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Sharakhov IV, Sharakhova MV. Chromosomal inversions and their impact on insect evolution. CURRENT OPINION IN INSECT SCIENCE 2024:101280. [PMID: 39374869 DOI: 10.1016/j.cois.2024.101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/20/2024] [Accepted: 10/02/2024] [Indexed: 10/09/2024]
Abstract
Insects can adapt quickly and effectively to rapid environmental change and maintain long-term adaptations, but the genetic mechanisms underlying this response are not fully understood. In this review, we summarize studies on the potential impact of chromosomal inversion polymorphisms on insect evolution at different spatial and temporal scales, ranging from long-term evolutionary stability to rapid emergence in response to emerging biotic and abiotic factors. The study of inversions has recently been advanced by comparative, population, and 3D genomics methods. The impact of inversions on insect genome evolution can be profound, including increased gene order rearrangements on sex chromosomes, accumulation of transposable elements, and facilitation of genome divergence. Understanding these processes provides critical insights into the evolutionary mechanisms shaping insect diversity.
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Affiliation(s)
- Igor V Sharakhov
- Department of Entomology and Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; The Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; The Center for Mathematics of Biosystems, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; Department of Genetics and Cell Biology, Tomsk State University, Tomsk 634050, Russia.
| | - Maria V Sharakhova
- Department of Entomology and Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; The Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
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2
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Karisa J, Ominde K, Tuwei M, Bartilol B, Ondieki Z, Musani H, Wanjiku C, Mwikali K, Babu L, Rono M, Eminov M, Mbogo C, Bejon P, Mwangangi J, Laroche M, Maia M. Utility of MALDI-TOF MS for determination of species identity and blood meal sources of primary malaria vectors on the Kenyan coast. Wellcome Open Res 2024; 8:151. [PMID: 38957296 PMCID: PMC11217722 DOI: 10.12688/wellcomeopenres.18982.2] [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] [Accepted: 05/21/2024] [Indexed: 07/04/2024] Open
Abstract
Background Protein analysis using matrix-assisted laser desorption/ionisation time-of-flight mass-spectrometry (MALDI-TOF MS) represents a promising tool for entomological surveillance. In this study we tested the discriminative power of this tool for measuring species and blood meal source of main Afrotropical malaria vectors on the Kenyan coast. Methods Mosquito collections were conducted along the coastal region of Kenya. MALDI-TOF MS spectra were obtained from each individual mosquito's cephalothorax as well as the abdomens of blood-engorged mosquitoes. The same mosquitoes were also processed using gold standard tests: polymerase chain reaction (PCR) for species identification and enzyme linked immunosorbent assay (ELISA) for blood meal source identification. Results Of the 2,332 mosquitoes subjected to MALDI-TOF MS, 85% (1,971/2,332) were considered for database creation and validation. There was an overall accuracy of 97.5% in the identification of members of the An. gambiae ( An. gambiae, 100%; An. arabiensis, 91.9%; An. merus, 97.5%; and An. quadriannulatus, 90.2%) and An. funestus ( An. funestus, 94.2%; An. rivulorum, 99.4%; and An. leesoni, 94.1%) complexes. Furthermore, MALDI-TOF MS also provided accurate (94.5% accuracy) identification of blood host sources across all mosquito species. Conclusions This study provides further evidence of the discriminative power of MALDI-TOF MS to identify sibling species and blood meal source of Afrotropical malaria vectors, further supporting its utility in entomological surveillance. The low cost per sample (<0.2USD) and high throughput nature of the method represents a cost-effective alternative to molecular methods and could enable programs to increase the number of samples analysed and therefore improve the data generated from surveillance activities.
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Affiliation(s)
- Jonathan Karisa
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- The Open University, Milton Keynes, United Kingdom, Walton Hall, Kents Hill, Milton Keynes MK7 6AA, UK
- Pwani University, Kilifi, Kenya, 195-80108, Kenya
| | - Kelly Ominde
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Mercy Tuwei
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- Pwani University, Kilifi, Kenya, 195-80108, Kenya
| | - Brian Bartilol
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Zedekiah Ondieki
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Harun Musani
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Caroline Wanjiku
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Kioko Mwikali
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Lawrence Babu
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Martin Rono
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- Pwani University, Kilifi, Kenya, 195-80108, Kenya
| | | | - Charles Mbogo
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- University of Oxford, Centre for Global Health and Tropical Medicine, Oxford, UK, Oxford, UK
| | - Joseph Mwangangi
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Maureen Laroche
- The University of Texas Medical Branch -, Galveston National Laboratory 301 University Blvd, Texas, Galveston TX 77555-1019, USA
| | - Marta Maia
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- University of Oxford, Centre for Global Health and Tropical Medicine, Oxford, UK, Oxford, UK
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3
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Gao L, Yang W, Wang J. Implications of mosquito metabolism on vector competence. INSECT SCIENCE 2024; 31:674-682. [PMID: 37907431 DOI: 10.1111/1744-7917.13288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 11/02/2023]
Abstract
Mosquito-borne diseases (MBDs) annually kill nearly half a million people. Due to the lack of effective vaccines and drugs on most MBDs, disease prevention relies primarily on controlling mosquitoes. Despite huge efforts having been put into mosquito control, eco-friendly and sustainable mosquito-control strategies are still lacking and urgently demanded. Most mosquito-transmitted pathogens have lost the capacity of de novo nutrition biosynthesis, and rely on their vertebrate and invertebrate hosts for sustenance during the long-term obligate parasitism process. Therefore, a better understanding of the metabolic interactions between mosquitoes and pathogens will contribute to the discovery of novel metabolic targets or regulators that lead to reduced mosquito populations or vector competence. This review summarizes the current knowledge about the effects of mosquito metabolism on the transmission of multiple pathogens. We also discuss that research in this area remains to be explored to develop multiple biological prevention and control strategies for MBDs.
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Affiliation(s)
- Li Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenxu Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingwen Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
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4
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Li XY, Si FL, Zhang XX, Zhang YJ, Chen B. Characteristics of Trypsin genes and their roles in insecticide resistance based on omics and functional analyses in the malaria vector Anopheles sinensis. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 201:105883. [PMID: 38685249 DOI: 10.1016/j.pestbp.2024.105883] [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: 01/09/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 05/02/2024]
Abstract
Trypsin is one of the most diverse and widely studied protease hydrolases. However, the diversity and characteristics of the Trypsin superfamily of genes have not been well understood, and their role in insecticide resistance is yet to be investigated. In this study, a total of 342 Trypsin genes were identified and classified into seven families based on homology, characteristic domains and phylogenetics in Anopheles sinensis, and the LY-Domain and CLECT-Domain families are specific to the species. Four Trypsin genes, (Astry2b, Astry43a, Astry90, Astry113c) were identified to be associated with pyrethroid resistance based on transcriptome analyses of three field resistant populations and qRT-PCR validation, and the knock-down of these genes significantly decrease the pyrethroid resistance of Anopheles sinensis based on RNAi. The activity of Astry43a can be reduced by five selected insecticides (indoxacarb, DDT, temephos, imidacloprid and deltamethrin); and however, the Astry43a could not directly metabolize these five insecticides, like the trypsin NYD-Tr did in earlier reports. This study provides the overall information frame of Trypsin genes, and proposes the role of Trypsin genes to insecticide resistance. Further researches are necessary to investigate the metabolism function of these trypsins to insecticides.
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Affiliation(s)
- Xiang-Ying Li
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Feng-Ling Si
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Xiao-Xiao Zhang
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Yu-Juan Zhang
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China
| | - Bin Chen
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, Chongqing Normal University, Chongqing 401331, China.
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5
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Kausar N, Shier WT, Ahmed M, Maryam, Albekairi NA, Alshammari A, Saleem M, Imran M, Muddassar M. Investigation of the insecticidal potential of curcumin derivatives that target the Helicoverpa armigera sterol carrier protein-2. Heliyon 2024; 10:e29695. [PMID: 38660259 PMCID: PMC11040122 DOI: 10.1016/j.heliyon.2024.e29695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Cotton bollworm (Helicoverpa armigera) is a highly polyphagous, widely prevalent, and persistent Old World insect pest that affects numerous important crops that are directly consumed by people, including tomato, cotton, pigeon pea, chickpea, rice, sorghum, and cowpea. Insects do not synthesize steroids but obtain them from their diet. Inhibition of dietary uptake of steroids by insects is a potentially effective insecticidal mechanism that should not be toxic to humans and other mammals, who synthesize their steroids. Ten curcumin derivatives were tested against H. armigera sterol carrier protein-2 (HaSCP-2) for their potential as insecticidal agents. Curcumin derivatives were initially docked at the binding site of HaSCP-2 to determine their binding affinities and plausible binding modes. The binding modes predominantly show hydrophobic interactions of derivatives with Phe53, Phe110, and Phe89 as core interacting residues in the active site. Validation of in silico results was carried out by performing a fluorescence binding and displacement assay to determine the binding affinities of curcumin derivatives. Among a collection of curcumin derivatives tested, Cur10 showed the lowest IC50 value of 9.64 μM, while Cur07 was 19.86 μM, and Cur06 was 20.79 μM. There was a significant negative correlation between the ability of the curcumin derivatives tested to displace the fluorescent probe from the sterol binding site of HaSCP-2 and to inhibit Sf9 insect cell growth in culture, which is consistent with the curcumin derivatives acting by the novel mechanism of blocking sterol uptake. Then molecular dynamics simulation studies validated the predicted binding modes and the interactions of curcumin derivatives with HaSCP-2 protein. In conclusion, these studies support the potential use of curcumin derivatives as insecticidal agents.
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Affiliation(s)
- Naeema Kausar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Wayne Thomas Shier
- College of Pharmacy, Department of Medicinal Chemistry, University of Minnesota, 55455, USA
| | - Mahmood Ahmed
- Department of Chemistry, Division of Science and Technology, University of Education, College Road, Lahore, Pakistan
| | - Maryam
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Muhammad Saleem
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Imran
- KAM-School of Life Sciences, FC College (A Chartered University), Lahore, 54000, Pakistan
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
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Schember I, Reid W, Sterling-Lentsch G, Halfon MS. Conserved and novel enhancers in the Aedes aegypti single-minded locus recapitulate embryonic ventral midline gene expression. PLoS Genet 2024; 20:e1010891. [PMID: 38683842 PMCID: PMC11081499 DOI: 10.1371/journal.pgen.1010891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 05/09/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Transcriptional cis-regulatory modules, e.g., enhancers, control the time and location of metazoan gene expression. While changes in enhancers can provide a powerful force for evolution, there is also significant deep conservation of enhancers for developmentally important genes, with function and sequence characteristics maintained over hundreds of millions of years of divergence. Not well understood, however, is how the overall regulatory composition of a locus evolves, with important outstanding questions such as how many enhancers are conserved vs. novel, and to what extent are the locations of conserved enhancers within a locus maintained? We begin here to address these questions with a comparison of the respective single-minded (sim) loci in the two dipteran species Drosophila melanogaster (fruit fly) and Aedes aegypti (mosquito). sim encodes a highly conserved transcription factor that mediates development of the arthropod embryonic ventral midline. We identify two enhancers in the A. aegypti sim locus and demonstrate that they function equivalently in both transgenic flies and transgenic mosquitoes. One A. aegypti enhancer is highly similar to known Drosophila counterparts in its activity, location, and autoregulatory capability. The other differs from any known Drosophila sim enhancers with a novel location, failure to autoregulate, and regulation of expression in a unique subset of midline cells. Our results suggest that the conserved pattern of sim expression in the two species is the result of both conserved and novel regulatory sequences. Further examination of this locus will help to illuminate how the overall regulatory landscape of a conserved developmental gene evolves.
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Affiliation(s)
- Isabella Schember
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, New York, United States of America
| | - William Reid
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, New York, United States of America
| | - Geyenna Sterling-Lentsch
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, New York, United States of America
| | - Marc S. Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, New York, United States of America
- Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, New York, United States of America
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, New York, United States of America
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, New York, United States of America
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7
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Roggenbuck EC, Hall EA, Hanson IB, Roby AA, Zhang KK, Alkatib KA, Carter JA, Clewner JE, Gelfius AL, Gong S, Gordon FR, Iseler JN, Kotapati S, Li M, Maysun A, McCormick EO, Rastogi G, Sengupta S, Uzoma CU, Wolkov MA, Clowney EJ. Let's talk about sex: Mechanisms of neural sexual differentiation in Bilateria. WIREs Mech Dis 2024; 16:e1636. [PMID: 38185860 DOI: 10.1002/wsbm.1636] [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: 05/09/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
In multicellular organisms, sexed gonads have evolved that facilitate release of sperm versus eggs, and bilaterian animals purposefully combine their gametes via mating behaviors. Distinct neural circuits have evolved that control these physically different mating events for animals producing eggs from ovaries versus sperm from testis. In this review, we will describe the developmental mechanisms that sexually differentiate neural circuits across three major clades of bilaterian animals-Ecdysozoa, Deuterosomia, and Lophotrochozoa. While many of the mechanisms inducing somatic and neuronal sex differentiation across these diverse organisms are clade-specific rather than evolutionarily conserved, we develop a common framework for considering the developmental logic of these events and the types of neuronal differences that produce sex-differentiated behaviors. This article is categorized under: Congenital Diseases > Stem Cells and Development Neurological Diseases > Stem Cells and Development.
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Affiliation(s)
- Emma C Roggenbuck
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elijah A Hall
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Isabel B Hanson
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Alyssa A Roby
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine K Zhang
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Kyle A Alkatib
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Joseph A Carter
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jarred E Clewner
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna L Gelfius
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Shiyuan Gong
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Finley R Gordon
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jolene N Iseler
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Samhita Kotapati
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Marilyn Li
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Areeba Maysun
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elise O McCormick
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Geetanjali Rastogi
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Srijani Sengupta
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Chantal U Uzoma
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Madison A Wolkov
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, Michigan, USA
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Himmel NJ, Moi D, Benton R. Remote homolog detection places insect chemoreceptors in a cryptic protein superfamily spanning the tree of life. Curr Biol 2023; 33:5023-5033.e4. [PMID: 37913770 DOI: 10.1016/j.cub.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/26/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Many proteins exist in the so-called "twilight zone" of sequence alignment, where low pairwise sequence identity makes it difficult to determine homology and phylogeny.1,2 As protein tertiary structure is often more conserved,3 recent advances in ab initio protein folding have made structure-based identification of putative homologs feasible.4,5,6 We present a pipeline for the identification and characterization of distant homologs and apply it to 7-transmembrane-domain ion channels (7TMICs), a protein group founded by insect odorant and gustatory receptors. Previous sequence and limited structure-based searches identified putatively related proteins, mainly in other animals and plants.7,8,9,10 However, very few 7TMICs have been identified in non-animal, non-plant taxa. Moreover, these proteins' remarkable sequence dissimilarity made it uncertain whether disparate 7TMIC types (Gr/Or, Grl, GRL, DUF3537, PHTF, and GrlHz) are homologous or convergent, leaving their evolutionary history unresolved. Our pipeline identified thousands of new 7TMICs in archaea, bacteria, and unicellular eukaryotes. Using graph-based analyses and protein language models to extract family-wide signatures, we demonstrate that 7TMICs have structure and sequence similarity, supporting homology. Through sequence- and structure-based phylogenetics, we classify eukaryotic 7TMICs into two families (Class-A and Class-B), which are the result of a gene duplication predating the split(s) leading to Amorphea (animals, fungi, and allies) and Diaphoretickes (plants and allies). Our work reveals 7TMICs as a cryptic superfamily, with origins close to the evolution of cellular life. More generally, this study serves as a methodological proof of principle for the identification of extremely distant protein homologs.
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Affiliation(s)
- Nathaniel J Himmel
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.
| | - David Moi
- Department of Computational Biology, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland.
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9
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Kalita AI, Marois E, Kozielska M, Weissing FJ, Jaouen E, Möckel MM, Rühle F, Butter F, Basilicata MF, Keller Valsecchi CI. The sex-specific factor SOA controls dosage compensation in Anopheles mosquitoes. Nature 2023; 623:175-182. [PMID: 37769784 PMCID: PMC10620080 DOI: 10.1038/s41586-023-06641-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/13/2023] [Indexed: 10/03/2023]
Abstract
The Anopheles mosquito is one of thousands of species in which sex differences play a central part in their biology, as only females need a blood meal to produce eggs. Sex differentiation is regulated by sex chromosomes, but their presence creates a dosage imbalance between males (XY) and females (XX). Dosage compensation (DC) can re-equilibrate the expression of sex chromosomal genes. However, because DC mechanisms have only been fully characterized in a few model organisms, key questions about its evolutionary diversity and functional necessity remain unresolved1. Here we report the discovery of a previously uncharacterized gene (sex chromosome activation (SOA)) as a master regulator of DC in the malaria mosquito Anopheles gambiae. Sex-specific alternative splicing prevents functional SOA protein expression in females. The male isoform encodes a DNA-binding protein that binds the promoters of active X chromosomal genes. Expressing male SOA is sufficient to induce DC in female cells. Male mosquitoes lacking SOA or female mosquitoes ectopically expressing the male isoform exhibit X chromosome misregulation, which is compatible with viability but causes developmental delay. Thus, our molecular analyses of a DC master regulator in a non-model organism elucidates the evolutionary steps that lead to the establishment of a chromosome-specific fine-tuning mechanism.
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Affiliation(s)
| | - Eric Marois
- INSERM U1257, CNRS UPR9022, Université de Strasbourg, Strasbourg, France
| | - Magdalena Kozielska
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Etienne Jaouen
- INSERM U1257, CNRS UPR9022, Université de Strasbourg, Strasbourg, France
| | | | - Frank Rühle
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich Loeffler Institute, Greifswald, Germany
| | - M Felicia Basilicata
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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10
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Lovero D, Porcelli D, Giordano L, Lo Giudice C, Picardi E, Pesole G, Pignataro E, Palazzo A, Marsano RM. Structural and Comparative Analyses of Insects Suggest the Presence of an Ultra-Conserved Regulatory Element of the Genes Encoding Vacuolar-Type ATPase Subunits and Assembly Factors. BIOLOGY 2023; 12:1127. [PMID: 37627011 PMCID: PMC10452791 DOI: 10.3390/biology12081127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Gene and genome comparison represent an invaluable tool to identify evolutionarily conserved sequences with possible functional significance. In this work, we have analyzed orthologous genes encoding subunits and assembly factors of the V-ATPase complex, an important enzymatic complex of the vacuolar and lysosomal compartments of the eukaryotic cell with storage and recycling functions, respectively, as well as the main pump in the plasma membrane that energizes the epithelial transport in insects. This study involves 70 insect species belonging to eight insect orders. We highlighted the conservation of a short sequence in the genes encoding subunits of the V-ATPase complex and their assembly factors analyzed with respect to their exon-intron organization of those genes. This study offers the possibility to study ultra-conserved regulatory elements under an evolutionary perspective, with the aim of expanding our knowledge on the regulation of complex gene networks at the basis of organellar biogenesis and cellular organization.
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Affiliation(s)
- Domenica Lovero
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
- MASMEC Biomed S.p.A., Via Delle Violette 14, 70026 Modugno, Italy
| | - Damiano Porcelli
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
- METALABS S.R.L., Corso A. De Gasperi 381/1, 70125 Bari, Italy
| | - Luca Giordano
- Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Aulweg 130, 35392 Giessen, Germany;
| | - Claudio Lo Giudice
- Istituto di Tecnologie Biomediche (ITB), Consiglio Nazionale Delle Ricerche, Via Giovanni Amendola, 122, 70126 Bari, Italy;
| | - Ernesto Picardi
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
| | - Graziano Pesole
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
| | - Eugenia Pignataro
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
| | - Antonio Palazzo
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
| | - René Massimiliano Marsano
- Dipartimento di Bioscienze Biotecnologie e Ambiente, Università Degli Studi di Bari Aldo Moro, Via Orabona 4, 70125 Bari, Italy; (D.L.); (D.P.); (E.P.); (G.P.); (E.P.); (A.P.)
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11
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Müller R, Bálint M, Hardes K, Hollert H, Klimpel S, Knorr E, Kochmann J, Lee KZ, Mehring M, Pauls SU, Smets G, Steinbrink A, Vilcinskas A. RNA interference to combat the Asian tiger mosquito in Europe: A pathway from design of an innovative vector control tool to its application. Biotechnol Adv 2023; 66:108167. [PMID: 37164239 DOI: 10.1016/j.biotechadv.2023.108167] [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: 12/31/2022] [Revised: 04/06/2023] [Accepted: 04/30/2023] [Indexed: 05/12/2023]
Abstract
The Asian tiger mosquito Aedes albopictus is currently spreading across Europe, facilitated by climate change and global transportation. It is a vector of arboviruses causing human diseases such as chikungunya, dengue hemorrhagic fever and Zika fever. For the majority of these diseases, no vaccines or therapeutics are available. Options for the control of Ae. albopictus are limited by European regulations introduced to protect biodiversity by restricting or phasing out the use of pesticides, genetically modified organisms (GMOs) or products of genome editing. Alternative solutions are thus urgently needed to avoid a future scenario in which Europe faces a choice between prioritizing human health or biodiversity when it comes to Aedes-vectored pathogens. To ensure regulatory compliance and public acceptance, these solutions should preferably not be based on chemicals or GMOs and must be cost-efficient and specific. The present review aims to synthesize available evidence on RNAi-based mosquito vector control and its potential for application in the European Union. The recent literature has identified some potential target sites in Ae. albopictus and formulations for delivery. However, we found little information concerning non-target effects on the environment or human health, on social aspects, regulatory frameworks, or on management perspectives. We propose optimal designs for RNAi-based vector control tools against Ae. albopictus (target product profiles), discuss their efficacy and reflect on potential risks to environmental health and the importance of societal aspects. The roadmap from design to application will provide readers with a comprehensive perspective on the application of emerging RNAi-based vector control tools for the suppression of Ae. albopictus populations with special focus on Europe.
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Affiliation(s)
- Ruth Müller
- Unit Entomology, Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerp, Belgium; Institute of Occupational, Social and Environmental Medicine, Goethe University, Theodor-Stern-Kai 9, 60590 Frankfurt am Main, Germany
| | - Miklós Bálint
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Kornelia Hardes
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch of Bioresources, Ohlebergsweg 12, 35392 Giessen, Germany; BMBF Junior Research Group in Infection Research "ASCRIBE", Germany
| | - Henner Hollert
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Department Media-related Toxicity, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany; Evolutionary Ecology and Environmental Toxicology, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Sven Klimpel
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Integrative Parasitology and Zoophysiology, Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany
| | - Eileen Knorr
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch of Bioresources, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Judith Kochmann
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany
| | - Kwang-Zin Lee
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch of Bioresources, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Marion Mehring
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; ISOE - Institute for Social-Ecological Research, Hamburger Allee 45, 60486 Frankfurt am Main, Germany
| | - Steffen U Pauls
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Greet Smets
- Perseus BV, Kortrijksesteenweg 127 B1, B-9830 Sint-Martens-Latem, Belgium
| | - Antje Steinbrink
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Vilcinskas
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Institute for Insect Biotechnology, Justus-Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch of Bioresources, Ohlebergsweg 12, 35392 Giessen, Germany.
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12
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Karisa J, Ominde K, Tuwei M, Bartilol B, Ondieki Z, Musani H, Wanjiku C, Mwikali K, Babu L, Rono M, Eminov M, Mbogo C, Bejon P, Mwangangi J, Laroche M, Maia M. Utility of MALDI-TOF MS for determination of species identity and blood meal sources of primary malaria vectors on the Kenyan coast. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18982.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Background: Protein analysis using matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) represents a promising tool for entomological surveillance. In this study we tested the discriminative power of this tool for measuring species and blood meal source of main Afrotropical malaria vectors on the Kenyan coast. Methods: Mosquito collections were conducted along the coastal region of Kenya. MALDI-TOF MS spectra were obtained from each individual mosquito’s cephalothorax as well as the abdomens of blood-engorged mosquitoes. The same mosquitoes were also processed using gold standard tests: polymerase chain reaction (PCR) for species identification and enzyme linked immunosorbent assay (ELISA) for blood meal source identification. Results: Of the 2,332 mosquitoes subjected to MALDI-TOF MS, 85% (1,971/2,332) were considered for database creation and validation. There was an overall accuracy of 97.5% in the identification of members of the An. gambiae (An. gambiae, 100%; An. arabiensis, 91.9%; An. merus, 97.5%; and An. quadriannulatus, 90.2%) and An. funestus (An. funestus, 94.2%; An. rivulorum, 99.4%; and An. leesoni, 94.1%) complexes. Furthermore, MALDI-TOF MS also provided accurate (94.5% accuracy) identification of blood host sources across all mosquito species. Conclusions: This study provides further evidence of the discriminative power of MALDI-TOF MS to identify sibling species and blood meal source of Afrotropical malaria vectors, further supporting its utility in entomological surveillance. The low cost per sample (<0.2USD) and high throughput nature of the method represents a cost-effective alternative to molecular methods and could enable programs to increase the number of samples analysed and therefore improve the data generated from surveillance activities.
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13
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Anderson N, Jaron KS, Hodson CN, Couger MB, Ševčík J, Weinstein B, Pirro S, Ross L, Roy SW. Gene-rich X chromosomes implicate intragenomic conflict in the evolution of bizarre genetic systems. Proc Natl Acad Sci U S A 2022; 119:e2122580119. [PMID: 35653559 PMCID: PMC9191650 DOI: 10.1073/pnas.2122580119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/08/2022] [Indexed: 11/18/2022] Open
Abstract
Haplodiploidy and paternal genome elimination (HD/PGE) are common in invertebrates, having evolved at least two dozen times, all from male heterogamety (i.e., systems with X chromosomes). However, why X chromosomes are important for the evolution of HD/PGE remains debated. The Haploid Viability Hypothesis posits that X-linked genes promote the evolution of male haploidy by facilitating purging recessive deleterious mutations. The Intragenomic Conflict Hypothesis holds that conflict between genes drives genetic system turnover; under this model, X-linked genes could promote the evolution of male haploidy due to conflicts with autosomes over sex ratios and genetic transmission. We studied lineages where we can distinguish these hypotheses: species with germline PGE that retain an XX/X0 sex determination system (gPGE+X). Because evolving PGE in these cases involves changes in transmission without increases in male hemizygosity, a high degree of X linkage in these systems is predicted by the Intragenomic Conflict Hypothesis but not the Haploid Viability Hypothesis. To quantify the degree of X linkage, we sequenced and compared 7 gPGE+X species’ genomes with 11 related species with typical XX/XY or XX/X0 genetic systems, representing three transitions to gPGE. We find highly increased X linkage in both modern and ancestral genomes of gPGE+X species compared to non-gPGE relatives and recover a significant positive correlation between percent X linkage and the evolution of gPGE. These empirical results substantiate longstanding proposals for a role for intragenomic conflict in the evolution of genetic systems such as HD/PGE.
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Affiliation(s)
- Noelle Anderson
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343
- Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343
| | - Kamil S. Jaron
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Christina N. Hodson
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Matthew B. Couger
- Department of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA 02115
| | - Jan Ševčík
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Brooke Weinstein
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343
- Quantitative and Systems Biology Graduate Group, University of California, Merced, CA 95343
| | | | - Laura Ross
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Scott William Roy
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343
- Department of Biology, San Francisco State University, San Francisco, CA 94132
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14
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Williamson NG, Walsh CM, Kijimoto T. Comparative metabolomic analysis of polyphenic horn development in the dung beetle Onthophagus taurus. PLoS One 2022; 17:e0265222. [PMID: 35298496 PMCID: PMC8929603 DOI: 10.1371/journal.pone.0265222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
Organisms alter their phenotypes in response to changing environmental conditions. The developmental basis of this phenomenon, phenotypic plasticity, is a topic of broad interest in many fields of biology. While insects provide a suitable model for studying the genetic basis of phenotypic plasticity, the physiological aspects of plasticity are not fully understood. Here, we report the physiological basis of polyphenism, an extreme form of phenotypic plasticity by utilizing a dung beetle species, Onthophagus taurus. We highlighted the metabolome between sexes as well as two distinct male morphs—large and small horns. Unlike results from previous transcriptomic studies, the comparative metabolomic study revealed that differences in metabolite level were more prominent between animals with different body sizes than different sexes. Our results also indicate that specific metabolites and biochemical pathways may be active during horn size determination.
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Affiliation(s)
- Naomi G. Williamson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
| | - Callee M. Walsh
- Shared Research Facilities, West Virginia University, Morgantown, West Virginia, United States of America
| | - Teiya Kijimoto
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, West Virginia, United States of America
- * E-mail:
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15
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Simakov O, Bredeson J, Berkoff K, Marletaz F, Mitros T, Schultz DT, O’Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS. Deeply conserved synteny and the evolution of metazoan chromosomes. SCIENCE ADVANCES 2022; 8:eabi5884. [PMID: 35108053 PMCID: PMC8809688 DOI: 10.1126/sciadv.abi5884] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 12/10/2021] [Indexed: 05/04/2023]
Abstract
Animal genomes show networks of deeply conserved gene linkages whose phylogenetic scope and chromosomal context remain unclear. Here, we report chromosome-scale conservation of synteny among bilaterians, cnidarians, and sponges and use comparative analysis to reconstruct ancestral chromosomes across major animal groups. Comparisons among diverse metazoans reveal the processes of chromosome evolution that produced contemporary karyotypes from their Precambrian progenitors. On the basis of these findings, we introduce a simple algebraic representation of chromosomal change and use it to establish a unified systematic framework for metazoan chromosome evolution. We find that fusion-with-mixing, a previously unappreciated mode of chromosome change, has played a central role. We find that relicts of several metazoan chromosomal units are preserved in unicellular eukaryotes. These conserved pre-metazoan linkages include the chromosomal unit that encodes the most diverse set of metazoan homeobox genes, suggesting a candidate genomic context for the early diversification of this key gene family.
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Affiliation(s)
- Oleg Simakov
- Department for Neurosciences and Developmental
Biology, University of Vienna, Vienna 1010, Austria
| | - Jessen Bredeson
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Kodiak Berkoff
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Ferdinand Marletaz
- Molecular Genetics Unit, Okinawa Institute of Science
and Technology Graduate University, 1919-1, Tancha, Onna, Okinawa 904-0495,
Japan
- Division of Biosciences, University College London,
Gower St., London WC1E 6BT, UK
| | - Therese Mitros
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
| | - Darrin T. Schultz
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
- Monterey Bay Aquarium Research Institute, Moss
Landing, CA 95039, USA
| | - Brendan L. O’Connell
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Paul Dear
- Mote Research Ltd, Babraham Hall, Babraham, Cambridge
CB2 4AT, UK
| | | | - Robert E. Steele
- Department of Biological Chemistry, University of
California, Irvine, Irvine, CA 92697-1700, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of
California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Charles N. David
- Faculty of Biology, Ludwig Maximilian University of
Munich, Munich 80539, Germany
| | - Daniel S. Rokhsar
- Department of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, CA 94720, USA
- Molecular Genetics Unit, Okinawa Institute of Science
and Technology Graduate University, 1919-1, Tancha, Onna, Okinawa 904-0495,
Japan
- Chan Zuckerberg Biohub, 499 Illinois St., San
Francisco, CA 94158, USA
- U.S. Department of Energy Joint Genome Institute,
Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720,
USA
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16
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Ranz JM, González PM, Su RN, Bedford SJ, Abreu-Goodger C, Markow T. Multiscale analysis of the randomization limits of the chromosomal gene organization between Lepidoptera and Diptera. Proc Biol Sci 2022; 289:20212183. [PMID: 35042416 PMCID: PMC8767184 DOI: 10.1098/rspb.2021.2183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022] Open
Abstract
How chromosome gene organization and gene content evolve among distantly related and structurally malleable genomes remains unresolved. This is particularly the case when considering different insect orders. We have compared the highly contiguous genome assemblies of the lepidopteran Danaus plexippus and the dipteran Drosophila melanogaster, which shared a common ancestor around 290 Ma. The gene content of 23 out of 30 D. plexippus chromosomes was significantly associated with one or two of the six chromosomal elements of the Drosophila genome, denoting common ancestry. Despite the phylogenetic distance, 9.6% of the 1-to-1 orthologues still reside within the same ancestral genome neighbourhood. Furthermore, the comparison D. plexippus-Bombyx mori indicated that the rates of chromosome repatterning are lower in Lepidoptera than in Diptera, although still within the same order of magnitude. Concordantly, 14 developmental gene clusters showed a higher tendency to retain full or partial clustering in D. plexippus, further supporting that the physical association between the SuperHox and NK clusters existed in the ancestral bilaterian. Our results illuminate the scope and limits of the evolution of the gene organization and content of the ancestral chromosomes to the Lepidoptera and Diptera while helping reconstruct portions of the genome in their most recent common ancestor.
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Affiliation(s)
- José M. Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Pablo M. González
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato GTO 36824, México
| | - Ryan N. Su
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Sarah J. Bedford
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine CA 92647, USA
| | - Cei Abreu-Goodger
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato GTO 36824, México
| | - Therese Markow
- Unidad de Genómica Avanzada (Langebio), CINVESTAV, Irapuato GTO 36824, México
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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17
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Deep Conservation of Hid-Like RHG Gene Family Homologs in Winged Insects Revealed by "Taxon Hopping" BLAST. INSECTS 2021; 12:insects12110957. [PMID: 34821758 PMCID: PMC8620624 DOI: 10.3390/insects12110957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022]
Abstract
Together with sickle (skl), the Drosophila paralogs reaper (rpr), head involution defective (hid), and grim (RHG) control a critical switch in the induction of programmed cell death. RHG homologs have been identified in other dipteran and lepidopteran species but not beyond. Revisiting this issue with a "taxon hopping" BLAST search strategy in current genome and transcriptome resources, I detected high confidence RHG homologs in Coleoptera, Hymenoptera, Hemiptera, and Dictyoptera. Analyses of gene structure and protein sequence conservation revealed aconserved splicing pattern and highly conserved amino acid residues at both the N- and C-terminal ends that identify hid as the most ancestrally organized RHG gene family member in Drosophila. hid-like RHG homologs were also detected in mosquitoes, redefining their michelob_x (mx) genes as an expansion of derived RHG homologs. Only singleton homologs were detected in the large majority of other insect clades. Lepidopteran RHG homologs, however, stand out by producing an evolutionarily-derived splice isoform, identified in previous work, in addition to the newly detected hid-like isoform. Exceptional sequence diversification of select RHG homologs at the family- and genus-level explain their previous elusiveness in important insect genome model species like the red flour beetle Tribolium castaneum and the pea aphid Acyrthosiphon pisum. Combined, these findings expand the minimal age of the RHG gene family by about 100 million years and open new avenues for molecular cell death studies in insects.
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18
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Horvath TD, Dagan S, Scaraffia PY. Unraveling mosquito metabolism with mass spectrometry-based metabolomics. Trends Parasitol 2021; 37:747-761. [PMID: 33896683 PMCID: PMC8282712 DOI: 10.1016/j.pt.2021.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023]
Abstract
Nearly half a million people die annually due to mosquito-borne diseases. Despite aggressive mosquito population-control efforts, current strategies are limited in their ability to control these vectors. A better understanding of mosquito metabolism through modern approaches can contribute to the discovery of novel metabolic targets and/or regulators and lead to the development of better mosquito-control strategies. Currently, cutting-edge technologies such as gas or liquid chromatography-mass spectrometry-based metabolomics are considered 'mature technologies' in many life-science disciplines but are still an emerging area of research in medical entomology. This review primarily discusses recent developments and progress in the application of mass spectrometry-based metabolomics to answer multiple biological questions related to mosquito metabolism.
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Affiliation(s)
- Thomas D Horvath
- Department of Immunology and Pathology, Baylor College of Medicine, and Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Shai Dagan
- Israel Institute for Biological Research, Ness Ziona, Israel, 74100, Israel
| | - Patricia Y Scaraffia
- Department of Tropical Medicine and Vector-Borne Infectious Disease Research Center, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, 70112, USA.
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19
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Keller Valsecchi CI, Marois E, Basilicata MF, Georgiev P, Akhtar A. Distinct mechanisms mediate X chromosome dosage compensation in Anopheles and Drosophila. Life Sci Alliance 2021; 4:4/9/e202000996. [PMID: 34266874 PMCID: PMC8321682 DOI: 10.26508/lsa.202000996] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
CRISPR knockout of msl-2 and epigenome analyses in Anopheles reveal that X chromosome dosage compensation in mosquitos and Drosophila is achieved by two different molecular mechanisms. Sex chromosomes induce potentially deleterious gene expression imbalances that are frequently corrected by dosage compensation (DC). Three distinct molecular strategies to achieve DC have been previously described in nematodes, fruit flies, and mammals. Is this a consequence of distinct genomes, functional or ecological constraints, or random initial commitment to an evolutionary trajectory? Here, we study DC in the malaria mosquito Anopheles gambiae. The Anopheles and Drosophila X chromosomes evolved independently but share a high degree of homology. We find that Anopheles achieves DC by a mechanism distinct from the Drosophila MSL complex–histone H4 lysine 16 acetylation pathway. CRISPR knockout of Anopheles msl-2 leads to embryonic lethality in both sexes. Transcriptome analyses indicate that this phenotype is not a consequence of defective X chromosome DC. By immunofluorescence and ChIP, H4K16ac does not preferentially enrich on the male X. Instead, the mosquito MSL pathway regulates conserved developmental genes. We conclude that a novel mechanism confers X chromosome up-regulation in Anopheles. Our findings highlight the pluralism of gene-dosage buffering mechanisms even under similar genomic and functional constraints.
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Affiliation(s)
| | - Eric Marois
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS) UPR9022, Inserm U1257, Strasbourg, France
| | - M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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20
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Gutiérrez Y, Fresch M, Hellmann SL, Hankeln T, Scherber C, Brockmeyer J. A multifactorial proteomics approach to sex‐specific effects of diet composition and social environment in an omnivorous insect. Ecol Evol 2021. [DOI: 10.1002/ece3.7676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Yeisson Gutiérrez
- Centro de Bioinformática y Biología Computacional de Colombia – BIOS Manizales Colombia
| | - Marion Fresch
- Department Food Chemistry Institute for Biochemistry and Technical Biochemistry University of Stuttgart Stuttgart Germany
| | - Sören L. Hellmann
- Institute of Organismic and Molecular Evolutionary Biology University of Mainz Mainz Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolutionary Biology University of Mainz Mainz Germany
| | - Christoph Scherber
- Institute of Landscape Ecology University of Münster Münster Germany
- Centre for Biodiversity Monitoring Zoological Research Museum Alexander Koenig Bonn Germany
| | - Jens Brockmeyer
- Department Food Chemistry Institute for Biochemistry and Technical Biochemistry University of Stuttgart Stuttgart Germany
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21
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Ahmed T, Liaqat I, Hyder MZ, Akhtar S, Bhatti AH, Butt SB, Imran Z, Yasmin T, Abbas S. Elucidation of larvicidal potential of metallic and environment friendly food-grade nanostructures against Aedes albopictus. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2021; 43:1903-1925. [PMID: 33179203 DOI: 10.1007/s10653-020-00771-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/30/2020] [Indexed: 06/11/2023]
Abstract
To combat health challenges associated with mosquito-borne diseases, the larvicidal activity of metallic nanoparticles, food-grade polymeric nano-capsules and insecticides was investigated against larvae of Aedes albopictus as an effective alternate control approach. The Ae. albopictus was identified using sequencing and phylogenetic analyses of COXI, CYTB and ITS2 genes. The characterization of synthesized nanostructures was performed through Zetasizer, UV-VIS spectroscopy, atomic force microscopy, scanning electron microscopy and energy dispersive X-ray spectroscopy. The mosquito larvae were exposed to varying concentration of nanostructures and insecticides, and their percentage mortality was evaluated at different time intervals of 24 h and 48 h exposure. The highest efficacy was observed in zinc oxide nanoparticles (ZnO-NPs) and polymeric nanocapsules FG-Cur E-III (LC50 = 0.24 mg/L, LC90 = 0.6 mg/L) and (LC50 = 3.8 mg/L, LC90 = 9.33 mg/L), respectively, after 24 h; while (LC50 = 0.18 mg/L, LC90 = 0.43 mg/L) and (LC50 = 1.95 mg/L, LC90 = 6.46 mg/L), respectively, after 48 h against fourth instar larvae of Ae. albopictus. Ag, CuO, NiTiO3 and CoTiO3 nanoparticles evaluated in this study also showed promising larvicidal activity. Although ZnO-NPs proved to be effective larvicides, their possible toxicity (producing ROS species) can limit their use. The curcumin nanostructures (FG-Cur E-III) stabilized by food-grade materials are thought to exert their larvicidal activity by binding to sterol carrier protein-2, and depriving the larvae from the essential dietary cholesterol, and bears effective larvicidal potential as safe alternative for chemical larvicides, due to their environment friendly, food-grade and easy biodegradability.
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Affiliation(s)
- Toqeer Ahmed
- Centre for Climate Research and Development (CCRD), COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Irfan Liaqat
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Muhammad Zeeshan Hyder
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan.
| | - Shaheen Akhtar
- Health Services Academy (HSA), Park Road, Islamabad, Pakistan
| | | | - Shahid Bilal Butt
- Preston Institute of Nano Sciences and Technology (PINSAT), Preston University, Islamabad, Pakistan
| | - Zahid Imran
- Department of Physics, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Tayyaba Yasmin
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Shabbar Abbas
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
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22
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Aromolaran O, Aromolaran D, Isewon I, Oyelade J. Machine learning approach to gene essentiality prediction: a review. Brief Bioinform 2021; 22:6219158. [PMID: 33842944 DOI: 10.1093/bib/bbab128] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022] Open
Abstract
Essential genes are critical for the growth and survival of any organism. The machine learning approach complements the experimental methods to minimize the resources required for essentiality assays. Previous studies revealed the need to discover relevant features that significantly classify essential genes, improve on the generalizability of prediction models across organisms, and construct a robust gold standard as the class label for the train data to enhance prediction. Findings also show that a significant limitation of the machine learning approach is predicting conditionally essential genes. The essentiality status of a gene can change due to a specific condition of the organism. This review examines various methods applied to essential gene prediction task, their strengths, limitations and the factors responsible for effective computational prediction of essential genes. We discussed categories of features and how they contribute to the classification performance of essentiality prediction models. Five categories of features, namely, gene sequence, protein sequence, network topology, homology and gene ontology-based features, were generated for Caenorhabditis elegans to perform a comparative analysis of their essentiality prediction capacity. Gene ontology-based feature category outperformed other categories of features majorly due to its high correlation with the genes' biological functions. However, the topology feature category provided the highest discriminatory power making it more suitable for essentiality prediction. The major limiting factor of machine learning to predict essential genes conditionality is the unavailability of labeled data for interest conditions that can train a classifier. Therefore, cooperative machine learning could further exploit models that can perform well in conditional essentiality predictions. SHORT ABSTRACT Identification of essential genes is imperative because it provides an understanding of the core structure and function, accelerating drug targets' discovery, among other functions. Recent studies have applied machine learning to complement the experimental identification of essential genes. However, several factors are limiting the performance of machine learning approaches. This review aims to present the standard procedure and resources available for predicting essential genes in organisms, and also highlight the factors responsible for the current limitation in using machine learning for conditional gene essentiality prediction. The choice of features and ML technique was identified as an important factor to predict essential genes effectively.
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Affiliation(s)
- Olufemi Aromolaran
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria.,Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Damilare Aromolaran
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria.,Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria.,Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
| | - Jelili Oyelade
- Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria.,Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
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23
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França LP, Amaral ACF, Ramos ADS, Ferreira JLP, Maria ACB, Oliveira KMT, Araujo ES, Branches ADS, Silva JN, Silva NG, Barros GDA, Chaves FCM, Tadei WP, Silva JRDA. Piper capitarianum essential oil: a promising insecticidal agent for the management of Aedes aegypti and Aedes albopictus. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:9760-9776. [PMID: 33159226 DOI: 10.1007/s11356-020-11148-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
Mosquitoes are responsible for serious public health problems worldwide, and as such, Aedes aegypti and Aedes albopictus are important vectors in the transmission of dengue, chikungunya, and Zika in Brazil and other countries of the world. Due to growing resistance to chemical insecticides among populations of vectors, environmentally friendly strategies for vector management are receiving ever more attention. Essential oils (EOs) extracted from plants have activities against insects with multiple mechanisms of action. These mechanisms hinder the development of resistance, and have the advantages of being less toxicity and biodegradable. Thus, the present study aimed to evaluate the chemical composition of the EOs obtained from Piper capitarianum Yunck, as well as evaluating their insecticidal potential against Aedes aegypti and A. albopictus, and their toxicity in relation to Artemia salina. The yields of the EOs extracted from the leaves, stems, and inflorescences of P. capitarianum were 1.2%, 0.9%, and 0.6%, respectively, and their main constituents were trans-caryophyllene (20.0%), α-humulene (10.2%), β-myrcene (10.5%), α-selinene (7.2%), and linalool (6.0%). The EO from the inflorescences was the most active against A. aegypti and A. albopictus, and exhibited the respective larvicidal (LC50 = 87.6 μg/mL and 76.1 μg/mL) and adulticide activities (LC50 = 126.2 μg/mL and 124.5 μg/mL). This EO was also the most active in the inhibition of AChE, since it presented an IC50 value of 14.2 μg/mL. Its larvicidal effect was observed under optical and scanning electron microscopy. Additionally, non-toxic effects against A. salina were observed. Docking modeling of trans-caryophyllene and α-humulene on sterol carrier protein-2 (SCP-2) suggests that both molecules have affinity with the active site of the enzyme, which indicates a possible mechanism of action. Therefore, the essential oil of P. capitarianum may be used in the development of new insecticide targets for the control of A. aegypti and A. albopictus in the Amazonian environment.
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Affiliation(s)
- Leandro P França
- Chromatography Laboratory, Chemistry Department, Federal University of Amazonas, Manaus, AM, Brazil
| | - Ana Claudia F Amaral
- Laboratory of Medicinal Plants and Derivatives, Department of Chemistry of Natural Products, Farmanguinhos, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Aline de S Ramos
- Laboratory of Medicinal Plants and Derivatives, Department of Chemistry of Natural Products, Farmanguinhos, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - José Luiz P Ferreira
- Laboratory of Medicinal Plants and Derivatives, Department of Chemistry of Natural Products, Farmanguinhos, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Ana Clara B Maria
- Laboratory of Medicinal Plants and Derivatives, Department of Chemistry of Natural Products, Farmanguinhos, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Kelson Mota T Oliveira
- Laboratory of Theoretical and Computational Chemistry, Chemistry Department, Federal University of Amazonas, Manaus, AM, Brazil
| | - Earle S Araujo
- Laboratory of Theoretical and Computational Chemistry, Chemistry Department, Federal University of Amazonas, Manaus, AM, Brazil
| | - Adjane Dalvana S Branches
- Laboratory of Theoretical and Computational Chemistry, Chemistry Department, Federal University of Amazonas, Manaus, AM, Brazil
| | - Jonathas N Silva
- Laboratory of Theoretical and Computational Chemistry, Chemistry Department, Federal University of Amazonas, Manaus, AM, Brazil
| | - Noam G Silva
- Laboratory of Theoretical and Computational Chemistry, Chemistry Department, Federal University of Amazonas, Manaus, AM, Brazil
| | - Gabriel de A Barros
- Laboratory of Theoretical and Computational Chemistry, Chemistry Department, Federal University of Amazonas, Manaus, AM, Brazil
| | | | - Wanderli P Tadei
- Laboratory of Malaria and Dengue, Institute for Research in the Amazon, Manaus, AM, Brazil
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24
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Valli M, Atanázio LCV, Monteiro GC, Coelho RR, Demarque DP, Andricopulo AD, Espindola LS, Bolzani VDS. The Potential of Biologically Active Brazilian Plant Species as a Strategy to Search for Molecular Models for Mosquito Control. PLANTA MEDICA 2021; 87:6-23. [PMID: 33348409 DOI: 10.1055/a-1320-4610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Natural products are a valuable source of biologically active compounds and continue to play an important role in modern drug discovery due to their great structural diversity and unique biological properties. Brazilian biodiversity is one of the most extensive in the world and could be an effective source of new chemical entities for drug discovery. Mosquitoes are vectors for the transmission of dengue, Zika, chikungunya, yellow fever, and many other diseases of public health importance. These diseases have a major impact on tropical and subtropical countries, and their incidence has increased dramatically in recent decades, reaching billions of people at risk worldwide. The prevention of these diseases is mainly through vector control, which is becoming more difficult because of the emergence of resistant mosquito populations to the chemical insecticides. Strategies to provide efficient and safe vector control are needed, and secondary metabolites from plant species from the Brazilian biodiversity, especially Cerrado, that are biologically active for mosquito control are herein highlighted. Also, this is a literature revision of targets as insights to promote advances in the task of developing active compounds for vector control. In view of the expansion and occurrence of arboviruses diseases worldwide, scientific reviews on bioactive natural products are important to provide molecular models for vector control and contribute with effective measures to reduce their incidence.
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Affiliation(s)
- Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), Institute of Physics of São Carlos, University of São Paulo (USP), São Carlos, Brazil
| | - Letícia Cristina Vieira Atanázio
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Gustavo Claro Monteiro
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Roberta Ramos Coelho
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Daniel Pecoraro Demarque
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Adriano Defini Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Centre for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), Institute of Physics of São Carlos, University of São Paulo (USP), São Carlos, Brazil
| | - Laila Salmen Espindola
- Laboratório de Farmacognosia, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, Brazil
| | - Vanderlan da Silva Bolzani
- Nuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
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25
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Ruiz JL, Ranford-Cartwright LC, Gómez-Díaz E. The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression. NAR Genom Bioinform 2021; 3:lqaa113. [PMID: 33987532 PMCID: PMC8092447 DOI: 10.1093/nargab/lqaa113] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/15/2020] [Accepted: 12/26/2020] [Indexed: 12/12/2022] Open
Abstract
Anopheles gambiae mosquitoes are primary human malaria vectors, but we know very little about their mechanisms of transcriptional regulation. We profiled chromatin accessibility by the assay for transposase-accessible chromatin by sequencing (ATAC-seq) in laboratory-reared A. gambiae mosquitoes experimentally infected with the human malaria parasite Plasmodium falciparum. By integrating ATAC-seq, RNA-seq and ChIP-seq data, we showed a positive correlation between accessibility at promoters and introns, gene expression and active histone marks. By comparing expression and chromatin structure patterns in different tissues, we were able to infer cis-regulatory elements controlling tissue-specific gene expression and to predict the in vivo binding sites of relevant transcription factors. The ATAC-seq assay also allowed the precise mapping of active regulatory regions, including novel transcription start sites and enhancers that were annotated to mosquito immune-related genes. Not only is this study important for advancing our understanding of mechanisms of transcriptional regulation in the mosquito vector of human malaria, but the information we produced also has great potential for developing new mosquito-control and anti-malaria strategies.
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Affiliation(s)
- José L Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, 18016 Granada, Spain
| | - Lisa C Ranford-Cartwright
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, 18016 Granada, Spain
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26
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Wang Y, Wang B, Liu M, Jiang K, Wang M, Wang L. Characterization and function analysis of a Kazal-type serine proteinase inhibitor in the red claw crayfish Cherax quadricarinatus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103871. [PMID: 32946920 DOI: 10.1016/j.dci.2020.103871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
Kazal-type serine proteinase inhibitors (KPIs) function in physiological and immunological processes requiring proteinase action. In the present study, the first Cherax quadricarinatus KPI gene (designated CqKPI) was identified and characterized. The open reading frame of CqKPI contains 405 nucleotides and encodes a protein of 134 amino acids. CqKPI has two Kazal domains comprising 44 amino acid residues with the conserved amino acid sequence C-X3-C-X7-C-X6-Y-X3-C-X6-C-X12-C. Each Kazal domain has six conserved cysteine residues, which can form a structural conformation of three pairs of disulfide bonds stabilizing the Kazal domain. CqKPI exhibited high similarity with previously identified KPIs from crayfish hemocytes. The results of tissue distribution showed that CqKPI had the highest expression level in hemocytes, and this was in agreement with phylogenic relationships. Recombinant CqKPI (rCqKPI) was heterologously expressed in Escherichia coli and purified for further study. The proteinase inhibition assays suggested that rCqKPI could potently inhibit elastase and weakly inhibit trypsin, subtilisin A, and proteinase K, but not α-chymotrypsin. It can firmly bind to Bacillus hwajinpoensis, Staphylococcus aureus, and Vibrio parahaemolyticus, with weak binding to Candida albicans. In addition, CqKPI inhibited bacterial secretory proteinase activity and inhibited the growth of B. hwajinpoensis and C. albicans. These data suggest that CqKPI might be involved in anti-bacterial immunity, acting as an inhibitor of the proteinase cascade in the resistance to invasion of pathogens.
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Affiliation(s)
- Yan Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baojie Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Mei Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Keyong Jiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Mengqiang Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China; The Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, SANYA Oceanographic Institution of the Ocean University of China, Sanya, 572024, China; Center for Marine Molecular Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Lei Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, 266237, China; CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266400, China.
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27
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Gamez S, Srivastav S, Akbari OS, Lau NC. Diverse Defenses: A Perspective Comparing Dipteran Piwi-piRNA Pathways. Cells 2020; 9:E2180. [PMID: 32992598 PMCID: PMC7601171 DOI: 10.3390/cells9102180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Animals face the dual threat of virus infections hijacking cellular function and transposons proliferating in germline genomes. For insects, the deeply conserved RNA interference (RNAi) pathways and other chromatin regulators provide an important line of defense against both viruses and transposons. For example, this innate immune system displays adaptiveness to new invasions by generating cognate small RNAs for targeting gene silencing measures against the viral and genomic intruders. However, within the Dipteran clade of insects, Drosophilid fruit flies and Culicids mosquitoes have evolved several unique mechanistic aspects of their RNAi defenses to combat invading transposons and viruses, with the Piwi-piRNA arm of the RNAi pathways showing the greatest degree of novel evolution. Whereas central features of Piwi-piRNA pathways are conserved between Drosophilids and Culicids, multiple lineage-specific innovations have arisen that may reflect distinct genome composition differences and specific ecological and physiological features dividing these two branches of Dipterans. This perspective review focuses on the most recent findings illuminating the Piwi/piRNA pathway distinctions between fruit flies and mosquitoes, and raises open questions that need to be addressed in order to ameliorate human diseases caused by pathogenic viruses that mosquitoes transmit as vectors.
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Affiliation(s)
- Stephanie Gamez
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA; (S.G.); (O.S.A.)
| | - Satyam Srivastav
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA;
| | - Omar S. Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA; (S.G.); (O.S.A.)
| | - Nelson C. Lau
- Department of Biochemistry and Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
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28
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Ribeiro JMC, Mans BJ. TickSialoFam (TSFam): A Database That Helps to Classify Tick Salivary Proteins, a Review on Tick Salivary Protein Function and Evolution, With Considerations on the Tick Sialome Switching Phenomenon. Front Cell Infect Microbiol 2020; 10:374. [PMID: 32850476 PMCID: PMC7396615 DOI: 10.3389/fcimb.2020.00374] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/17/2020] [Indexed: 01/09/2023] Open
Abstract
Tick saliva contains a complex mixture of peptides and non-peptides that counteract their hosts' hemostasis, immunity, and tissue-repair reactions. Recent transcriptomic studies have revealed over one thousand different transcripts coding for secreted polypeptides in a single tick species. Not only do these gene products belong to many expanded families, such as the lipocalins, metalloproteases, Antigen-5, cystatins, and apyrases, but also families that are found exclusively in ticks, such as the evasins, Isac, DAP36, and many others. Phylogenetic analysis of the deduced protein sequences indicate that the salivary genes exhibit an increased rate of evolution due to a lower evolutionary constraint and/or positive selection, allowing for a large diversity of tick salivary proteins. Thus, for each new tick species that has its salivary transcriptome sequenced and assembled, a formidable task of annotation of these transcripts awaits. Currently, as of November 2019, there are over 287 thousand coding sequences deposited at the National Center for Biotechnology Information (NCBI) that are derived from tick salivary gland mRNA. Here, from these 287 thousand sequences we identified 45,264 potential secretory proteins which possess a signal peptide and no transmembrane domains on the mature peptide. By using the psiblast tools, position-specific matrices were constructed and assembled into the TickSialoFam (TSF) database. The TSF is a rpsblastable database that can help with the annotation of tick sialotranscriptomes. The TSA database identified 136 tick salivary secreted protein families, as well as 80 families of endosomal-related products, mostly having a protein modification function. As the number of sequences increases, and new annotation details become available, new releases of the TSF database may become available.
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Affiliation(s)
- José M. C. Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, United States
| | - Ben J. Mans
- Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research, Pretoria, South Africa
- The Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, South Africa
- Department of Life and Consumer Sciences, University of South Africa, Pretoria, South Africa
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29
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Song X, Pei L, Zhang Y, Chen X, Zhong Q, Ji Y, Tang J, Feng F, Li B. Functional diversification of three delta-class glutathione S-transferases involved in development and detoxification in Tribolium castaneum. INSECT MOLECULAR BIOLOGY 2020; 29:320-336. [PMID: 31999035 DOI: 10.1111/imb.12637] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
Glutathione S-transferases (GSTs) are members of a multifunctional enzyme superfamily. Forty-one GSTs have been identified in Tribolium castaneum; however, none of the 41 GSTs has been functionally characterized. Here, three delta-class GSTs, TcGSTd1, TcGSTd2 and TcGSTd3, of T. castaneum were successfully cloned and expressed in Escherichia coli. All of the studied GSTs catalysed the conjugation of reduced glutathione with 1-chloro-2,4-dinitrobenzene. Insecticide treatment showed that the expression levels of TcGSTd3 and TcGSTd2 were significantly increased after exposure to phoxim and lambda-cyhalothrin, whereas TcGSTd1 was slightly upregulated only in response to phoxim. A disc diffusion assay showed that overexpression of TcGSTD3, but not TcGSTD1 or TcGSTD2, in E. coli increased resistance to paraquat-induced oxidative stress. RNA interference knockdown of TcGSTd1 caused metamorphosis deficiencies and reduced fecundity by regulating insulin/target-of-rapamycin signalling pathway-mediated ecdysteroid biosynthesis, and knockdown of TcGSTd3 led to reduced fertility and a decreased hatch rate of the offspring, probably caused by the reduced antioxidative activity in the reproductive organs. These results indicate that TcGSTd3 and TcGSTd2 may play vital roles in cellular detoxification, whereas TcGSTd1 may play essential roles in normal development of T. castaneum. These delta-class GSTs in T. castaneum have obtained different functions during the evolution.
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Affiliation(s)
- X Song
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - L Pei
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Y Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - X Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Q Zhong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Y Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - J Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - B Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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30
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Heames B, Schmitz J, Bornberg-Bauer E. A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila. J Mol Evol 2020; 88:382-398. [PMID: 32253450 PMCID: PMC7162840 DOI: 10.1007/s00239-020-09939-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/13/2020] [Indexed: 12/13/2022]
Abstract
Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Drosophila genus. Across the annotated proteomes of twelve species, we find 6297 orphan genes within 4953 taxon-specific clusters of orthologs. By inferring the ancestral DNA as non-coding for between 550 and 2467 (8.7-39.2%) of these genes, we describe for the first time how de novo emergence contributes to the abundance of clade-specific Drosophila genes. In support of them having functional roles, we show that de novo genes have robust expression and translational support. However, the distinct nucleotide sequences of de novo genes, which have characteristics intermediate between intergenic regions and conserved genes, reflect their recent birth from non-coding DNA. We find that de novo genes encode more disordered proteins than both older genes and intergenic regions. Together, our results suggest that gene emergence from non-coding DNA provides an abundant source of material for the evolution of new proteins. Following gene birth, gradual evolution over large evolutionary timescales moulds sequence properties towards those of conserved genes, resulting in a continuum of properties whose starting points depend on the nucleotide sequences of an initial pool of novel genes.
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Affiliation(s)
- Brennen Heames
- Institute for Evolution and Biodiversity, 48149, Münster, Germany
| | - Jonathan Schmitz
- Institute for Evolution and Biodiversity, 48149, Münster, Germany
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Chasapi A, Aivaliotis M, Angelis L, Chanalaris A, Iliopoulos I, Kappas I, Karapiperis C, Kyrpides NC, Pafilis E, Panteris E, Topalis P, Tsiamis G, Vizirianakis IS, Vlassi M, Promponas VJ, Ouzounis CA. Establishment of computational biology in Greece and Cyprus: Past, present, and future. PLoS Comput Biol 2019; 15:e1007532. [PMID: 31856214 PMCID: PMC6922331 DOI: 10.1371/journal.pcbi.1007532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Anastasia Chasapi
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Michalis Aivaliotis
- School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessalonica, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Lefteris Angelis
- School of Informatics, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Anastasios Chanalaris
- Botnar Research Centre, NDORMS, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ioannis Iliopoulos
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece
| | - Ilias Kappas
- School of Biology, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Christos Karapiperis
- School of Informatics, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Evangelos Pafilis
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Eleftherios Panteris
- First Psychiatric Clinic, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - George Tsiamis
- Department of Environmental Engineering, School of Engineering, University of Patras, Patras, Greece
| | - Ioannis S. Vizirianakis
- Department of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Metaxia Vlassi
- Institute of Biosciences & Applications, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- * E-mail: (VJP); (CAO)
| | - Christos A. Ouzounis
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
- * E-mail: (VJP); (CAO)
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32
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Bartys N, Kierzek R, Lisowiec-Wachnicka J. The regulation properties of RNA secondary structure in alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194401. [PMID: 31323437 DOI: 10.1016/j.bbagrm.2019.07.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
Abstract
The RNA secondary structure is important for many functional processes in the cell. The secondary and tertiary structures of cellular RNAs are essential for the activity of these molecules in processes such as transcription, splicing, translation, and localization. New high-throughput analytical methods, including next generation sequencing, have allowed for the in-depth characterization of the 'RNA structurome': a new term describing how the RNA structure controls the activity of RNA by itself and how it regulates the expression of genes. In this review, we present many examples of the influence of structural motifs of RNA, long range interactions and global RNA structure on the alternative splicing processes. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Natalia Bartys
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
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Zhang XR, Zhang JQ, Shao YY, Xing XR, Wang J, Liu ZX, Li YJ, Ofori AD, Tu QB, Wang J, Sheng S, Wu FA. Identification of glutathione-S-transferase genes by transcriptome analysis in Meteorus pulchricornis (Hymenoptera: Braconidae) and their expression patterns under stress of phoxim and cypermethrin. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100607. [PMID: 31319266 DOI: 10.1016/j.cbd.2019.100607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 01/08/2023]
Abstract
Meteorus pulchricornis (Wesmael) (Hymenoptera: Braconidae) is a preponderant endoparasitoid wasp, attacking the larvae of many lepidopteran pests. We present the first body transcriptome dataset for M. pulchricornis. In total, 50,781,796 clean reads were obtained and 33,144 unigenes were assembled; 15,458 unigenes showed a significant similarity (E value < 10-5) to known proteins in the NCBI non-redundant protein database. Gene ontology and cluster of orthologous group analyses were performed to classify the functions of genes. To better understand the role of glutathione-S-transferases (GSTs) in detoxification mechanism in M. pulchricornis, we identified seventeen GST genes (MpulGSTs) from the body transcriptome. Among these, fifteen MpulGSTs belonged to cytosolic GSTs and the other two belonged to microsomal classes. The cytosolic GSTs were classified into four different clades: four in delta, three in omega, seven in sigma, and one in zeta. The expression levels of these MpulGSTs after exposure to sub-lethal concentrations of phoxim and cypermethrin were determined using real-time quantitative polymerase chain reaction: seven MpulGSTs (MpulGSTD3, MpulGSTS1, MpulGSTS2, MpulGSTS4, MpulGSTS6 MpulGSTO3, and MpulGSTmic1) and 11 MpulGSTs (MpulGSTD1, MpulGSTD2, MpulGSTD3, MpulGSTO2, MpulGSTS1, MpulGSTS2, MpulGSTS3, MpulGSTS4, MpulGSTS5, MpulGSTS7, and MpulGSTmic1) were highly expressed, respectively. These results suggested that GST genes may play a pivotal role in detoxification process in M. pulchricornis. Our findings would provide a theoretical base for elucidating insecticide susceptibility and should promote functional research on specific GST genes in parasitoid wasps.
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Affiliation(s)
- Xiao-Rui Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Jia-Qi Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Ying-Ying Shao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Xiao-Rong Xing
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Jiao Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Zhi-Xiang Liu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Yi-Jiangcheng Li
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Andrews Danso Ofori
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Qing-Bo Tu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; School of Hanlin, Nanjing University of China Medicine, Taizhou 225300, PR China
| | - Jun Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China
| | - Sheng Sheng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China.
| | - Fu-An Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China.
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Lee BY, Choi BS, Kim MS, Park JC, Jeong CB, Han J, Lee JS. The genome of the freshwater water flea Daphnia magna: A potential use for freshwater molecular ecotoxicology. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 210:69-84. [PMID: 30826642 DOI: 10.1016/j.aquatox.2019.02.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
The water flea Daphnia magna is a small planktonic cladoceran. D. magna has been used as a model species for ecotoxicology, as it is sensitive to environmental stressors and environmental changes. Since Daphnia is affected by culture environment and each population/strain has its own ecological and genetic characteristics, its population/strain-based genome information is useful for environmental genomic studies. In this study, we assembled and characterized the genome of D. magna. Using a high-density genetic map of D. magna xinb3, the draft genome was integrated to 10 linkage groups (LGs). The total length of the integrated genome was about 123 Mb with N50 = 10.1 Mb, and the number of scaffolds was 4193 including 10 LGs. A total of 15,721 genes were annotated after manual curation. Orthologous genes were characterized in the genome and compared with other genomes of Daphnia. In addition, we identified defense related genes such as cytochrome P450 (CYP) genes, glutathione S-transferase (GST) genes, and ATP-binding cassette (ABC) genes from the assembled D. magna genome for its potential use in molecular ecotoxicological studies in the freshwater environment. This genomic resource will be helpful to study for a better understanding on molecular mechanism in response to various pollutants.
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Affiliation(s)
- Bo-Young Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Min-Sub Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jeonghoon Han
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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35
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Qi Y, Wu Y, Saunders R, Chen XG, Mao C, Biedler JK, Tu ZJ. Guy1, a Y-linked embryonic signal, regulates dosage compensation in Anopheles stephensi by increasing X gene expression. eLife 2019; 8:43570. [PMID: 30888319 PMCID: PMC6440743 DOI: 10.7554/elife.43570] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/16/2019] [Indexed: 12/22/2022] Open
Abstract
We previously showed that Guy1, a primary signal expressed from the Y chromosome, is a strong candidate for a male-determining factor that confers female-specific lethality in Anopheles stephensi (Criscione et al., 2016). Here, we present evidence that Guy1 increases X gene expression in Guy1-transgenic females from two independent lines, providing a mechanism underlying the Guy1-conferred female lethality. The median level gene expression (MGE) of X-linked genes is significantly higher than autosomal genes in Guy1-transgenic females while there is no significant difference in MGE between X and autosomal genes in wild-type females. Furthermore, Guy1 significantly upregulates at least 40% of the 996 genes across the X chromosome in transgenic females. Guy1-conferred female-specific lethality is remarkably stable and completely penetrant. These findings indicate that Guy1 regulates dosage compensation in An. stephensi and components of dosage compensation may be explored to develop novel strategies to control mosquito-borne diseases.
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Affiliation(s)
- Yumin Qi
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Yang Wu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangdong, China
| | - Randy Saunders
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Xiao-Guang Chen
- Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Chunhong Mao
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, United States
| | - James Kite Biedler
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Zhijian Jake Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
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36
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Perry C, Scanlan J, Robin C. Mining insect genomes for functionally affiliated genes. CURRENT OPINION IN INSECT SCIENCE 2019; 31:114-122. [PMID: 31109664 DOI: 10.1016/j.cois.2018.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
Several hundred insect genome assemblies are already publicly available, and this total grows on a weekly basis. A major challenge now confronting insect science is how best to use genomic data to improve our understanding of insect biology. We consider a framework for genome analysis based on functional affiliation, that is, groups of genes involved in the same biological process or pathway, and explore how such an approach furthers our understanding of several aspects of insect phenotype. We anticipate that this approach will prove useful for future research across the breadth of insect studies, whatever organism or trait it involves.
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Affiliation(s)
- Caitlyn Perry
- The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia.
| | - Jack Scanlan
- The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
| | - Charles Robin
- The University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
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37
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Ding BY, Yang L, Peng YY, Chang TY, Ye C, Shang F, Niu J, Wang JJ. RNA-sequencing of a citrus bud-feeder, Podagricomela weisei (Coleoptera: Chrysomelidae), reveals xenobiotic metabolism/core RNAi machinery-associated genes and conserved miRNAs. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:339-350. [PMID: 30682656 DOI: 10.1016/j.cbd.2019.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 11/15/2022]
Abstract
The citrus leaf-mining beetle, Podagricomela weisei Heikertinger, is an important citrus pest that ingests the mesophyll and new shoots. The mechanism underlying the xenobiotic metabolism of P. weisei is not well understood, in part because of a lack of available genomic and transcriptomic data, which has hampered the development of novel pest management approaches [e.g., RNA interference (RNAi)]. In this study, we completed the deep sequencing of the P. weisei transcriptome to identify factors potentially involved in xenobiotic metabolism and the core RNAi machinery. The sequencing of the P. weisei transcriptome generated >27 million clean reads, ultimately yielding 90,410 unigenes with an N50 of 1065 bp. The unigenes were used as queries to search the Nr database, which revealed that 21,847 unigenes were homologous to known genes in various species. Transcripts encoding genes involved in xenobiotic metabolism were identified, including genes encoding cytochrome P450 monooxygenase (P450, 47 unigenes), glutathione S-transferase (GST, 12 unigenes), esterase (EST, 25 unigenes), and the ATP-binding cassette transporter (ABC transporter, 32 unigenes). A parallel sequencing of small RNAs detected 30 conserved miRNAs, with the most abundant being Pwe-miR-1-3p, with an expression level reaching 517,996 reads in the prepared library, followed by Pwe-miR-8-3p (149,402 reads). Genes encoding components of the miRNA, siRNA, and piRNA pathways were also identified, and the results indicated that P. weisei possesses only one of each gene in all three pathways. In summary, this is the first detailed analysis of the transcriptome and small RNAs of P. weisei. The datasets presented herein may form the basis for future molecular characterizations of P. weisei as well as the development of enhanced pest control strategies.
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Affiliation(s)
- Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Li Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yuan-Yuan Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Teng-Yu Chang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Chao Ye
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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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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Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging. Proc Natl Acad Sci U S A 2018; 115:E7568-E7577. [PMID: 30038005 PMCID: PMC6094101 DOI: 10.1073/pnas.1803062115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mosquito blood cells are immune cells that help control infection by vector-borne pathogens. Despite their importance, little is known about mosquito blood cell biology beyond morphological and functional criteria used for their classification. Here, we combined the power of single-cell RNA sequencing, high-content imaging flow cytometry, and single-molecule RNA hybridization to analyze a subset of blood cells of the malaria mosquito Anopheles gambiae By demonstrating that blood cells express nearly half of the mosquito transcriptome, our dataset represents an unprecedented view into their transcriptional program. Analyses of differentially expressed genes identified transcriptional signatures of two cell types and provide insights into the current classification of these cells. We further demonstrate the active transfer of a cellular marker between blood cells that may confound their identification. We propose that cell-to-cell exchange may contribute to cellular diversity and functional plasticity seen across biological systems.
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Comparative immunological study of the snail Physella acuta (Hygrophila, Pulmonata) reveals shared and unique aspects of gastropod immunobiology. Mol Immunol 2018; 101:108-119. [PMID: 29920433 DOI: 10.1016/j.molimm.2018.05.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 12/22/2022]
Abstract
The freshwater snail Physella acuta was selected to expand the perspective of comparative snail immunology. Analysis of Physella acuta, belonging to the Physidae, taxonomic sister family to Planorbidae, affords family-level comparison of immune features characterized from Biomphalaria glabrata, the model snail often used to interpret general gastropod immunity. To capture constitutive and induced immune sequences, transcriptomes of an individual Physella acuta snail, 12 h post injection with bacteria (Gram -/+) and one sham-exposed snail were recorded with 454 pyrosequencing. Assembly yielded a combined reference transcriptome containing 24,288 transcripts. Additionally, genomic Illumina reads were obtained (∼15-fold coverage). Recovery of transcripts for two macin-like antimicrobial peptides (AMPs), 12 aplysianins, four LBP/BPIs and three physalysins indicated that Physella acuta shares a similar organization of antimicrobial defenses with Biomphalaria glabrata, contrasting a modest AMP arsenal with a diverse set of antimicrobial proteins. The lack of predicted transmembrane domains in all seven Physella acuta PGRP transcripts supports the notion that gastropods do not employ cell-bound PGRP receptors, different from ecdysozoan invertebrates yet similar to mammals (vertebrate deuterostomes). The well-documented sequence diversification by Biomphalaria glabrata FREPs (immune lectins comprising immunoglobulin superfamily domains and fibrinogen domains), resulting from somatic mutations of a large FREP gene family is hypothesized to be unique to Planorbidae; Physella acuta revealed just two bonafide FREP genes and these were not diversified. Furthermore, the flatworm parasite Echinostoma paraensei, confirmed here to infect both snail species, did not evoke from Physella acuta the abundant expression of FREP proteins at 2, 4 and 8 days post exposure that was previously observed from Biomphalaria glabrata. The Physella acuta reference transcriptome also revealed 24 unique transcripts encoding proteins consisting of a single fibrinogen-related domain (FReDs), with a short N-terminal sequence encoding either a signal peptide, transmembrane domain or no predicted features. The Physella acuta FReDs are candidate immune genes based on implication of similar sequences in immunity of bivalve molluscs. Overall, comparative analysis of snails of sister families elucidated the potential for taxon-specific immune features and investigation of strategically selected species will provide a more comprehensive view of gastropod immunity.
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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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42
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Artemov GN, Bondarenko SM, Naumenko AN, Stegniy VN, Sharakhova MV, Sharakhov IV. Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome. BMC Genomics 2018; 19:278. [PMID: 29688842 PMCID: PMC5914054 DOI: 10.1186/s12864-018-4663-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 04/12/2018] [Indexed: 02/06/2023] Open
Abstract
Background Malaria mosquitoes have had a remarkable stability in the number of chromosomes in their karyotype (2n = 6) during 100 million years of evolution. Moreover, autosomal arms were assumed to maintain their integrity even if their associations with each other changed via whole-arm translocations. Here we use high-coverage comparative physical genome mapping of three Anopheles species to test the extent of evolutionary conservation of chromosomal arms in malaria mosquitoes. Results In this study, we developed a physical genome map for Anopheles atroparvus, one of the dominant malaria vectors in Europe. Using fluorescence in situ hybridization (FISH) of DNA probes with the ovarian nurse cell polytene chromosomes and synteny comparison, we anchored 56 genomic scaffolds to the An. atroparvus chromosomes. The obtained physical map represents 89.6% of the An. atroparvus genome. This genome has the second highest mapping coverage among Anophelinae assemblies after An. albimanus, which has 98.2% of the genome assigned to its chromosomes. A comparison of the An. atroparvus, An. albimanus, and An. gambiae genomes identified partial-arm translocations between the autosomal arms that break down the integrity of chromosome elements in evolution affecting the structure of the genetic material in the pericentromeric regions. Unlike An. atroparvus and An. albimanus, all chromosome elements of An. gambiae are fully syntenic with chromosome elements of the putative ancestral Anopheles karyotype. We also detected nonrandom distribution of large conserved synteny blocks and confirmed a higher rate of inversion fixation in the X chromosome compared with autosomes. Conclusions Our study demonstrates the power of physical mapping for understanding the genome evolution in malaria mosquitoes. The results indicate that syntenic relationships among chromosome elements of Anopheles species have not been fully preserved because of multiple partial-arm translocations. Electronic supplementary material The online version of this article (10.1186/s12864-018-4663-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gleb N Artemov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia
| | - Semen M Bondarenko
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia
| | - Anastasia N Naumenko
- Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA, 24061, USA
| | - Vladimir N Stegniy
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia
| | - Maria V Sharakhova
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia. .,Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA, 24061, USA.
| | - Igor V Sharakhov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk, 634050, Russia. .,Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA, 24061, USA.
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43
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Wiegmann BM, Richards S. Genomes of Diptera. CURRENT OPINION IN INSECT SCIENCE 2018; 25:116-124. [PMID: 29602357 DOI: 10.1016/j.cois.2018.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Diptera (true flies) are among the most diverse holometabolan insect orders and were the first eukaryotic order to have a representative genome fully sequenced. 110 fly species have publically available genome assemblies and many hundreds of population-level genomes have been generated in the model organisms Drosophila melanogaster and the malaria mosquito Anopheles gambiae. Comparative genomics carried out in a phylogenetic context is illuminating many aspects of fly biology, providing unprecedented insight into variability in genome structure, gene content, genetic mechanisms, and rates and patterns of evolution in genes, populations, and species. Despite the rich availability of genomic resources in flies, there remain many fly lineages to which new genome sequencing efforts should be directed. Such efforts would be most valuable in fly families or clades that exhibit multiple origins of key fly behaviors such as blood feeding, phytophagy, parasitism, pollination, and mycophagy.
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Affiliation(s)
- Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, United States.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77006, United States
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Voolstra CR, Li Y, Liew YJ, Baumgarten S, Zoccola D, Flot JF, Tambutté S, Allemand D, Aranda M. Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals. Sci Rep 2017; 7:17583. [PMID: 29242500 PMCID: PMC5730576 DOI: 10.1038/s41598-017-17484-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 11/28/2017] [Indexed: 02/07/2023] Open
Abstract
Stony corals form the foundation of coral reef ecosystems. Their phylogeny is characterized by a deep evolutionary divergence that separates corals into a robust and complex clade dating back to at least 245 mya. However, the genomic consequences and clade-specific evolution remain unexplored. In this study we have produced the genome of a robust coral, Stylophora pistillata, and compared it to the available genome of a complex coral, Acropora digitifera. We conducted a fine-scale gene-based analysis focusing on ortholog groups. Among the core set of conserved proteins, we found an emphasis on processes related to the cnidarian-dinoflagellate symbiosis. Genes associated with the algal symbiosis were also independently expanded in both species, but both corals diverged on the identity of ortholog groups expanded, and we found uneven expansions in genes associated with innate immunity and stress response. Our analyses demonstrate that coral genomes can be surprisingly disparate. Future analyses incorporating more genomic data should be able to determine whether the patterns elucidated here are not only characteristic of the differences between S. pistillata and A. digitifera but also representative of corals from the robust and complex clade at large.
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Affiliation(s)
- Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Yong Li
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yi Jin Liew
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sebastian Baumgarten
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Biology of Host-Parasite Interactions Unit, Institut Pasteur, 25 rue du Dr Roux, 75015, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 quai Antoine Ier, 98000, Monaco, Monaco
| | - Jean-François Flot
- Université libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Bruxelles, Belgium
| | - Sylvie Tambutté
- Centre Scientifique de Monaco, 8 quai Antoine Ier, 98000, Monaco, Monaco
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 quai Antoine Ier, 98000, Monaco, Monaco
| | - Manuel Aranda
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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45
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Irregular designs and Darwinism in biology: Genomes as the test case. J Biosci 2017; 42:523-525. [PMID: 29229869 DOI: 10.1007/s12038-017-9720-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Bilandžija H, Laslo M, Porter ML, Fong DW. Melanization in response to wounding is ancestral in arthropods and conserved in albino cave species. Sci Rep 2017; 7:17148. [PMID: 29215078 PMCID: PMC5719348 DOI: 10.1038/s41598-017-17471-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/27/2017] [Indexed: 01/15/2023] Open
Abstract
Many species adapted to aphotic subterranean habitats have lost all body pigmentation. Yet, melanization is an important component of wound healing in arthropods. We amputated appendages in a variety of cave-adapted and surface-dwelling arthropods. A dark clot formed at the site of injury in most species tested, including even albino cave-adapted species. The dark coloration of the clots was due to melanin deposition. The speed of wound melanization was uncorrelated with a difference in metabolic rate between surface and cave populations of an amphipod. The chelicerate Limulus polyphemus, all isopod crustaceans tested, and the cave shrimp Troglocaris anophthalmus did not melanize wounds. The loss of wound melanization in T. anophthalmus was an apomorphy associated with adaptation to subterranean habitats, but in isopods it appeared to be a symplesiomorphy unrelated to colonization of subterranean habitats. We conclude that wound melanization i) is an important part of innate immunity because it was present in all major arthropod lineages, ii) is retained in most albino cave species, and iii) has been lost several times during arthropod evolution, indicating melanization is not an indispensable component of wound healing in arthropods.
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Affiliation(s)
- Helena Bilandžija
- Department of Molecular Biology, Ruđer Bošković Institute, Zagreb, 10000, Croatia
| | - Mara Laslo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Megan L Porter
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
| | - Daniel W Fong
- Department of Biology, American University, Washington, DC, 20016, USA.
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Alonso J, Martinez M. Insights into the molecular evolution of peptidase inhibitors in arthropods. PLoS One 2017; 12:e0187643. [PMID: 29108008 PMCID: PMC5673224 DOI: 10.1371/journal.pone.0187643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/23/2017] [Indexed: 11/19/2022] Open
Abstract
Peptidase inhibitors are key proteins involved in the control of peptidases. In arthropods, peptidase inhibitors modulate the activity of peptidases involved in endogenous physiological processes and peptidases of the organisms with which they interact. Exploring available arthropod genomic sequences is a powerful way to obtain the repertoire of peptidase inhibitors in every arthropod species and to understand the evolutionary mechanisms involved in the diversification of this kind of proteins. A genomic comparative analysis of peptidase inhibitors in species belonging to different arthropod taxonomic groups was performed. The results point out: i) species or clade-specific presence is shown for several families of peptidase inhibitors; ii) multidomain peptidase inhibitors are commonly found in many peptidase inhibitor families; iii) several families have a wide range of members in different arthropod species; iv) several peptidase inhibitor families show species-specific (or clade-specific) gene family expansions; v) functional divergence may be assumed for particular clades; vi) passive expansions may be used by natural selection to fix adaptations. In conclusion, conservation and divergence of duplicated genes and the potential recruitment as peptidase inhibitors of proteins from other families are the main mechanisms used by arthropods to fix diversity. This diversity would be associated to the control of target peptidases and, as consequence, to adapt to specific environments.
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Affiliation(s)
- Joaquin Alonso
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, Madrid, Spain
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Liu HW, Li YS, Tang X, Guo PC, Wang DD, Zhou CY, Xia QY, Zhao P. A midgut-specific serine protease, BmSP36, is involved in dietary protein digestion in the silkworm, Bombyx mori. INSECT SCIENCE 2017; 24:753-767. [PMID: 27311916 DOI: 10.1111/1744-7917.12369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
Serine proteases play important roles in digestion and immune responses during insect development. In the present study, the serine protease gene BmSP36, which encodes a 292-residue protein, was cloned from the midgut cells of Bombyx mori. BmSP36 contains an intact catalytic triad (H57, D102 and S195) and a conserved substrate-binding site (G189, H216 and G226), suggesting that it is a serine protease with chymotrypsin-like specificity. The temporal and spatial expression patterns of BmSP36 indicated that its messenger RNA and protein expression mainly occurred in the midgut at the feeding stages. Western blotting, immunofluorescence and liquid chromatography-tandem mass spectrometry analyses revealed secretion of BmSP36 protein from epithelial cells into the midgut lumen. The transcriptional and translational expression of BmSP36 was down-regulated after starvation but up-regulated after refeeding. Moreover, expression of the BmSP36 gene could be up-regulated by a juvenile hormone analogue. These results enable us to better define the potential role of BmSP36 in dietary protein digestion at the feeding stages during larval development.
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Affiliation(s)
- Hua-Wei Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - You-Shan Li
- Vitamin D Research Institute, Shaanxi Sci-Tech University, Hanzhong, Shaanxi Province, China
| | - Xin Tang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Peng-Chao Guo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Dan-Dan Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Chun-Yan Zhou
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Qing-You Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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Mandrioli M, Zambonini G, Manicardi GC. Comparative Gene Mapping as a Tool to Understand the Evolution of Pest Crop Insect Chromosomes. Int J Mol Sci 2017; 18:ijms18091919. [PMID: 28880213 PMCID: PMC5618568 DOI: 10.3390/ijms18091919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 11/22/2022] Open
Abstract
The extent of the conservation of synteny and gene order in aphids has been previously investigated only by comparing a small subset of linkage groups between the pea aphid Acyrthosiphon pisum and a few other aphid species. Here we compared the localization of eight A. pisum scaffolds (covering more than 5 Mb and 83 genes) in respect to the Drosophila melanogaster Muller elements identifying orthologous loci spanning all the four A. pisum chromosomes. Comparison of the genetic maps revealed a conserved synteny across different loci suggesting that the study of the fruit fly Muller elements could favour the identification of chromosomal markers useful for the study of chromosomal rearrangements in aphids. A. pisum is the first aphid species to have its genome sequenced and the finding that there are several chromosomal regions in synteny between Diptera and Hemiptera indicates that the genomic tools developed in A. pisum will be broadly useful not only for the study of other aphids but also for other insect species.
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Affiliation(s)
- Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
| | - Giada Zambonini
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
| | - Gian Carlo Manicardi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.
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50
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Zhang J, Huang J, Zhu F, Zhang J. Differential gene expression in Anopheles stephensi following infection with drug-resistant Plasmodium yoelii. Parasit Vectors 2017; 10:401. [PMID: 28851458 PMCID: PMC5576267 DOI: 10.1186/s13071-017-2326-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/08/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The transmission of drug-resistant parasites by the mosquito may be influenced by the altered biological fitness of drug-resistant parasites and different immune reactions or metabolic change in the mosquito. At this point, little is known about the variations in mosquito immunity and metabolism when mosquitoes are infected with drug-resistant parasites. To understand the differential gene expression in Anopheles following infection with drug-resistant Plasmodium, we conducted a genome-wide transcriptomic profiling analysis of Anopheles stephensi following feeding on mice with drug-resistant or drug-sensitive P. yoelii, observed changes in gene expression profiles and identified transcripts affected by the drug-resistant parasite. RESULTS To study the impact of drug-resistant Plasmodium infections on An. stephensi gene transcription, we analyzed the three major transition stages of Plasmodium infections: at 24 h and 13 and 19 days after blood-feeding. Six cDNA libraries (R-As24h, R-As13d, R-As19d,S-As24h, S-As13dand S-As19d) were constructed, and RNA sequencing was subsequently performed. In total, approximately 50.1 million raw reads, 47.9 million clean reads and 7.18G clean bases were obtained. Following differentially expressed gene (DEG) analysis, GO enrichment analysis of DEGs, and functional classification by KEGG, we showed that the variations in gene expression in An. stephensi infected by the drug-resistant P. yoelii NSM occurred mainly at 13 days after blood meal during sporozoite migration through the hemolymph. The differentially expressed genes included those functioning in some important immune reaction and iron metabolism pathways, such as pattern recognition receptors, regulators of the JNK pathway, components of the phagosome pathway, regulators of the melanization response, activators of complement reactions, insulin signaling cascade members, oxidative stress and detoxification proteins. CONCLUSIONS Our study shows that drug-resistant P. yoelii NSM has an impact on the transcript abundance levels of An.stephensi mostly at 13 days after blood meal during sporozoite migration through the hemolymph and that most differentially expressed genes were downregulated. Our results highlight the need for a better understanding of selective pressures from these differentially expressed genes of the drug-resistant Plasmodium in the mosquito and the different transmission patterns of drug-resistant Plasmodium by Anopheles.
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Affiliation(s)
- Jingru Zhang
- Department of Pathobiology, the Third Military Medical University, Chongqing, People's Republic of China
| | - Jiacheng Huang
- Students brigade 5, The Third Military Medical University, Chongqing, People's Republic of China
| | - Feng Zhu
- Department of Pathobiology, the Third Military Medical University, Chongqing, People's Republic of China
| | - Jian Zhang
- Department of Pathobiology, the Third Military Medical University, Chongqing, People's Republic of China.
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