSTe2 was also able to eliminate DDE although the metabolite could not be identified. Molecular modeling revealed subtle differences in the binding pocket of both enzymes and a better fit of DDT within the H-site of AaGSTe2. The overexpression but much lower DDT metabolic activity of AaGSTd3, might suggest that AaGSTd3 sequesters DDT. These findings highlight the complexity of insecticide resistance in the major malaria vectors and the difficulties associated with control of the vectors using DDT, which is still used for indoor residual spraying.
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Affiliation(s)
- Xueping Lu
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Eba Alemayehu Simma
- Department of Biology, College of Natural Sciences, Jimma University, Jimma, Ethiopia.
| | - Pieter Spanoghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
| | - Wannes Dermauw
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium; Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, 9820 Merelbeke, Belgium.
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Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
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Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
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5
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Kelley M, Uhran M, Herbert C, Yoshida G, Watts ER, Limbach PA, Benoit JB. Abundances of transfer RNA modifications and transcriptional levels of tRNA-modifying enzymes are sex-associated in mosquitoes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 143:103741. [PMID: 35181477 PMCID: PMC9034435 DOI: 10.1016/j.ibmb.2022.103741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 06/03/2023]
Abstract
As carriers of multiple human diseases, understanding the mechanisms behind mosquito reproduction may have implications for remediation strategies. Transfer RNA (tRNA) acts as the adapter molecule of amino acids and are key components in protein synthesis. A critical factor in the function of tRNAs is chemical modifications which contribute to codon-anticodon interactions. Here, we provide an assessment of tRNA modifications between sexes for three mosquito species and examine the correlation of transcript levels underlying key proteins involved in tRNA modification. Thirty-three tRNA modifications were detected among mosquito species and most of these modifications are higher in females compared to males for three mosquito species. Analysis of previous male and female RNA-seq datasets indicated a similar increase in transcript levels of tRNA-modifying enzymes in females among six mosquito species, supporting our observed female enrichment of tRNA modifications. Tissues-specific expressional studies revealed higher transcript levels for tRNA-modifying enzymes in the ovaries for Aedes aegypti, but not male reproductive tissues. These studies suggest that tRNA modifications may be critical to reproduction in mosquitoes, representing a potential novel target for control through suppression of fecundity.
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Affiliation(s)
- Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA.
| | - Melissa Uhran
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Cassandra Herbert
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - George Yoshida
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Emmarie R Watts
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA.
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6
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Pezenti LF, Levy SM, de Souza RF, Sosa-Gómez DR, da Rosa R. Testes morphology and the identification of transcripts of the hormonal pathways of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae). ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 65:101111. [PMID: 34571334 DOI: 10.1016/j.asd.2021.101111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Anticarsia gemmatalis is one of the main defoliating pests of soybeans in Brazil. In the current study, we characterized the histomorphology of the testes and the spermatogenesis process in A. gemmatalis. We also identified transcripts involved in the biosynthesis, metabolism, and signaling of juvenile and ecdysteroid hormones, in order to provide information about potential mechanisms of regulation of hormonal pathways in this species. Our analyses revealed that the A. gemmatalis larvae have a pair of kidney-shaped testicles. These are divided into four testicular follicles, where there are germ cell cysts at different stages of development. In the pupal stage, the testicles are fused, so adults have a single spherical testis, with a variable number of follicles. The A. gemmatalis has centripetal spermatogenesis and exhibits spermatic dimorphism. We identified 31 transcripts that encode proteins involved in juvenile hormone and ecdysteroid pathways, such as mevalonate kinase, CYP14A1, ecdysone receptor, among others. Our results on the morphology of the testes and spermatogenesis process, as well as identification of the genes involved in hormonal pathways in A. gemmatalis, provide important data for understanding the biology of this agricultural pest, which can be used as a basis for further research in other economically important lepidopterans.
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Affiliation(s)
- Larissa Forim Pezenti
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil; Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Sheila Michele Levy
- Laboratório de Insetos, Departamento de Histologia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Rogério Fernandes de Souza
- Laboratório de Bioinformática, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
| | - Daniel Ricardo Sosa-Gómez
- Empresa Brasileira de Pesquisa Agropecuária/Centro Nacional de Pesquisa de Soja (Embrapa Soja), Londrina, Paraná, Brazil.
| | - Renata da Rosa
- Laboratório de Citogenética Animal, Departamento de Biologia Geral, Universidade Estadual de Londrina, Londrina, Paraná, Brazil.
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7
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Montino A, Balakrishnan K, Dippel S, Trebels B, Neumann P, Wimmer EA. Mutually Exclusive Expression of Closely Related Odorant-Binding Proteins 9A and 9B in the Antenna of the Red Flour Beetle Tribolium castaneum. Biomolecules 2021; 11:1502. [PMID: 34680135 PMCID: PMC8533528 DOI: 10.3390/biom11101502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 01/01/2023] Open
Abstract
Olfaction is crucial for insects to find food sources, mates, and oviposition sites. One of the initial steps in olfaction is facilitated by odorant-binding proteins (OBPs) that translocate hydrophobic odorants through the aqueous olfactory sensilla lymph to the odorant receptor complexes embedded in the dendritic membrane of olfactory sensory neurons. The Tribolium castaneum (Coleoptera, Tenebrionidae) OBPs encoded by the gene pair TcasOBP9A and TcasOBP9B represent the closest homologs to the well-studied Drosophila melanogaster OBP Lush (DmelOBP76a), which mediates pheromone reception. By an electroantennographic analysis, we can show that these two OBPs are not pheromone-specific but rather enhance the detection of a broad spectrum of organic volatiles. Both OBPs are expressed in the antenna but in a mutually exclusive pattern, despite their homology and gene pair character by chromosomal location. A phylogenetic analysis indicates that this gene pair arose at the base of the Cucujiformia, which dates the gene duplication event to about 200 Mio years ago. Therefore, this gene pair is not the result of a recent gene duplication event and the high sequence conservation in spite of their expression in different sensilla is potentially the result of a common function as co-OBPs.
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Affiliation(s)
- Alice Montino
- GZMB, Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Ernst-Caspari-Haus, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany; (A.M.); (S.D.)
- Goettingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, Georg-August University School of Science, University of Goettingen, 37077 Goettingen, Germany
| | - Karthi Balakrishnan
- Department of Forest Zoology and Forest Conservation, Buesgen-Institute, Georg-August-University Goettingen, Buesgenweg 3, 37077 Goettingen, Germany;
| | - Stefan Dippel
- GZMB, Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Ernst-Caspari-Haus, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany; (A.M.); (S.D.)
- Department of Biology—Animal Physiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany;
| | - Björn Trebels
- Department of Biology—Animal Physiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany;
| | - Piotr Neumann
- GZMB, Department of Molecular Structural Biology, Institute of Microbiology & Genetics, Ernst-Caspari-Haus, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany;
| | - Ernst A. Wimmer
- GZMB, Department of Developmental Biology, Johann-Friedrich-Blumenbach-Institute for Zoology and Anthropology, Ernst-Caspari-Haus, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany; (A.M.); (S.D.)
- Goettingen Graduate Center for Neurosciences, Biophysics, and Molecular Biosciences, Georg-August University School of Science, University of Goettingen, 37077 Goettingen, Germany
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8
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Sun X, Liu W, Li R, Zhao C, Pan L, Yan C. A chromosome level genome assembly of Propsilocerus akamusi to understand its response to heavy metal exposure. Mol Ecol Resour 2021; 21:1996-2012. [PMID: 33710757 DOI: 10.1111/1755-0998.13377] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/27/2022]
Abstract
Chironomidae species are universally used for studying the impact of pollutants in aquatic systems. The nonbiting midge Propsilocerus akamusi is often found in urban streams and is suitable for use as a toxicological bioindicator. However, few studies have previously examined metal stress in this species. We sequenced the genome of this urban midge to address this question. Here, we present the first chromosome-level genome of P. akamusi, obtained from Illumina short-read and PacBio long-read sequences with Hi-C technology. The size of the very small assembled genome was 85.83 Mb with a contig N50 of 6.2 Mb and a scaffold N50 of 26.1 Mb. This assembly revealed significant expansion of haemoglobin (Hb) genes, some of which formed large tandem repeats. Transcriptomic studies for copper tolerance identified four genes in the tandem array that were highly expressed, all of which presented intron loss. This characteristic might highlight the potential role of Hb genes in copper tolerance. Additionally, detoxification genes, chemosensory genes and heat shock protein genes of this midge were identified, some of which are associated with metal stress. The high-quality assembled genome of P. akamusi and the transcriptomic analyses provide new insight into the molecular mechanisms of heavy metal stress. Our comparison of the P. akamusi genome with other dipteran genomes provides valuable resources for understanding the evolutionary history, genetics, and ecology of this species as well as those of other midges.
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Affiliation(s)
- Xiaoya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China.,Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Wenbin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China.,Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Ruoqun Li
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China.,Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Cong Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China.,Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Lina Pan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China.,Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Chuncai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China.,Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
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9
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Zhang YJ, Lan Y, Chen B. ASDB: A comprehensive omics database for Anopheles sinensis. Genomics 2021; 113:976-982. [PMID: 33588073 DOI: 10.1016/j.ygeno.2021.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 01/10/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Anopheles sinensis is a key disease vector for human malaria and parasitic diseases such as malayan filariasis, and it is considered to be one of the most important malaria vectors in China and Southeast Asia. As high-throughput sequencing and assembly technology are widely used in An. sinensis, a lot of omics data have been generated, and abundant genome, mRNA transcriptome, miRNA transcriptome and resequencing results have been accumulated. In addition, lots of valuable morphological images and publications have been produced with the in-depth studies on An. sinensis. However, the increased quantity, variety, and structure complexity of the omics data create inconveniences for researchers to use and manage this information. We have built an An. sinensis omics database (ASDB, http://asdb.jungleran.com/) - a comprehensive and integrated database to promote scientific research on An. sinensis. Docker was used to deploy a development environment and Drupal to build ASDB. ASDB provides a Blast tool to do sequence alignment of genome sequence, gene sequence and protein sequence of An. sinensis. It also offers JBrowse (a next-generation genome visualization and analysis web platform) to facilitate researchers visualize the gene structure, non-coding RNA (include miRNA, snRNA, tRNA and so on) structure and genomic variation sites as desired. ASDB has integrated various latest omics data of An. Sinensis, including de novo genome and its annotation data, genome variation data (such as SNP and InDel), transcriptome and its expression value, miRNA expression value and miRNA-mRNA interaction, metagenomes. The database has also included the morphological images of different developmental stages and tissues, and important literatures associated with An. sinensis. ASDB provides a user-friendly search and displays pages. The integration of these resources will contribute to the study of basic biology and functional genome of An. sinensis.
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Affiliation(s)
- Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, China.
| | - Yang Lan
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, China
| | - Bin Chen
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing 401331, China.
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10
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Wimalasiri-Yapa BMCR, Barrero RA, Stassen L, Hafner LM, McGraw EA, Pyke AT, Jansen CC, Suhrbier A, Yakob L, Hu W, Devine GJ, Frentiu FD. Temperature modulates immune gene expression in mosquitoes during arbovirus infection. Open Biol 2021; 11:200246. [PMID: 33401993 PMCID: PMC7881175 DOI: 10.1098/rsob.200246] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
The principal vector of dengue, Zika and chikungunya viruses is the mosquito Aedes aegypti, with its ability to transmit pathogens influenced by ambient temperature. We use chikungunya virus (CHIKV) to understand how the mosquito transcriptome responds to arbovirus infection at different ambient temperatures. We exposed CHIKV-infected mosquitoes to 18, 28 and 32°C, and found that higher temperature correlated with higher virus levels, particularly at 3 days post infection, but lower temperature resulted in reduced virus levels. RNAseq analysis indicated significantly altered gene expression levels in CHIKV infection. The highest number of significantly differentially expressed genes was observed at 28°C, with a more muted effect at the other temperatures. At the higher temperature, the expression of many classical immune genes, including Dicer-2, was not substantially altered in response to CHIKV. The upregulation of Toll, IMD and JAK-STAT pathways was only observed at 28°C. Functional annotations suggested that genes in immune response and metabolic pathways related to energy supply and DNA replication were involved in temperature-dependent changes. Time post infection also led to substantially different gene expression profiles, and this varied with temperature. In conclusion, temperature significantly modulates mosquito gene expression in response to infection, potentially leading to impairment of immune defences at higher temperatures.
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Affiliation(s)
- B. M. C. Randika Wimalasiri-Yapa
- Institute of Health and Biomedical Innovation, and School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- Department of Medical Laboratory Sciences, Faculty of Health Science, Open University of Sri Lanka, Nugegoda, Colombo, Sri Lanka
| | - Roberto A. Barrero
- eResearch Office, Division of Research and Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Liesel Stassen
- Institute of Health and Biomedical Innovation, and School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Louise M. Hafner
- Institute of Health and Biomedical Innovation, and School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Elizabeth A. McGraw
- Center for Infectious Disease Dynamics, Department of Entomology, The Pennsylvania State University, University Park, PA 16801, USA
| | - Alyssa T. Pyke
- Public Health Virology Laboratory, Forensic and Scientific Services, Coopers Plains, Queensland, Australia
| | - Cassie C. Jansen
- Communicable Diseases Branch, Department of Health, Queensland Government, Herston, Queensland, Australia
| | - Andreas Suhrbier
- Inflammation Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Laith Yakob
- London School of Hygiene and Tropical Medicine, London, UK
| | - Wenbiao Hu
- School of Public Health and Social Work, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Gregor J. Devine
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Francesca D. Frentiu
- Institute of Health and Biomedical Innovation, and School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
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11
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Runtuwene LR, Kawashima S, Pijoh VD, Tuda JSB, Hayashida K, Yamagishi J, Sugimoto C, Nishiyama S, Sasaki M, Orba Y, Sawa H, Takasaki T, James AA, Kobayashi T, Eshita Y. The Lethal(2)-Essential-for-Life [ L(2)EFL] Gene Family Modulates Dengue Virus Infection in Aedes aegypti. Int J Mol Sci 2020; 21:ijms21207520. [PMID: 33053895 PMCID: PMC7593908 DOI: 10.3390/ijms21207520] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 12/25/2022] Open
Abstract
Efforts to determine the mosquito genes that affect dengue virus replication have identified a number of candidates that positively or negatively modify amplification in the invertebrate host. We used deep sequencing to compare the differential transcript abundances in Aedes aegypti 14 days post dengue infection to those of uninfected A. aegypti. The gene lethal(2)-essential-for-life [l(2)efl], which encodes a member of the heat shock 20 protein (HSP20) family, was upregulated following dengue virus type 2 (DENV-2) infection in vivo. The transcripts of this gene did not exhibit differential accumulation in mosquitoes exposed to insecticides or pollutants. The induction and overexpression of l(2)efl gene products using poly(I:C) resulted in decreased DENV-2 replication in the cell line. In contrast, the RNAi-mediated suppression of l(2)efl gene products resulted in enhanced DENV-2 replication, but this enhancement occurred only if multiple l(2)efl genes were suppressed. l(2)efl homologs induce the phosphorylation of eukaryotic initiation factor 2α (eIF2α) in the fruit fly Drosophila melanogaster, and we confirmed this finding in the cell line. However, the mechanism by which l(2)efl phosphorylates eIF2α remains unclear. We conclude that l(2)efl encodes a potential anti-dengue protein in the vector mosquito.
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Affiliation(s)
- Lucky R. Runtuwene
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan;
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- AIDS Research Centre, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Correspondence: (L.R.R.); (Y.E.)
| | - Shuichi Kawashima
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan;
| | - Victor D. Pijoh
- Faculty of Medicine, Sam Ratulangi University, Kampus Unsrat, Bahu Manado 95-115, Indonesia; (V.D.P.); (J.S.B.T.)
| | - Josef S. B. Tuda
- Faculty of Medicine, Sam Ratulangi University, Kampus Unsrat, Bahu Manado 95-115, Indonesia; (V.D.P.); (J.S.B.T.)
| | - Kyoko Hayashida
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan; (K.H.); (J.Y.); (C.S.)
| | - Junya Yamagishi
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan; (K.H.); (J.Y.); (C.S.)
- Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan
| | - Chihiro Sugimoto
- Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan; (K.H.); (J.Y.); (C.S.)
| | - Shoko Nishiyama
- Laboratory of Zoonotic Diseases, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu-shi, Gifu 501-1193, Japan;
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan; (M.S.); (Y.O.); (H.S.)
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan; (M.S.); (Y.O.); (H.S.)
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan; (M.S.); (Y.O.); (H.S.)
| | - Tomohiko Takasaki
- National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
- Kanagawa Prefectural Institute of Public Health, Kanagawa 253-0087, Japan
| | - Anthony A. James
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, University of California, Irvine, CA 92697, USA;
| | - Takashi Kobayashi
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan;
| | - Yuki Eshita
- Department of Infectious Disease Control, Faculty of Medicine, Oita University, Oita 879-5593, Japan;
- Departments of Medical Entomology, Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Rajathewi, Bangkok 10400, Thailand
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10 Kita-ku, Sapporo, Hokkaido 001-0020, Japan
- Correspondence: (L.R.R.); (Y.E.)
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12
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CrustyBase: an interactive online database for crustacean transcriptomes. BMC Genomics 2020; 21:637. [PMID: 32928113 PMCID: PMC7490944 DOI: 10.1186/s12864-020-07063-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/10/2020] [Indexed: 11/10/2022] Open
Abstract
Transcriptome sequencing has opened the field of genomics to a wide variety of researchers, owing to its efficiency, applicability across species and ability to quantify gene expression. The resulting datasets are a rich source of information that can be mined for many years into the future, with each dataset providing a unique angle on a specific context in biology. Maintaining accessibility to this accumulation of data presents quite a challenge for researchers.The primary focus of conventional genomics databases is the storage, navigation and interpretation of sequence data, which is typically classified down to the level of a species or individual. The addition of expression data adds a new dimension to this paradigm - the sampling context. Does gene expression describe different tissues, a temporal distribution or an experimental treatment? These data not only describe an individual, but the biological context surrounding that individual. The structure and utility of a transcriptome database must therefore reflect these attributes. We present an online database which has been designed to maximise the accessibility of crustacean transcriptome data by providing intuitive navigation within and between datasets and instant visualization of gene expression and protein structure.The site is accessible at https://crustybase.org and currently holds 10 datasets from a range of crustacean species. It also allows for upload of novel transcriptome datasets through a simple web interface, allowing the research community to contribute their own data to a pool of shared knowledge.
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13
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Ahmed TH, Saunders TR, Mullins D, Rahman MZ, Zhu J. Molecular action of pyriproxyfen: Role of the Methoprene-tolerant protein in the pyriproxyfen-induced sterilization of adult female mosquitoes. PLoS Negl Trop Dis 2020; 14:e0008669. [PMID: 32866146 PMCID: PMC7485974 DOI: 10.1371/journal.pntd.0008669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/11/2020] [Accepted: 08/03/2020] [Indexed: 01/02/2023] Open
Abstract
Exposure of adult mosquitoes to pyriproxyfen (PPF), an analog of insect juvenile hormone (JH), has shown promise to effectively sterilize female mosquitoes. However, the underlying mechanisms of the PPF-induced decrease in mosquito fecundity are largely unknown. We performed a comprehensive study to dissect the mode of PPF action in Aedes aegypti mosquitoes. Exposure to PPF prompted the overgrowth of primary follicles in sugar-fed Ae. aegypti females but blocked the development of primary follicles at Christopher’s Stage III after blood feeding. Secondary follicles were precociously activated in PPF-treated mosquitoes. Moreover, PPF substantially altered the expression of many genes that are essential for mosquito physiology and oocyte development in the fat body and ovary. In particular, many metabolic genes were differentially expressed in response to PPF treatment, thereby affecting the mobilization and utilization of energy reserves. Furthermore, PPF treatment on the previtellogenic female adults considerably modified mosquito responses to JH and 20-hydroxyecdysone (20E), two major hormones that govern mosquito reproduction. Krüppel homolog 1, a JH-inducible transcriptional regulator, showed consistently elevated expression after PPF exposure. Conversely, PPF upregulated the expression of several key players of the 20E regulatory cascades, including HR3 and E75A, in the previtellogenic stage. After blood-feeding, the expression of these 20E response genes was significantly weaker in PPF-treated mosquitoes than the solvent-treated control groups. RNAi-mediated knockdown of the Methoprene-tolerant (Met) protein, the JH receptor, partially rescued the impaired follicular development after PPF exposure and substantially increased the hatching of the eggs produced by PPF-treated female mosquitoes. Thus, the results suggested that PPF relied on Met to exert its sterilizing effects on female mosquitoes. In summary, this study finds that PPF exposure disturbs normal hormonal responses and metabolism in Ae. aegypti, shedding light on the molecular targets and the downstream signaling pathways activated by PPF. Aedes aegypti mosquitoes are responsible for the transmission of dengue, yellow fever, chikungunya, and Zika fever. Insecticides are widely used as the primary tool in the prevention and control of these infectious diseases. In light of the rapid increase of insecticide resistance in mosquito populations, there is an urgent need to find new classes of insecticides with a different mode of action. Here we found that pyriproxyfen, an analog of insect juvenile hormone (JH), had a large impact on the oocyte development, both before and after blood feeding, in female mosquitoes. Pyriproxyfen disturbed normal hormonal responses and caused metabolic shifting in female adults. These actions appear to collectively impair oocyte development and substantially reduce viable progenies of female mosquitoes. Besides, we demonstrated the involvement of the JH receptor Met in pyriproxyfen-induced female sterilization. This study significantly advances our understanding of mosquito reproductive biology and the molecular basis of pyriproxyfen action, which are invaluable for the development of new mosquito control strategies.
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Affiliation(s)
- Tahmina Hossain Ahmed
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - T. Randolph Saunders
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Donald Mullins
- Department of Entomology, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Mohammad Zillur Rahman
- Quantitative Science Core, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Jinsong Zhu
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail:
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14
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He Y, Han SB, Geng YN, Yang SL, Wu YM. Quantitative analysis of proteins related to chemoresistance to paclitaxel and carboplatin in human SiHa cervical cancer cells via iTRAQ. J Gynecol Oncol 2020; 31:e28. [PMID: 31912682 PMCID: PMC7189068 DOI: 10.3802/jgo.2020.31.e28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 09/24/2019] [Accepted: 10/16/2019] [Indexed: 11/30/2022] Open
Abstract
Objective This study aimed to identify proteins related to paclitaxel and carboplatin chemoresistance in cervical cancer. Methods Quantitative proteomic analysis was performed on normal SiHa cells and those treated with paclitaxel and carboplatin for 14 days, with isobaric tags for relative and absolute quantitation (iTRAQ) analysis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to identify related processes and differentially expressed proteins. Results A total of 67 and 96 differentially expressed proteins were identified in the paclitaxel- and carboplatin- treated groups, respectively. GO and KEGG enrichment analyses identified 53 (43 upregulated and 10 downregulated) and 85 differentially expressed proteins (70 upregulated and 15 downregulated) in the paclitaxel- and carboplatin-treated groups, respectively. The cell counting kit-8 results revealed that APOA1 was overexpressed in both the paclitaxel- and carboplatin- resistant SiHa cells compared with the control cells. Immunohistochemistry showed that APOA1 was highly expressed in the paclitaxel- and carboplatin- resistant squamous cell carcinoma of the cervix. Conclusion This study is the first to use iTRAQ to identify paclitaxel- and carboplatin- resistance proteins in cervical cells. We identified several proteins previously unassociated with paclitaxel and carboplatin resistance in cervical cancer, thereby expanding our understanding of paclitaxel and carboplatin resistance mechanisms. Moreover, these findings indicate that the APOA1 protein could serve as a potential marker for monitoring and predicting paclitaxel and carboplatin resistance levels.
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Affiliation(s)
- Yue He
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Su Bin Han
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Yu Ning Geng
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Shu Li Yang
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Yu Mei Wu
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China.
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15
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Xu Y, Dong Y, Xu Y, Lai Z, Jin B, Hao Y, Gao Y, Sun Y, Chen XG, Gu J. Differentiation of Long Non-Coding RNA and mRNA Expression Profiles in Male and Female Aedes albopictus. Front Genet 2019; 10:975. [PMID: 31681418 PMCID: PMC6802003 DOI: 10.3389/fgene.2019.00975] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/13/2019] [Indexed: 11/13/2022] Open
Abstract
The Asia tiger mosquito (Aedes albopictus) is an important vector of arboviruses, and females can transmit pathogens such as the dengue, zika, and chikungunya viruses. Understanding sex-related differences in this mosquito is fundamental for vector control. However, there are no reports of systematic characterization of long non-coding RNAs (lncRNAs) in male and female Ae. albopictus. To investigate the roles of coding and non-coding RNAs in both sexes of Ae. albopictus, RNA sequencing was performed on male and female samples. The results showed 305 differentially expressed protein-coding genes (DEGs) between males and females, of which 198 were highly expressed in males and 125 were highly expressed in females. Sex-associated gene ontology terms were enriched. Analysis with the FEELnc software identified 2,623 novel lncRNAs, of which 26 showed male high expression and 11 showed female high expression. Quantitative real-time PCR of randomly selected DEGs and lncRNAs supported the validity of the RNA sequencing results. Knocking down male high-expressed gene AALF000433 in male adults reduced the egg hatching rate. This study provides valuable data on sex-specific expression of protein-coding genes and lncRNAs in adult Ae. albopictus, which will guide further studies aimed at understanding sex development and determination mechanisms in this species.
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Affiliation(s)
- Ye Xu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yunqiao Dong
- Reproductive Medical Center of Guangdong Women and Children Hospital, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yazhou Xu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zetian Lai
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Binbin Jin
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yanqiang Hao
- Department of Laboratory Medicine, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yonghui Gao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yan Sun
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xiao-Guang Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jinbao Gu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
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16
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Imrie L, Le Bihan T, O'Toole Á, Hickner PV, Dunn WA, Weise B, Rund SSC. Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics. PLoS One 2019; 14:e0220225. [PMID: 31356616 PMCID: PMC6663012 DOI: 10.1371/journal.pone.0220225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
The malaria mosquito, Anopheles stephensi, and other mosquitoes modulate their biology to match the time-of-day. In the present work, we used a non-hypothesis driven approach (untargeted proteomics) to identify proteins in mosquito tissue, and then quantified the relative abundance of the identified proteins from An. stephensi bodies. Using these quantified protein levels, we then analyzed the data for proteins that were only detectable at certain times-of-the day, highlighting the need to consider time-of-day in experimental design. Further, we extended our time-of-day analysis to look for proteins which cycle in a rhythmic 24-hour ("circadian") manner, identifying 31 rhythmic proteins. Finally, to maximize the utility of our data, we performed a proteogenomic analysis to improve the genome annotation of An. stephensi. We compare peptides that were detected using mass spectrometry but are 'missing' from the An. stephensi predicted proteome, to reference proteomes from 38 other primarily human disease vector species. We found 239 such peptide matches and reveal that genome annotation can be improved using proteogenomic analysis from taxonomically diverse reference proteomes. Examination of 'missing' peptides revealed reading frame errors, errors in gene-calling, overlapping gene models, and suspected gaps in the genome assembly.
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Affiliation(s)
- Lisa Imrie
- SynthSys–Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thierry Le Bihan
- SynthSys–Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Rapid Novor, Kitchener, Ontario, Canada
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul V. Hickner
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - W. Augustine Dunn
- Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Benjamin Weise
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel S. C. Rund
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
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17
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Moyes CL, Wiebe A, Gleave K, Trett A, Hancock PA, Padonou GG, Chouaïbou MS, Sovi A, Abuelmaali SA, Ochomo E, Antonio-Nkondjio C, Dengela D, Kawada H, Dabire RK, Donnelly MJ, Mbogo C, Fornadel C, Coleman M. Analysis-ready datasets for insecticide resistance phenotype and genotype frequency in African malaria vectors. Sci Data 2019; 6:121. [PMID: 31308378 PMCID: PMC6629700 DOI: 10.1038/s41597-019-0134-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/19/2019] [Indexed: 12/19/2022] Open
Abstract
The impact of insecticide resistance in malaria vectors is poorly understood and quantified. Here a series of geospatial datasets for insecticide resistance in malaria vectors are provided, so that trends in resistance in time and space can be quantified, and the impact of resistance found in wild populations on malaria transmission in Africa can be assessed. Specifically, data have been collated and geopositioned for the prevalence of insecticide resistance, as measured by standard bioassays, in representative samples of individual species or species complexes. Data are provided for the Anopheles gambiae species complex, the Anopheles funestus subgroup, and for nine individual vector species. Data are also given for common genetic markers of resistance to support analyses of whether these markers can improve the ability to monitor resistance in low resource settings. Allele frequencies for known resistance-associated markers in the Voltage-gated sodium channel (Vgsc) are provided. In total, eight analysis-ready, standardised, geopositioned datasets encompassing over 20,000 African mosquito collections between 1957 and 2017 are released.
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Affiliation(s)
- Catherine L Moyes
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX1 7LF, UK.
| | - Antoinette Wiebe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX1 7LF, UK
| | - Katherine Gleave
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L1, UK
| | - Anna Trett
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L1, UK
| | - Penelope A Hancock
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX1 7LF, UK
| | - Germain Gil Padonou
- Centre de Recherche Entomologique de Cotonou (CREC), 06BP2604, Cotonou, Benin
| | - Mouhamadou S Chouaïbou
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, 01BP1303, Abj 01, Abidjan, Côte d'Ivoire
| | - Arthur Sovi
- Centre de Recherche Entomologique de Cotonou (CREC), 06BP2604, Cotonou, Benin
- Faculty of Agronomy, University of Parakou, BP123, Parakou, Benin
| | - Sara A Abuelmaali
- Department of Medical Entomology, National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan
| | - Eric Ochomo
- Kenya Medical Research Institute, Center for Global Health Research, Kisumu, Kenya
| | - Christophe Antonio-Nkondjio
- Laboratoire de Recherche sur le Paludisme, Organisation de Coordination pour la lutte Contre les Endémies en Afrique Centrale (OCEAC), P.O. Box 288, Yaoundé, Cameroon
| | - Dereje Dengela
- U.S. PMI VectorLink Project, Abt Associates, 6130 Executive Boulevard, Rockville, MD, 20852, USA
| | - Hitoshi Kawada
- Department of Vector Ecology and Environment, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Roch K Dabire
- Department of Medical Biology and Public Health, Institut de Recherche en Science de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Martin J Donnelly
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L1, UK
| | - Charles Mbogo
- KEMRI Centre for Geographic Medicine Research-Coast, P.O Box 230-80108, Kilifi, Kenya
- KEMRI-Wellcome Trust Research Program, P.O Box 43640-00100, Nairobi, Kenya
| | - Christen Fornadel
- US President's Malaria Initiative, US Agency for International Development, Washington, DC, USA
| | - Michael Coleman
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool L1, UK
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18
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RNASeq Analysis of Aedes albopictus Mosquito Midguts after Chikungunya Virus Infection. Viruses 2019; 11:v11060513. [PMID: 31167461 PMCID: PMC6631752 DOI: 10.3390/v11060513] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 06/02/2019] [Indexed: 01/01/2023] Open
Abstract
Chikungunya virus (CHIKV) is an emerging pathogen around the world and causes significant morbidity in patients. A single amino acid mutation in the envelope protein of CHIKV has led to a shift in vector preference towards Aedesalbopictus. While mosquitoes are known to mount an antiviral immune response post-infection, molecular interactions during the course of infection at the tissue level remain largely uncharacterised. We performed whole transcriptome analysis on dissected midguts of Aedes albopictus infected with CHIKV to identify differentially expressed genes. For this, RNA was extracted at two days post-infection (2-dpi) from pooled midguts. We initially identified 25 differentially expressed genes (p-value < 0.05) when mapped to a reference transcriptome. Further, multiple differentially expressed genes were identified from a custom de novo transcriptome, which was assembled using the reads that did not align with the reference genome. Thirteen of the identified transcripts, possibly involved in immunity, were validated by qRT-PCR. Homologues of seven of these genes were also found to be significantly upregulated in Aedes aegypti midguts 2 dpi, indicating a conserved mechanism at play. These results will help us to characterise the molecular interaction between Aedes albopictus and CHIKV and can be utilised to reduce the impact of this viral infection.
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19
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Ruzzante L, Reijnders MJ, Waterhouse RM. Of Genes and Genomes: Mosquito Evolution and Diversity. Trends Parasitol 2019; 35:32-51. [DOI: 10.1016/j.pt.2018.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/07/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022]
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20
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Nowling RJ, Emrich SJ. Adjusted likelihood-ratio test for variants with unknown genotypes. J Bioinform Comput Biol 2018; 16:1840020. [DOI: 10.1142/s0219720018400206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Association tests performed with the Likelihood-Ratio Test (LR Test) can be an alternative to [Formula: see text], which is often used in population genetics to find variants of interest. Because the LR Test has several properties that could make it preferable to [Formula: see text], we propose a novel approach for modeling unknown genotypes in highly-similar species. To show the effectiveness of this LR Test approach, we apply it to single-nucleotide polymorphisms (SNPs) associated with the recent speciation of the malaria vectors Anopheles gambiae and Anopheles coluzzii and compare to [Formula: see text].
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Affiliation(s)
- Ronald J. Nowling
- Electrical Engineering and Computer Science, Milwaukee School of Engineering, 1025 North Broadway, Milwaukee, WI 53202, USA
| | - Scott J. Emrich
- Electrical Engineering and Computer Science, University of Tennessee, 1520 Middle Drive, Knoxville, TN 37996, USA
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21
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Shrinet J, Srivastava P, Kumar A, Dubey SK, Sirisena PDNN, Srivastava P, Sunil S. Differential Proteome Analysis of Chikungunya Virus and Dengue Virus Coinfection in Aedes Mosquitoes. J Proteome Res 2018; 17:3348-3359. [DOI: 10.1021/acs.jproteome.8b00211] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jatin Shrinet
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), 110067 New Delhi, India
| | - Priyanshu Srivastava
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), 110067 New Delhi, India
| | - Ankit Kumar
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), 110067 New Delhi, India
| | - Sunil Kumar Dubey
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), 110067 New Delhi, India
| | | | - Pratibha Srivastava
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), 110067 New Delhi, India
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), 110067 New Delhi, India
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22
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Morales-Hojas R, Hinsley M, Armean IM, Silk R, Harrup LE, Gonzalez-Uriarte A, Veronesi E, Campbell L, Nayduch D, Saski C, Tabachnick WJ, Kersey P, Carpenter S, Fife M. The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus. BMC Genomics 2018; 19:624. [PMID: 30134833 PMCID: PMC6106943 DOI: 10.1186/s12864-018-5014-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 08/14/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The new genomic technologies have provided novel insights into the genetics of interactions between vectors, viruses and hosts, which are leading to advances in the control of arboviruses of medical importance. However, the development of tools and resources available for vectors of non-zoonotic arboviruses remains neglected. Biting midges of the genus Culicoides transmit some of the most important arboviruses of wildlife and livestock worldwide, with a global impact on economic productivity, health and welfare. The absence of a suitable reference genome has hindered genomic analyses to date in this important genus of vectors. In the present study, the genome of Culicoides sonorensis, a vector of bluetongue virus (BTV) in the USA, has been sequenced to provide the first reference genome for these vectors. In this study, we also report the use of the reference genome to perform initial transcriptomic analyses of vector competence for BTV. RESULTS Our analyses reveal that the genome is 189 Mb, assembled in 7974 scaffolds. Its annotation using the transcriptomic data generated in this study and in a previous study has identified 15,612 genes. Gene expression analyses of C. sonorensis females infected with BTV performed in this study revealed 165 genes that were differentially expressed between vector competent and refractory females. Two candidate genes, glutathione S-transferase (gst) and the antiviral helicase ski2, previously recognized as involved in vector competence for BTV in C. sonorensis (gst) and repressing dsRNA virus propagation (ski2), were confirmed in this study. CONCLUSIONS The reference genome of C. sonorensis has enabled preliminary analyses of the gene expression profiles of vector competent and refractory individuals. The genome and transcriptomes generated in this study provide suitable tools for future research on arbovirus transmission. These provide a valuable resource for these vector lineage, which diverged from other major Dipteran vector families over 200 million years ago. The genome will be a valuable source of comparative data for other important Dipteran vector families including mosquitoes (Culicidae) and sandflies (Psychodidae), and together with the transcriptomic data can yield potential targets for transgenic modification in vector control and functional studies.
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Affiliation(s)
- Ramiro Morales-Hojas
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK. .,Rothamsted Insect Survey, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Malcolm Hinsley
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Irina M Armean
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rhiannon Silk
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Lara E Harrup
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Asier Gonzalez-Uriarte
- Bioinformatics group, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Eva Veronesi
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK.,National Centre for Vector Entomology, Institute of Parasitology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Lahcen Campbell
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dana Nayduch
- USDA-ARS, Center for Grain and Animal Health Research, Arthropod Borne Animal Diseases Research Unit, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - Christopher Saski
- Department of Genetics and Biochemistry, Clemson University Genomics Institute, BRC #310, 105 Collins Street, Clemson, SC, 29634, USA
| | - Walter J Tabachnick
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, University of Florida, IFAS, 200 9th St., SE, Vero Beach, FL, 32962, USA
| | - Paul Kersey
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Simon Carpenter
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
| | - Mark Fife
- The Pirbright Institute, Ash Road, Woking, Surrey, GU24 0NF, UK
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23
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Friedrich M, Chahine H, Al-Jageta C, Badreddine H. Massive parallel expansions of Methuselah/Methuselah-like receptors in schizophoran Diptera. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:384-389. [PMID: 30058118 DOI: 10.1002/jez.b.22813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/14/2018] [Accepted: 06/11/2018] [Indexed: 01/16/2023]
Abstract
The Methuselah/Methuselah-like (Mth/Mthl) family of G-protein coupled receptors (GPCRs) is represented by 16 homologs in the fruit fly Drosophila melanogaster. Three of them have thus far been functionally characterized and found to play critical roles in cell adhesion, immunity, lifespan, and oxidative stress regulation. Evolutionary studies have shown that the large number of D. melanogaster Mth/Mthl GPCRs arose by at least two rounds of gene duplications. The first produced the "mth superclade" subfamily and was followed by the expansion of the "melanogaster subgroup" cluster within the "mth superclade" of Mth/Mthl GPCRs. The adaptive significance of the Mth/Mthl receptor repertoire expansion in Drosophila remains elusive. Studying the Mth/Mthl gene family content in newly available dipteran genomes, we find that the first expansion of the mthl superclade predates the diversification of schizophoran Diptera approximately 65 million years ago. Unexpectedly, we further find that the subsequent expansion of the melanogaster subgroup cluster was paralleled by independent mth superclade Mth/Mthl GPCR expansions in other schizophoran clades (Muscidae and Tephritidae). Our study thus reveals an even more dynamic diversification of mth superclade GPCRs than previously appreciated and linked to the emergence of schizophoran flies, the most dramatic radiation in the dipteran tree of life.
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Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan.,Department of Anatomy and Cell Biology, School of Medicine, Wayne State University, Detroit, Michigan
| | - Hanady Chahine
- Department of Biological Sciences, Wayne State University, Detroit, Michigan
| | - Cristina Al-Jageta
- Department of Biological Sciences, Wayne State University, Detroit, Michigan
| | - Hamzah Badreddine
- Department of Biological Sciences, Wayne State University, Detroit, Michigan
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24
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Bao R, Dia SE, Issa HA, Alhusein D, Friedrich M. Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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25
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Shrinet J, Bhavesh NS, Sunil S. Understanding Oxidative Stress in Aedes during Chikungunya and Dengue Virus Infections Using Integromics Analysis. Viruses 2018; 10:v10060314. [PMID: 29890729 PMCID: PMC6024870 DOI: 10.3390/v10060314] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/26/2018] [Accepted: 04/27/2018] [Indexed: 12/15/2022] Open
Abstract
Arboviral infection causes dysregulation of cascade of events involving numerous biomolecules affecting fitness of mosquito to combat virus. In response of the viral infection mosquito’s defense mechanism get initiated. Oxidative stress is among the first host responses triggered by the vector. Significant number of information is available showing changes in the transcripts and/or proteins upon Chikungunya virus and Dengue virus mono-infections and as co-infections. In the present study, we collected different -omics data available in the public database along with the data generated in our laboratory related to mono-infections or co-infections of these viruses. We analyzed the data and classified them into their respective pathways to study the role of oxidative stress in combating arboviral infection in Aedes mosquito. The analysis revealed that the oxidative stress related pathways functions in harmonized manner.
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Affiliation(s)
- Jatin Shrinet
- Vector Borne Diseases, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Neel Sarovar Bhavesh
- Transcriptional Regulation, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Sujatha Sunil
- Vector Borne Diseases, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.
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26
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Subramanyam S, Shreve JT, Nemacheck JA, Johnson AJ, Schemerhorn B, Shukle RH, Williams CE. Modulation of nonessential amino acid biosynthetic pathways in virulent Hessian fly larvae (Mayetiola destructor), feeding on susceptible host wheat (Triticum aestivum). JOURNAL OF INSECT PHYSIOLOGY 2018; 105:54-63. [PMID: 29336997 DOI: 10.1016/j.jinsphys.2018.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 12/29/2017] [Accepted: 01/06/2018] [Indexed: 05/29/2023]
Abstract
Compatible interactions between wheat (Triticum aestivum), and its dipteran pest Hessian fly (Hf, Mayetiola destructor) result in successful establishment of larval feeding sites rendering the host plant susceptible. Virulent larvae employ an effector-based feeding strategy to reprogram the host physiology resulting in formation of a protein- and sugar-rich nutritive tissue beneficial to developing larvae. Previous studies documented increased levels of nonessential amino acids (NAA; that need not be received through insect diet) in the susceptible wheat in response to larval feeding, suggesting importance of plant-derived NAA in larval nutrition. Here, we investigated the modulation of genes from NAA biosynthetic pathways (NAABP) in virulent Hf larvae. Transcript profiling for 16 NAABP genes, annotated from the recently assembled Hf genome, was carried out in the feeding first-, and second-instars and compared with that of the first-instar neonate (newly hatched, migrating, assumed to be non-feeding) larvae. While Tyr, Gln, Glu, and Pro NAABP genes transcript abundance declined in the feeding instars as compared to the neonates, those for Ala, and Ser increased in the feeding larval instars, despite higher levels of these NAA in the susceptible host plant. Asp, Asn, Gly and Cys NAABP genes exhibited variable expression profiles in the feeding first- and second-instars. Our results indicate that while Hf larvae utilize the plant-derived NAA, de novo synthesis of several NAA may be necessary to: (i) provide larvae with the requisite amount for sustaining growth before nutritive tissue formation and, (ii) overcome any inadequate amounts in the host plant, post-nutritive tissue formation.
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Affiliation(s)
| | - Jacob T Shreve
- Department of Entomology, Purdue University, West Lafayette, IN 47907, United States
| | - Jill A Nemacheck
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN 47907, United States
| | - Alisha J Johnson
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN 47907, United States
| | - Brandi Schemerhorn
- Department of Entomology, Purdue University, West Lafayette, IN 47907, United States; USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN 47907, United States
| | - Richard H Shukle
- Department of Entomology, Purdue University, West Lafayette, IN 47907, United States; USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN 47907, United States
| | - Christie E Williams
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, United States; USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, IN 47907, United States
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27
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017. [PMID: 28756775 DOI: 10.1186/s12915-017-0399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. RESULTS We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. CONCLUSIONS Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan
- Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
- Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
- Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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28
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Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol 2017; 15:62. [PMID: 28756775 PMCID: PMC5535294 DOI: 10.1186/s12915-017-0399-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
Background The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0399-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evelyn E Schwager
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Thomas Clarke
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.,Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
| | - Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Torsten Wierschin
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany
| | - Matthias Pechmann
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Yasuko Akiyama-Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Osaka Medical College, Takatsuki, Osaka, Japan
| | - Lauren Esposito
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA, 94118, USA
| | - Jesper Bechsgaard
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Trine Bilde
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Alexandra D Buffry
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - HarshaVardhan Doddapaneni
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cornelius Eibner
- Department of Genetics, Friedrich-Schiller-University Jena, Philosophenweg 12, 07743, Jena, Germany
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Peter Funch
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark
| | - Jessica Garb
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA, 01854, USA
| | - Luis B Gonzalez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Vanessa L Gonzalez
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA
| | - Sam Griffiths-Jones
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Cheryl Hayashi
- Department of Biology, University of California, Riverside, Riverside, CA, 92521, USA.,Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.,Department of Developmental Biology, University of Cologne, Cologne Biocenter, Institute of Zoology, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Rodrigo Nunes da Fonseca
- Nucleo em Ecologia e Desenvolvimento SocioAmbiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, 27941-222, Brazil
| | - Christian L B Paese
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Matthew Ronshaugen
- Faculty of Biology Medicine and Health, University of Manchester, D.1416 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Christoph Schomburg
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Anna Schönauer
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Montserrat Torres-Oliva
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Natascha Turetzek
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany
| | - Bram Vanthournout
- Department of Bioscience, Aarhus University, Ny Munkegade 116, building 1540, 8000, Aarhus C, Denmark.,Evolution and Optics of Nanostructure group (EON), Biology Department, Ghent University, Gent, Belgium
| | - John H Werren
- Biology Department, University of Rochester, Rochester, NY, 14627, USA
| | - Carsten Wolff
- Humboldt-Universität of Berlin, Institut für Biologie, Philippstr.13, 10115, Berlin, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Gregor Bucher
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach-Institute, GZMB, Georg-August-University, Göttingen Campus, Justus von Liebig Weg 11, 37077, Göttingen, Germany.
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Jonathan Coddington
- Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC, 20013-7012, USA.
| | - Hiroki Oda
- JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan. .,Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan.
| | - Mario Stanke
- Ernst Moritz Arndt University Greifswald, Institute for Mathematics and Computer Science, Walther-Rathenau-Str. 47, 17487, Greifswald, Germany.
| | - Nadia A Ayoub
- Department of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA, 24450, USA.
| | - Nikola-Michael Prpic
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Jean-François Flot
- Université libre de Bruxelles (ULB), Evolutionary Biology & Ecology, C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.
| | - Nico Posnien
- Department for Developmental Biology, University Goettingen, Johann-Friedrich-Blumenbach-Institut for Zoology and Anthropology, GZMB Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077, Goettingen, Germany.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK.
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Sheppard AD, Rund SSC, George GF, Clark E, Acri DJ, Duffield GE. Light manipulation of mosquito behaviour: acute and sustained photic suppression of biting activity in the Anopheles gambiae malaria mosquito. Parasit Vectors 2017; 10:255. [PMID: 28619089 PMCID: PMC5472875 DOI: 10.1186/s13071-017-2196-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 05/12/2017] [Indexed: 11/22/2022] Open
Abstract
Background Host-seeking behaviours in anopheline mosquitoes are time-of-day specific, with a greater propensity for nocturnal biting. We investigated how a short exposure to light presented during the night or late day can inhibit biting activity and modulate flight activity behaviour. Results Anopheles gambiae (s.s.), maintained on a 12:12 LD cycle, were exposed transiently to white light for 10-min at the onset of night and the proportion taking a blood meal in a human biting assay was recorded every 2 h over an 8-h duration. The pulse significantly reduced biting propensity in mosquitoes 2 h following administration, in some trials for 4 h, and with no differences detected after 6 h. Conversely, biting levels were significantly elevated when mosquitoes were exposed to a dark treatment during the late day, suggesting that light suppresses biting behaviour even during the late daytime. These data reveal a potent effect of a discrete light pulse on biting behaviour that is both immediate and sustained. We expanded this approach to develop a method to reduce biting propensity throughout the night by exposing mosquitoes to a series of 6- or 10-min pulses presented every 2 h. We reveal both an immediate suppressive effect of light during the exposure period and 2 h after the pulse. This response was found to be effective during most times of the night: however, differential responses that were time-of-day specific suggest an underlying circadian property of the mosquito physiology that results in an altered treatment efficacy. Finally, we examined the immediate and sustained effects of light on mosquito flight activity behaviour following exposure to a 30-min pulse, and observed activity suppression during early night, and elevated activity during the late night. Conclusions As mosquitoes and malaria parasites are becoming increasingly resistant to insecticide and drug treatment respectively, there is a necessity for the development of innovative control strategies beyond insecticide-treated nets (ITNs) and residual spraying. These data reveal the potent inhibitory effects of light exposure and the utility of multiple photic pulses presented at intervals during the night/late daytime, may prove to be an effective tool that complements established control methods.
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Affiliation(s)
- Aaron D Sheppard
- Department of Biological Sciences and Eck Institute for Global Health, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Samuel S C Rund
- Department of Biological Sciences and Eck Institute for Global Health, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Gary F George
- Department of Biological Sciences and Eck Institute for Global Health, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Erin Clark
- Department of Biological Sciences and Eck Institute for Global Health, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Dominic J Acri
- Department of Biological Sciences and Eck Institute for Global Health, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Giles E Duffield
- Department of Biological Sciences and Eck Institute for Global Health, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN, 46556, USA.
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30
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Li Y, Piermarini PM, Esquivel CJ, Price DP, Drumm HE, Schilkey FD, Hansen IA. RNA-Seq Comparison of Larval and Adult Malpighian Tubules of the Yellow Fever Mosquito Aedes aegypti Reveals Life Stage-Specific Changes in Renal Function. Front Physiol 2017; 8:283. [PMID: 28536536 PMCID: PMC5422481 DOI: 10.3389/fphys.2017.00283] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 04/19/2017] [Indexed: 11/20/2022] Open
Abstract
Introduction: The life history of Aedes aegypti presents diverse challenges to its diuretic system. During the larval and pupal life stages mosquitoes are aquatic. With the emergence of the adult they become terrestrial. This shifts the organism within minutes from an aquatic environment to a terrestrial environment where dehydration has to be avoided. In addition, female mosquitoes take large blood meals, which present an entirely new set of challenges to salt and water homeostasis. Methods: To determine differences in gene expression associated with these different life stages, we performed an RNA-seq analysis of the main diuretic tissue in A. aegypti, the Malpighian tubules. We compared transcript abundance in 4th instar larvae to that of adult females and analyzed the data with a focus on transcripts that encode proteins potentially involved in diuresis, like water and solute channels as well as ion transporters. We compared our results against the model of potassium- and sodium chloride excretion in the Malpighian tubules proposed by Hine et al. (2014), which involves at least eight ion transporters and a proton-pump. Results: We found 3,421 of a total number of 17,478 (19.6%) unique transcripts with a P < 0.05 and at least a 2.5 fold change in expression levels between the two groups. We identified two novel transporter genes that are highly expressed in the adult Malpighian tubules, which have not previously been part of the transport model in this species and may play important roles in diuresis. We also identified candidates for hypothesized sodium and chloride channels. Detoxification genes were generally higher expressed in larvae. Significance: This study represents the first comparison of Malpighian tubule transcriptomes between larval and adult A. aegypti mosquitoes, highlighting key differences in their renal systems that arise as they transform from an aquatic filter-feeding larval stage to a terrestrial, blood-feeding adult stage.
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Affiliation(s)
- Yiyi Li
- Department of Biology, New Mexico State UniversityLas Cruces, NM, USA.,Department of Computer Science, New Mexico State UniversityLas Cruces, NM, USA
| | - Peter M Piermarini
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State UniversityWooster, OH, USA
| | - Carlos J Esquivel
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State UniversityWooster, OH, USA
| | | | - Hannah E Drumm
- Department of Biology, New Mexico State UniversityLas Cruces, NM, USA
| | | | - Immo A Hansen
- Department of Biology, New Mexico State UniversityLas Cruces, NM, USA.,Department of Computer Science, New Mexico State UniversityLas Cruces, NM, USA.,Institute of Applied Biosciences, New Mexico State UniversityLas Cruces, NM, USA
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31
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Shrinet J, Srivastava P, Sunil S. Transcriptome analysis of Aedes aegypti in response to mono-infections and co-infections of dengue virus-2 and chikungunya virus. Biochem Biophys Res Commun 2017; 492:617-623. [PMID: 28161634 DOI: 10.1016/j.bbrc.2017.01.162] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/24/2017] [Accepted: 01/29/2017] [Indexed: 12/24/2022]
Abstract
Chikungunya virus (CHIKV) and Dengue virus (DENV) spread via the bite of infected Aedes mosquitoes. Both these viruses exist as co-infections in the host as well as the vector and are known to exploit their cellular machinery for their replication. While there are studies reporting the changes in Aedes transcriptome when infected with DENV and CHIKV individually, the effect both these viruses have on the mosquitoes when present as co-infections is not clearly understood. In the present study, we infected Aedes aegypti mosquitoes with DENV and CHIKV individually and as co-infection through nanoinjections. We performed high throughput RNA sequencing of the infected Aedes aegypti to understand the changes in the Aedes transcriptome during the early stages of infection, i.e., 24 h post infection and compared the transcriptome profiles during DENV and CHIKV mono-infections with that of co-infections. We identified 190 significantly regulated genes identified in CHIKV infected library, 37 genes from DENV library and 100 genes from co-infected library and they were classified into different pathways. Our study reveal that distinct pathways and transcripts are being regulated during the three types of infection states in Aedes aegypti mosquitoes.
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Affiliation(s)
- Jatin Shrinet
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pratibha Srivastava
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sujatha Sunil
- Vector Borne Diseases Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India.
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32
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Morphological and Transcriptomic Analysis of a Beetle Chemosensory System Reveals a Gnathal Olfactory Center. BMC Biol 2016; 14:90. [PMID: 27751175 PMCID: PMC5067906 DOI: 10.1186/s12915-016-0304-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/05/2016] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The red flour beetle Tribolium castaneum is an emerging insect model organism representing the largest insect order, Coleoptera, which encompasses several serious agricultural and forest pests. Despite the ecological and economic importance of beetles, most insect olfaction studies have so far focused on dipteran, lepidopteran, or hymenopteran systems. RESULTS Here, we present the first detailed morphological description of a coleopteran olfactory pathway in combination with genome-wide expression analysis of the relevant gene families involved in chemoreception. Our study revealed that besides the antennae, also the mouthparts are highly involved in olfaction and that their respective contribution is processed separately. In this beetle, olfactory sensory neurons from the mouthparts project to the lobus glomerulatus, a structure so far only characterized in hemimetabolous insects, as well as to a so far non-described unpaired glomerularly organized olfactory neuropil in the gnathal ganglion, which we term the gnathal olfactory center. The high number of functional odorant receptor genes expressed in the mouthparts also supports the importance of the maxillary and labial palps in olfaction of this beetle. Moreover, gustatory perception seems equally distributed between antenna and mouthparts, since the number of expressed gustatory receptors is similar for both organs. CONCLUSIONS Our analysis of the T. castaneum chemosensory system confirms that olfactory and gustatory perception are not organotopically separated to the antennae and mouthparts, respectively. The identification of additional olfactory processing centers, the lobus glomerulatus and the gnathal olfactory center, is in contrast to the current picture that in holometabolous insects all olfactory inputs allegedly converge in the antennal lobe. These findings indicate that Holometabola have evolved a wider variety of solutions to chemoreception than previously assumed.
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33
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Leite DJ, Ninova M, Hilbrant M, Arif S, Griffiths-Jones S, Ronshaugen M, McGregor AP. Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum. Genome Biol Evol 2016; 8:2133-44. [PMID: 27324919 PMCID: PMC4987109 DOI: 10.1093/gbe/evw143] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development.
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Affiliation(s)
- Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, United Kingdom
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Saad Arif
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | | | | | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
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Sen R, Nayak L, De RK. A review on host-pathogen interactions: classification and prediction. Eur J Clin Microbiol Infect Dis 2016; 35:1581-99. [PMID: 27470504 DOI: 10.1007/s10096-016-2716-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023]
Abstract
The research on host-pathogen interactions is an ever-emerging and evolving field. Every other day a new pathogen gets discovered, along with comes the challenge of its prevention and cure. As the intelligent human always vies for prevention, which is better than cure, understanding the mechanisms of host-pathogen interactions gets prior importance. There are many mechanisms involved from the pathogen as well as the host sides while an interaction happens. It is a vis-a-vis fight of the counter genes and proteins from both sides. Who wins depends on whether a host gets an infection or not. Moreover, a higher level of complexity arises when the pathogens evolve and become resistant to a host's defense mechanisms. Such pathogens pose serious challenges for treatment. The entire human population is in danger of such long-lasting persistent infections. Some of these infections even increase the rate of mortality. Hence there is an immediate emergency to understand how the pathogens interact with their host for successful invasion. It may lead to discovery of appropriate preventive measures, and the development of rational therapeutic measures and medication against such infections and diseases. This review, a state-of-the-art updated scenario of host-pathogen interaction research, has been done by keeping in mind this urgency. It covers the biological and computational aspects of host-pathogen interactions, classification of the methods by which the pathogens interact with their hosts, different machine learning techniques for prediction of host-pathogen interactions, and future scopes of this research field.
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Affiliation(s)
- R Sen
- Machine Intelligence Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700108, India
| | - L Nayak
- Machine Intelligence Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700108, India
| | - R K De
- Machine Intelligence Unit, Indian Statistical Institute, 203, Barrackpore Trunk Road, Kolkata, 700108, India.
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Suh A, Witt CC, Menger J, Sadanandan KR, Podsiadlowski L, Gerth M, Weigert A, McGuire JA, Mudge J, Edwards SV, Rheindt FE. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nat Commun 2016; 7:11396. [PMID: 27097561 PMCID: PMC4844689 DOI: 10.1038/ncomms11396] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 03/21/2016] [Indexed: 02/08/2023] Open
Abstract
Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity. Lymphatic filariasis and loiasis are diseases caused by insect-borne filarial nematodes. Here, Suh et al. identify a retrotransposon that is present in the genomes of these nematodes and seven tropical bird lineages, indicating two waves of horizontal gene transfer around 17–25 million years ago.
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Affiliation(s)
- Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, SE-752 36 Uppsala, Sweden
| | - Christopher C Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Juliana Menger
- Department of Conservation Biology, Helmholtz Centre for Environmental Research (UFZ), D-04318 Leipzig, Germany.,Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany.,Instituto Nacional de Pesquisas da Amazônia (INPA), AM 69067-375 Manaus, Brazil
| | - Keren R Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Lars Podsiadlowski
- Institute of Evolutionary Biology and Ecology, University of Bonn, D-53121 Bonn, Germany
| | - Michael Gerth
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, D-04103 Leipzig, Germany.,Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico 87505, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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Mangia C, Vismarra A, Kramer L, Bell-Sakyi L, Porretta D, Otranto D, Epis S, Grandi G. Evaluation of the in vitro expression of ATP binding-cassette (ABC) proteins in an Ixodes ricinus cell line exposed to ivermectin. Parasit Vectors 2016; 9:215. [PMID: 27090214 PMCID: PMC4835901 DOI: 10.1186/s13071-016-1497-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/05/2016] [Indexed: 11/10/2022] Open
Abstract
Background Ticks are among the most important vectors of pathogens causing human and animal disease. Acaricides are used to control tick infestation, although there are increasing reports of resistance. Recently, over-expression of ATP-binding cassette (ABC) transporter proteins (P-glycoproteins, PgP) has been implicated in resistance to the acaricide ivermectin in the ticks Rhipicephalus (Boophilus) microplus and Rhipicephalus sanguineus sensu lato. Ixodid tick cell lines have been used to investigate drug resistance mechanisms. The aim of the present study was to evaluate expression of several PgPs in the Ixodes ricinus-derived cell line IRE/CTVM19 and to determine modulation of expression following treatment with ivermectin. Findings IRE/CTVM19 cells were treated with different concentrations of ivermectin (0, 11, 22 or 33 μM) and incubated for 10 days. Evaluation of viability and relative expression of ABCB1, ABCB6, ABCB8 and ABCB10 genes were carried out at day 10 post treatment. Cell viability ranged between 84 % and 92 % with no significant differences between untreated and treated cells. qRT-PCR showed that ABC pump expression was not significantly modulated by ivermectin treatment. Expression of the ABCB8 PgP subfamily revealed a biphasic trend, based on the ivermectin concentration. ABCB6 and ABCB10 gene expression was not modulated by ivermectin treatment and ABCB1 expression was not detected. Conclusions This is the first report of PgP expression in an I. ricinus-derived tick cell line. Development of an in vitro model for the study of acaricide resistance mechanisms would greatly facilitate screening for drug resistance in ticks.
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Affiliation(s)
- Carlo Mangia
- Department of Veterinary Sciences, University of Parma, 43126, Parma, Italy
| | - Alice Vismarra
- Department of Veterinary Sciences, University of Parma, 43126, Parma, Italy
| | - Laura Kramer
- Department of Veterinary Sciences, University of Parma, 43126, Parma, Italy.
| | - Lesley Bell-Sakyi
- The Pirbright Institute, Ash Road, Pirbright, Surrey GU24 0NF, Pirbright, UK
| | - Daniele Porretta
- Department of Environmental Biology, University of Rome 'La Sapienza', Rome, Italy
| | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, 70010, Bari, Italy
| | - Sara Epis
- Department of Veterinary Science and Public Health, University of Milan, Milan, Italy
| | - Giulio Grandi
- National Veterinary Institute, SVA, SE-751 89, Uppsala, Sweden
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Kiware SS, Russell TL, Mtema ZJ, Malishee AD, Chaki P, Lwetoijera D, Chanda J, Chinula D, Majambere S, Gimnig JE, Smith TA, Killeen GF. A generic schema and data collection forms applicable to diverse entomological studies of mosquitoes. SOURCE CODE FOR BIOLOGY AND MEDICINE 2016; 11:4. [PMID: 27022408 PMCID: PMC4809029 DOI: 10.1186/s13029-016-0050-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/17/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Standardized schemas, databases, and public data repositories are needed for the studies of malaria vectors that encompass a remarkably diverse array of designs and rapidly generate large data volumes, often in resource-limited tropical settings lacking specialized software or informatics support. RESULTS Data from the majority of mosquito studies conformed to a generic schema, with data collection forms recording the experimental design, sorting of collections, details of sample pooling or subdivision, and additional observations. Generically applicable forms with standardized attribute definitions enabled rigorous, consistent data and sample management with generic software and minimal expertise. Forms use now includes 20 experiments, 8 projects, and 15 users at 3 research and control institutes in 3 African countries, resulting in 11 peer-reviewed publications. CONCLUSION We have designed generic data schema that can be used to develop paper or electronic based data collection forms depending on the availability of resources. We have developed paper-based data collection forms that can be used to collect data from majority of entomological studies across multiple study areas using standardized data formats. Data recorded on these forms with standardized formats can be entered and linked with any relational database software. These informatics tools are recommended because they ensure that medical entomologists save time, improve data quality, and data collected and shared across multiple studies is in standardized formats hence increasing research outputs.
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Affiliation(s)
- Samson S Kiware
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania ; Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI 53201-1881 USA
| | - Tanya L Russell
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania ; Pacific Malaria Initiative Support Centre, School of Population Health, University of Queensland, Brisbane, 4006 Australia
| | - Zacharia J Mtema
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania
| | - Alpha D Malishee
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania
| | - Prosper Chaki
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania
| | - Dickson Lwetoijera
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania ; Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK
| | | | | | - Silas Majambere
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania ; Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK
| | - John E Gimnig
- Division of Parasitic Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Thomas A Smith
- Department of Public Health and Epidemiology, Swiss Tropical Institute, Socinstrasse 57, Basel, CH 4002 Switzerland
| | - Gerry F Killeen
- Environmental Health and Ecological Sciences Thematic Group, Ifakara Health Institute, P.O. Box 53, Ifakara, Tanzania ; Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK
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Jung S, Lee T, Ficklin S, Yu J, Cheng CH, Main D. Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw010. [PMID: 26989146 PMCID: PMC4795932 DOI: 10.1093/database/baw010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/21/2016] [Indexed: 11/12/2022]
Abstract
The Genome Database for Rosaceae (GDR) and CottonGen are comprehensive online data repositories that provide access to integrated genomic, genetic and breeding data through search, visualization and analysis tools for Rosaceae crops and Gossypium (cotton). These online databases use Chado, an open-source, generic and ontology-driven database schema for biological data, as the primary data storage platform. Chado is highly normalized and uses ontologies to indicate the 'types' of data. Therefore, Chado is flexible such that it has been used to house genomic, genetic and breeding data for GDR and CottonGen. These data include whole genome sequence and annotation, transcripts, molecular markers, genetic maps, Quantitative Trait Loci, Mendelian Trait Loci, traits, germplasm, pedigrees, large scale phenotypic and genotypic data, ontologies and publications. We provide information about how to store these types of data in Chado using GDR and CottonGen as examples sites that were converted from an older legacy infrastructure. Database URL: GDR (www.rosaceae.org), CottonGen (www.cottongen.org).
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Affiliation(s)
- Sook Jung
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Taein Lee
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Stephen Ficklin
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Jing Yu
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University Pullman, WA, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University Pullman, WA, USA
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Macharia R, Mireji P, Murungi E, Murilla G, Christoffels A, Aksoy S, Masiga D. Genome-Wide Comparative Analysis of Chemosensory Gene Families in Five Tsetse Fly Species. PLoS Negl Trop Dis 2016; 10:e0004421. [PMID: 26886411 PMCID: PMC4757090 DOI: 10.1371/journal.pntd.0004421] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/11/2016] [Indexed: 12/04/2022] Open
Abstract
For decades, odour-baited traps have been used for control of tsetse flies (Diptera; Glossinidae), vectors of African trypanosomes. However, differential responses to known attractants have been reported in different Glossina species, hindering establishment of a universal vector control tool. Availability of full genome sequences of five Glossina species offers an opportunity to compare their chemosensory repertoire and enhance our understanding of their biology in relation to chemosensation. Here, we identified and annotated the major chemosensory gene families in Glossina. We identified a total of 118, 115, 124, and 123 chemosensory genes in Glossina austeni, G. brevipalpis, G. f. fuscipes, G. pallidipes, respectively, relative to 127 reported in G. m. morsitans. Our results show that tsetse fly genomes have fewer chemosensory genes when compared to other dipterans such as Musca domestica (n>393), Drosophila melanogaster (n = 246) and Anopheles gambiae (n>247). We also found that Glossina chemosensory genes are dispersed across distantly located scaffolds in their respective genomes, in contrast to other insects like D. melanogaster whose genes occur in clusters. Further, Glossina appears to be devoid of sugar receptors and to have expanded CO2 associated receptors, potentially reflecting Glossina's obligate hematophagy and the need to detect hosts that may be out of sight. We also identified, in all species, homologs of Ir84a; a Drosophila-specific ionotropic receptor that promotes male courtship suggesting that this is a conserved trait in tsetse flies. Notably, our selection analysis revealed that a total of four gene loci (Gr21a, GluRIIA, Gr28b, and Obp83a) were under positive selection, which confers fitness advantage to species. These findings provide a platform for studies to further define the language of communication of tsetse with their environment, and influence development of novel approaches for control. Chemical sensing is crucial to survival of tsetse flies; the sole cyclical vectors of African trypanosomes that cause the neglected zoonotic tropical disease sleeping sickness in humans. For many years, vector control has been used to mitigate trypanosome infections among rural populations of sub-Saharan Africa. Nevertheless, development of an all-inclusive strategy to control tsetse flies using odour-baited traps has been limited by disparate responses to the odors exhibited by various tsetse species. In this study, proteins that are putatively involved in chemical sensing were identified and compared among five tsetse species and their close relatives with an aim of enhancing our knowledge on tsetse olfaction. Our findings suggest that the chemosensory genes are conserved across tsetse fly species despite their documented differential responses in odours. We found no species-specific sequence variations among the five species to suggest that differential response to odours is due to loss or gain of genes. It could therefore be hypothesized that the observed differences emerge during the downstream processing of odour molecules involving post translational modification of the chemosensory proteins. We thus recommend functional studies on the identified proteins to determine their roles and molecular interactions.
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Affiliation(s)
- Rosaline Macharia
- Molecular Biology and Bioinformatics Unit, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Paul Mireji
- Department of Epidemiology of Microbial Diseases, Yale School of Public Heath, New Haven, Connecticut, United States of America
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
- * E-mail: (PM); (DM)
| | - Edwin Murungi
- Department of Biochemistry and Molecular Biology, Egerton University, Njoro, Kenya
| | - Grace Murilla
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Alan Christoffels
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Heath, New Haven, Connecticut, United States of America
| | - Daniel Masiga
- Molecular Biology and Bioinformatics Unit, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- * E-mail: (PM); (DM)
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Franco TA, Oliveira DS, Moreira MF, Leal WS, Melo ACA. Silencing the odorant receptor co-receptor RproOrco affects the physiology and behavior of the Chagas disease vector Rhodnius prolixus. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 69:82-90. [PMID: 25747010 DOI: 10.1016/j.ibmb.2015.02.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 02/09/2015] [Accepted: 02/21/2015] [Indexed: 06/04/2023]
Abstract
Olfaction is one of the main sensory modalities that allow insects to interpret their environment. Several proteins, including odorant-binding proteins (OBPs) and odorant receptors (ORs), are involved in this process. Odorant receptors are ion channels formed by a binding unit OR and an odorant receptor co-receptor (Orco). The main goal of this study was to characterize the Orco gene of Rhodnius prolixus (RproOrco) and to infer its biological functions using gene silencing. The full-length RproOrco gene sequence was downloaded from VectorBase. This gene has 7 introns and is located in the genome SuperContig GL563069: 1,017,713-1,023,165. RproOrco encodes a protein of 473 amino acids, with predicted 7 transmembrane domains, and is highly expressed in the antennae during all R. prolixus developmental stages. The RNAi technique effectively silenced RproOrco, reducing the gene's expression by approximately 73%. Interestingly, the effect of gene silencing persisted for more than 100 days, indicating a prolonged effect of dsRNA that was maintained even after molting. The phenotypic effects of silencing involved the following: (1) loss of the ability to find a vertebrate host in a timely manner, (2) decreased ingested blood volume, (3) delayed and decreased molt rate, (4) increased mortality rate, and (5) decreased egg laying. Our data strongly suggest that dsOrco disrupts R. prolixus host-finding behavior, which is further reflected in the blood ingestion, molting, mortality, and egg laying data. This study clearly demonstrates that Orco is an excellent target for controlling triatomine populations. Thus, the data presented here open new possibilities for the control of vector-borne diseases.
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Affiliation(s)
- Thiago A Franco
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Daniele S Oliveira
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Monica F Moreira
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909, Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil
| | - Walter S Leal
- Department of Molecular and Cellular Biology, University of California, 95616, Davis, CA, USA
| | - Ana C A Melo
- Universidade Federal do Rio de Janeiro, Instituto de Química, 21941-909, Rio de Janeiro, RJ, Brazil; Department of Molecular and Cellular Biology, University of California, 95616, Davis, CA, USA; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil.
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Hajdusek O, Sima R, Perner J, Loosova G, Harcubova A, Kopacek P. Tick iron and heme metabolism - New target for an anti-tick intervention. Ticks Tick Borne Dis 2016; 7:565-72. [PMID: 26810909 DOI: 10.1016/j.ttbdis.2016.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 12/28/2022]
Abstract
Ticks are blood-feeding parasites and vectors of serious human and animal diseases. Ixodes ricinus is a common tick in Europe, transmitting tick-borne encephalitis, Lyme borreliosis, anaplasmosis, or babesiosis. Immunization of hosts with recombinant tick proteins has, in theory, the potential to interfere with tick feeding and block transmission of pathogens from the tick to the host. However, the efficacy of tick antigens has, to date, not been fully sufficient to achieve this. We have focused on 11 in silico identified genes encoding proteins potentially involved in tick iron and heme metabolism. Quantitative real-time PCR (qRT-PCR) expression profiling was carried out to preferentially target proteins that are up-regulated during the blood meal. RNA interference (RNAi) was then used to score the relative importance of these genes in tick physiology. Finally, we performed vaccination screens to test the suitability of these proteins as vaccine candidates. These newly identified tick antigens have the potential to improve the available anti-tick vaccines.
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Affiliation(s)
- Ondrej Hajdusek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
| | - Radek Sima
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
| | - Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
| | - Gabriela Loosova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
| | - Adela Harcubova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
| | - Petr Kopacek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic.
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Chen M, Wang C, Wang W, Ji G, Hu B, Du M, Liu G, Li Z, Wang W, Lin X, Zheng W, Chen J. De Novo Assembly and Characterization of Early Embryonic Transcriptome of the Horseshoe Crab Tachypleus tridentatus. PLoS One 2016; 11:e0145825. [PMID: 26731763 PMCID: PMC4711587 DOI: 10.1371/journal.pone.0145825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/02/2015] [Indexed: 01/09/2023] Open
Abstract
The horseshoe crab Tachypleus tridentatus is a unique marine species and a potential model for marine invertebrate. Limited genomic and transcriptional data are currently available to understand the molecular mechanisms underlying the embryonic development of T. tridentatus. Here, we reported for the first time the de novo transcriptome assembly for T. tridentatus at embryonic developmental stage using Illumina RNA-seq platform. Approximate 38 million reads were obtained and further assembled into 133,212 unigenes. Sequence homology analysis against public databases revealed that 33,796 unigenes could be annotated with gene descriptions. Of the annotated unigenes, we identified a number of key components of several conserved metazoan signaling pathways (Hedgehog, Wnt, TGF-beta and Notch pathways) and other important regulatory genes involved in embryonic development. Targeted searching of Pax family genes which play critical roles in the formation of tissue and organ during embryonic development identified a complete set of Pax family genes. Moreover, the full length T. tridentatus Pax1/9a (TtPax1/9a) and Pax1/9b (TtPax1/9b) cDNA sequences were determined based on the transcriptome, demonstrating the immediate application of our database. Using quantitative real time PCR, we analyzed the expression patterns of TtPax1/9a and TtPax1/9b in different tissues of horseshoe crab. Taking advantage of Drosophila model, we further found that TtPax1/9b, but not TtPax1/9a, can partly rescue the Drosophila homolog Poxm dysfunction-caused lethality at the larval stage. Our study provides the embryonic transcriptome of T. tridentatus which could be immediately used for gene discovery and characterization, functional genomics studies in T. tridentatus. This transcriptome database will also facilitate the investigations of molecular mechanisms underlying embryonic development of T. tridentatus and other marine arthropods as well.
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Affiliation(s)
- Mingliang Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Chenying Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Wei Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Gubiao Ji
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Bin Hu
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Mi Du
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Guosheng Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Zengpeng Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Weiyi Wang
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Xiangzhi Lin
- Center of Marine Biotechnology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Weibing Zheng
- Center of Marine Biotechnology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
| | - Jianming Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian Province, China
- * E-mail:
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Souza TM, Menezes ESB, Oliveira RV, Almeida Filho LCP, Martins JM, Moreno FB, Monteiro-Moreira ACO, Moura AAA, Carvalho AFU. Further evidences for the mode of action of the larvicidal m-pentadecadienyl-phenol isolated from Myracrodruon urundeuva seeds against Aedes aegypti. Acta Trop 2015; 152:49-55. [PMID: 26299195 DOI: 10.1016/j.actatropica.2015.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/11/2015] [Accepted: 08/14/2015] [Indexed: 12/25/2022]
Abstract
Nowadays, dengue fever is considered the most important arbovirosis worldwide and its control is still based upon combating the vector Aedes aegypti. Besides monitoring of mosquito populations resistant to conventional insecticides, the search for new environmentally safe insecticides and conduction of molecular studies focusing on the elucidation of mode of action and possible resistance mechanisms are considered the key for a sustainable management of the mosquito vector. Thus, the present work aimed to assess changes in protein expression of 3rd-instar larvae of Ae. aegypti after exposure to the natural insecticide m-pentadecadienyl-phenol. Bidimensional electrophoresis followed by mass spectrometry resulted in identification of 12 proteins differentially expressed between control and treated groups. Larvae exposed to the toxic compound for 24h showed elevated detoxification response (glutathione-S-transferase), increased levels of stress-related proteins (HSP70) as well as evidence of lysosome stabilization to enable survival. Furthermore, expression of proteins involved in protection of peritrophic membrane and metabolism of lipids indicated systemic effect of toxic effects in treated larvae.
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Affiliation(s)
- Terezinha M Souza
- Department of Biochemistry and Molecular Biology, Campus Pici, Federal University of Ceara, 60440-900 Fortaleza, CE, Brazil
| | - Erika S Bezerra Menezes
- Department of Animal Science, Campus do Pici, Federal University of Ceara, 60455-760 Fortaleza, CE, Brazil
| | - Rodrigo V Oliveira
- Department of Animal Science, Campus do Pici, Federal University of Ceara, 60455-760 Fortaleza, CE, Brazil
| | - Luiz Carlos P Almeida Filho
- Department of Biochemistry and Molecular Biology, Campus Pici, Federal University of Ceara, 60440-900 Fortaleza, CE, Brazil
| | - Jorge M Martins
- Department of Animal Science, Campus do Pici, Federal University of Ceara, 60455-760 Fortaleza, CE, Brazil
| | - Frederico B Moreno
- School of Pharmacy, The University of Fortaleza, 60810-431, Fortaleza, CE, Brazil
| | | | - Arlindo A Araripe Moura
- Department of Animal Science, Campus do Pici, Federal University of Ceara, 60455-760 Fortaleza, CE, Brazil
| | - Ana F Urano Carvalho
- Departament of Biology, Campus do Pici, Federal University of Ceara, 60455-760 Fortaleza, CE, Brazil.
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Etebari K, Osei-Amo S, Blomberg SP, Asgari S. Dengue virus infection alters post-transcriptional modification of microRNAs in the mosquito vector Aedes aegypti. Sci Rep 2015; 5:15968. [PMID: 26514826 PMCID: PMC4626843 DOI: 10.1038/srep15968] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/06/2015] [Indexed: 12/21/2022] Open
Abstract
Recent discoveries regarding the importance of isomiRs have increased our understanding of the regulatory complexities of the miRNAome. Observed changes in the miRNA profiles in mosquitoes infected with flaviviruses have implicated small RNAs in the interactions between viruses and their vectors. Here we analysed the isomiR profiles of both uninfected and infected Aedes aegypti mosquitoes with the major human pathogen dengue virus (DENV). We found that several specific isomiRs were significantly altered in their abundance patterns in response to DENV infection potentially affecting their target repertoire. Notable among these were isomiR variants which displayed arm-switching. We also demonstrate that modifications to the 3p end of miRNAs are vastly more prevalent than those at the 5p ends. We also observed that in only 45% of Ae. aegypti miRNAs the most abundant read matches the exact sequence reported in miRBase. Further, we found positive correlations between the number of mature miRNA reads, pre-miRNA length, GC content and secondary structure minimum free energy with the number of isomiRs. The findings presented here provide some evidence that isomiR production is not a random phenomenon and may be important in DENV replication in its vector.
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Affiliation(s)
- Kayvan Etebari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Solomon Osei-Amo
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Simon Phillip Blomberg
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane QLD 4072 Australia
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Substrate specificity and transport mechanism of amino-acid transceptor Slimfast from Aedes aegypti. Nat Commun 2015; 6:8546. [PMID: 26449545 PMCID: PMC4608377 DOI: 10.1038/ncomms9546] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 09/03/2015] [Indexed: 12/11/2022] Open
Abstract
Anautogenous mosquitoes depend on vertebrate blood as nutrient source for their eggs. A highly efficient set of membrane transporters mediates the massive movement of nutrient amino acids between mosquito tissues after a blood meal. Here we report the characterization of the amino-acid transporter Slimfast (Slif) from the yellow-fever mosquito Aedes aegypti using codon-optimized heterologous expression. Slif is a well-known component of the target-of-rapamycin signalling pathway and fat body nutrient sensor, but its substrate specificity and transport mechanism were unknown. We found that Slif transports essential cationic and neutral amino acids with preference for arginine. It has an unusual dual-affinity mechanism with only the high affinity being Na+ dependent. Tissue-specific expression and blood meal-dependent regulation of Slif are consistent with conveyance of essential amino acids from gut to fat body. Slif represents a novel transport system and type of transceptor for sensing and transporting essential amino acids during mosquito reproduction. Anautogenous mosquitoes need to obtain essential amino acids from a blood meal for reproduction. Here, the authors examine the amino acid transporter Slimfast from the yellow-fever mosquito and describe both its specificity and mechanism of action.
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46
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Constructing a Genome-Wide LD Map of Wild A. gambiae Using Next-Generation Sequencing. BIOMED RESEARCH INTERNATIONAL 2015; 2015:238139. [PMID: 26421280 PMCID: PMC4573223 DOI: 10.1155/2015/238139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/24/2015] [Indexed: 12/16/2022]
Abstract
Anopheles gambiae is the major malaria vector in Africa. Examining the molecular basis of A. gambiae traits requires knowledge of both genetic variation and genome-wide linkage disequilibrium (LD) map of wild A. gambiae populations from malaria-endemic areas. We sequenced the genomes of nine wild A. gambiae mosquitoes individually using next-generation sequencing technologies and detected 2,219,815 common single nucleotide polymorphisms (SNPs), 88% of which are novel. SNPs are not evenly distributed across A. gambiae chromosomes. The low SNP-frequency regions overlay heterochromatin and chromosome inversion domains, consistent with the lower recombinant rates at these regions. Nearly one million SNPs that were genotyped correctly in all individual mosquitoes with 99.6% confidence were extracted from these high-throughput sequencing data. Based on these SNP genotypes, we constructed a genome-wide LD map for wild A. gambiae from malaria-endemic areas in Kenya and made it available through a public Website. The average size of LD blocks is less than 40 bp, and several large LD blocks were also discovered clustered around the para gene, which is consistent with the effect of insecticide selective sweeps. The SNPs and the LD map will be valuable resources for scientific communities to dissect the A. gambiae genome.
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Janssen R, Schönauer A, Weber M, Turetzek N, Hogvall M, Goss GE, Patel NH, McGregor AP, Hilbrant M. The evolution and expression of panarthropod frizzled genes. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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48
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Carpi G, Walter KS, Bent SJ, Hoen AG, Diuk-Wasser M, Caccone A. Whole genome capture of vector-borne pathogens from mixed DNA samples: a case study of Borrelia burgdorferi. BMC Genomics 2015; 16:434. [PMID: 26048573 PMCID: PMC4458057 DOI: 10.1186/s12864-015-1634-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/18/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Rapid and accurate retrieval of whole genome sequences of human pathogens from disease vectors or animal reservoirs will enable fine-resolution studies of pathogen epidemiological and evolutionary dynamics. However, next generation sequencing technologies have not yet been fully harnessed for the study of vector-borne and zoonotic pathogens, due to the difficulty of obtaining high-quality pathogen sequence data directly from field specimens with a high ratio of host to pathogen DNA. RESULTS We addressed this challenge by using custom probes for multiplexed hybrid capture to enrich for and sequence 30 Borrelia burgdorferi genomes from field samples of its arthropod vector. Hybrid capture enabled sequencing of nearly the complete genome (~99.5 %) of the Borrelia burgdorferi pathogen with 132-fold coverage, and identification of up to 12,291 single nucleotide polymorphisms per genome. CONCLUSIONS The proprosed culture-independent method enables efficient whole genome capture and sequencing of pathogens directly from arthropod vectors, thus making population genomic study of vector-borne and zoonotic infectious diseases economically feasible and scalable. Furthermore, given the similarities of invertebrate field specimens to other mixed DNA templates characterized by a high ratio of host to pathogen DNA, we discuss the potential applicabilty of hybrid capture for genomic study across diverse study systems.
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Affiliation(s)
- Giovanna Carpi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA.
| | - Katharine S Walter
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA.
| | - Stephen J Bent
- Robinson Research Institute, University of Adelaide, 5005, Adelaide, SA, Australia.
| | - Anne Gatewood Hoen
- The Geisel School of Medicine, Dartmouth College, 03755, Hanover, NH, USA.
| | - Maria Diuk-Wasser
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. .,Department of Ecology, Evolution and Environmental Biology, Columbia University, 10027, New York, NY, USA.
| | - Adalgisa Caccone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 06520, New Haven, CT, USA. .,Department of Ecology and Evolutionary Biology, Yale University, 06520, New Haven, CT, USA.
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Price DP, Schilkey FD, Ulanov A, Hansen IA. Small mosquitoes, large implications: crowding and starvation affects gene expression and nutrient accumulation in Aedes aegypti. Parasit Vectors 2015; 8:252. [PMID: 25924822 PMCID: PMC4415286 DOI: 10.1186/s13071-015-0863-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 04/16/2015] [Indexed: 01/13/2023] Open
Abstract
Background Environmental factors such as temperature, nutrient availability, and larval density determine the outcome of postembryonic development in mosquitoes. Suboptimal temperatures, crowding, and starvation during the larval phase reduce adult mosquito size, nutrient stores and affect vectorial capacity. Methods In this study we compared adult female Aedes aegypti, Rockefeller strain, raised under standard laboratory conditions (Large) with those raised under crowded and nutritionally deprived conditions (Small). To compare the gene expression and nutritional state of the major energy storage and metabolic organ, the fat body, we performed transcriptomics using Illumina based RNA-seq and metabolomics using GC/MS on females before and 24 hours following blood feeding. Results Analysis of fat body gene expression between the experimental groups revealed a large number of significantly differentially expressed genes. Transcripts related to immunity, reproduction, autophagy, several metabolic pathways; including amino acid degradation and metabolism; and membrane transport were differentially expressed. Metabolite profiling identified 60 metabolites within the fat body to be significantly affected between small and large mosquitoes, with the majority of detected free amino acids at a higher level in small mosquitoes compared to large. Conclusions Gene expression and metabolites in the adult fat body reflect the individual post-embryonic developmental history of a mosquito larva. These changes affect nutritional storage and utilization, immunity, and reproduction. Therefore, it is apparent that changes in larval environment due to weather conditions, nutrition availability, vector control efforts, and other factors can affect adult vectorial capacity in the field. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-0863-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David P Price
- Department of Biology, New Mexico State University, Las Cruces, NM, USA. .,Molecular Biology Program, New Mexico State University, Las Cruces, USA.
| | | | - Alexander Ulanov
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana-Champaign, Illinois, USA.
| | - Immo A Hansen
- Department of Biology, New Mexico State University, Las Cruces, NM, USA. .,Molecular Biology Program, New Mexico State University, Las Cruces, USA.
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Juneja P, Ariani CV, Ho YS, Akorli J, Palmer WJ, Pain A, Jiggins FM. Exome and transcriptome sequencing of Aedes aegypti identifies a locus that confers resistance to Brugia malayi and alters the immune response. PLoS Pathog 2015; 11:e1004765. [PMID: 25815506 PMCID: PMC4376896 DOI: 10.1371/journal.ppat.1004765] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 02/25/2015] [Indexed: 11/18/2022] Open
Abstract
Many mosquito species are naturally polymorphic for their abilities to transmit parasites, a feature which is of great interest for controlling vector-borne disease. Aedes aegypti, the primary vector of dengue and yellow fever and a laboratory model for studying lymphatic filariasis, is genetically variable for its capacity to harbor the filarial nematode Brugia malayi. The genome of Ae. aegypti is large and repetitive, making genome resequencing difficult and expensive. We designed exome captures to target protein-coding regions of the genome, and used association mapping in a wild Kenyan population to identify a single, dominant, sex-linked locus underlying resistance. This falls in a region of the genome where a resistance locus was previously mapped in a line established in 1936, suggesting that this polymorphism has been maintained in the wild for the at least 80 years. We then crossed resistant and susceptible mosquitoes to place both alleles of the gene into a common genetic background, and used RNA-seq to measure the effect of this locus on gene expression. We found evidence for Toll, IMD, and JAK-STAT pathway activity in response to early stages of B. malayi infection when the parasites are beginning to die in the resistant genotype. We also found that resistant mosquitoes express anti-microbial peptides at the time of parasite-killing, and that this expression is suppressed in susceptible mosquitoes. Together, we have found that a single resistance locus leads to a higher immune response in resistant mosquitoes, and we identify genes in this region that may be responsible for this trait.
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Affiliation(s)
- Punita Juneja
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Cristina V. Ariani
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Yung Shwen Ho
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
| | - Jewelna Akorli
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, Accra, Ghana
| | - William J. Palmer
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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