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Shen X, Jin J, Zhang G, Yan B, Yu X, Wu H, Yang M, Zhang F. The chromosome-level genome assembly of Aphidoletes aphidimyza Rondani (Diptera: Cecidomyiidae). Sci Data 2024; 11:785. [PMID: 39019956 PMCID: PMC11255235 DOI: 10.1038/s41597-024-03614-4] [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: 12/08/2023] [Accepted: 07/05/2024] [Indexed: 07/19/2024] Open
Abstract
Aphidoletes aphidimyza is widely recognized as an effective predator of aphids in agricultural systems. However, there is limited understanding of its predation mechanisms. In this study, we generated a high-quality chromosome level of the A. aphidimyza genome by combining PacBio, Illumina, and Hi-C data. The genome has a size of 192.08 Mb, with a scaffold N50 size of 46.85 Mb, and 99.08% (190.35 Mb) of the assembly is located on four chromosomes. The BUSCO analysis of our assembly indicates a completeness of 97.8% (n = 1,367), including 1,307 (95.6%) single-copy BUSCOs and 30 (2.2%) duplicated BUSCOs. Additionally, we annotated a total of 13,073 protein-coding genes, 18.43% (35.40 Mb) repetitive elements, and 376 non-coding RNAs. Our study is the first time to report the chromosome-scale genome for the species of A. aphidimyza. It provides a valuable genomic resource for the molecular study of A. aphidimyza.
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Affiliation(s)
- Xiuxian Shen
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, College of Agriculture, Guizhou University, Guiyang, 550025, China
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianfeng Jin
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guoqiang Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bin Yan
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Xiaofei Yu
- College of Tobacco Science, Guizhou University, Guiyang, 550025, China
| | - Huizi Wu
- Zunyi Branch of Guizhou Tobacco Company, Zunyi, 564200, China
| | - Maofa Yang
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, College of Agriculture, Guizhou University, Guiyang, 550025, China.
- College of Tobacco Science, Guizhou University, Guiyang, 550025, China.
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
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Habtewold T, Wagah M, Tambwe MM, Moore S, Windbichler N, Christophides G, Johnson H, Heaton H, Collins J, Krasheninnikova K, Pelan SE, Pointon DLB, Sims Y, Torrance JW, Tracey A, Uliano Da Silva M, Wood JMD, von Wyschetzki K, McCarthy SA, Neafsey DE, Makunin A, Lawniczak MK, Lawniczak M. A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain. Wellcome Open Res 2024; 8:74. [PMID: 37424773 PMCID: PMC10326452 DOI: 10.12688/wellcomeopenres.18854.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
We present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
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Affiliation(s)
- Tibebu Habtewold
- Department of Life Sciences, Imperial College London, London, UK
| | - Martin Wagah
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | - Mgeni Mohamed Tambwe
- Vector Control Product Testing Unit, Ifakara Health institute, Bagamoyo, Tanzania
| | - Sarah Moore
- Vector Control Product Testing Unit, Ifakara Health institute, Bagamoyo, Tanzania
- Vector Biology Unit, Swiss Tropical and Public Health Institute, Bagamoyo, Tanzania
| | | | | | - Harriet Johnson
- Scientific Operations, Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | | | | | - Ying Sims
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | | | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective
- Department of Life Sciences, Imperial College London, London, UK
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
- Vector Control Product Testing Unit, Ifakara Health institute, Bagamoyo, Tanzania
- Vector Biology Unit, Swiss Tropical and Public Health Institute, Bagamoyo, Tanzania
- Scientific Operations, Wellcome Sanger Institute, Hinxton, UK
- CSSE, Auburn University, Auburn, Alabama, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Daniel E. Neafsey
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Alex Makunin
- Tree of Life, Wellcome Sanger Institute, Hinxton, UK
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Ryazansky SS, Chen C, Potters M, Naumenko AN, Lukyanchikova V, Masri RA, Brusentsov II, Karagodin DA, Yurchenko AA, Dos Anjos VL, Haba Y, Rose NH, Hoffman J, Guo R, Menna T, Kelley M, Ferrill E, Schultz KE, Qi Y, Sharma A, Deschamps S, Llaca V, Mao C, Murphy TD, Baricheva EM, Emrich S, Fritz ML, Benoit JB, Sharakhov IV, McBride CS, Tu Z, Sharakhova MV. The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes. BMC Biol 2024; 22:16. [PMID: 38273363 PMCID: PMC10809549 DOI: 10.1186/s12915-024-01825-0] [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: 08/25/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. METHODS In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus. RESULTS We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes. CONCLUSION The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.
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Affiliation(s)
- Sergei S Ryazansky
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Molecular Genetics of Cell, NRC "Kurchatov Institute", Moscow, Russia
| | - Chujia Chen
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Mark Potters
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Anastasia N Naumenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Group of Genomic Mechanisms of Development, Institute of Cytology and Genetics, Novosibirsk, Russia
- Laboratory of Structural and Functional Genomics, Novosibirsk State University, Novosibirsk, Russia
| | - Reem A Masri
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Ilya I Brusentsov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Dmitriy A Karagodin
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Andrey A Yurchenko
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Vitor L Dos Anjos
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Jinna Hoffman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Rong Guo
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Theresa Menna
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily Ferrill
- County of San Diego Vector Control Program, San Diego, CA, USA
| | - Karen E Schultz
- Mosquito and Vector Management District of Santa Barbara County, Santa Barbara, CA, USA
| | - Yumin Qi
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | - Atashi Sharma
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
| | | | | | - Chunhong Mao
- Biocomplexity Institute & Initiative University of Virginia, Charlottesville, VA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Elina M Baricheva
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Scott Emrich
- Department of Electrical Engineering & Computer Science, the University of Tennessee, Knoxville, TN, USA
| | - Megan L Fritz
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Zhijian Tu
- Genetics, Bioinformatics, Computational Biology Program, Virginia Polytechnic and State University, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Polytechnic and State University, Blacksburg, USA
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA, USA.
- Laboratory of Cell Differentiation Mechanisms, Institute of Cytology and Genetics, Novosibirsk, Russia.
- Fralin Life Sciences Institute, Virginia Polytechnic and State University, Blacksburg, VA, USA.
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Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024; 2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [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] [Indexed: 06/01/2024]
Abstract
Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.
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Affiliation(s)
- Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Frankfurt, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ann Kathrin Huylmans
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Alun R C Jones
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Eckart Stolle
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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5
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Smith LB, Chagas AC, Martin-Martin I, Ribeiro JMC, Calvo E. An insight into the female and male Sabethes cyaneus mosquito salivary glands transcriptome. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 153:103898. [PMID: 36587808 PMCID: PMC9899327 DOI: 10.1016/j.ibmb.2022.103898] [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: 11/29/2022] [Revised: 12/26/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Mosquitoes are responsible for the death and debilitation of millions of people every year due to the pathogens they can transmit while blood feeding. While a handful of mosquitoes, namely those in the Aedes, Anopheles, and Culex genus, are the dominant vectors, many other species belonging to different genus are also involved in various pathogen cycles. Sabethes cyaneus is one of the many poorly understood mosquito species involved in the sylvatic cycle of Yellow Fever Virus. Here, we report the expression profile differences between male and female of Sa.cyaneus salivary glands (SGs). We find that female Sa.cyaneus SGs have 165 up-regulated and 18 down-regulated genes compared to male SGs. Most of the up-regulated genes have unknown functions, however, odorant binding proteins, such as those in the D7 protein family, and mucins were among the top 30 genes. We also performed various in vitro activity assays of female SGs. In the activity analysis we found that female SG extracts inhibit coagulation by blocking factor Xa and has endonuclease activity. Knowledge about mosquitoes and their physiology are important for understanding how different species differ in their ability to feed on and transmits pathogens to humans. These results provide us with an insight into the Sabethes SG activity and gene expression that expands our understanding of mosquito salivary glands.
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Affiliation(s)
- Leticia Barion Smith
- Laboratory of Malaria and Vector Research, National Institutes of Health, 12735 Twinbrook Parkway, Room 2W09, Bethesda, MD, 20892, USA
| | - Andrezza Campos Chagas
- Laboratory of Malaria and Vector Research, National Institutes of Health, 12735 Twinbrook Parkway, Room 2W09, Bethesda, MD, 20892, USA
| | - Ines Martin-Martin
- Laboratory of Malaria and Vector Research, National Institutes of Health, 12735 Twinbrook Parkway, Room 2W09, Bethesda, MD, 20892, USA
| | - Jose M C Ribeiro
- Laboratory of Malaria and Vector Research, National Institutes of Health, 12735 Twinbrook Parkway, Room 2W09, Bethesda, MD, 20892, USA
| | - Eric Calvo
- Laboratory of Malaria and Vector Research, National Institutes of Health, 12735 Twinbrook Parkway, Room 2W09, Bethesda, MD, 20892, USA.
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Liang J, Bondarenko SM, Sharakhov IV, Sharakhova MV. Visualization of the Linear and Spatial Organization of Chromosomes in Mosquitoes. Cold Spring Harb Protoc 2022; 2022:585-590. [PMID: 35960626 DOI: 10.1101/pdb.top107732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mosquitoes are vectors of dangerous human diseases such as malaria, dengue, Zika, West Nile fever, and lymphatic filariasis. Visualization of the linear and spatial organization of mosquito chromosomes is important for understanding genome structure and function. Utilization of chromosomal inversions as markers for population genetics studies yields insights into mosquito adaptation and evolution. Cytogenetic approaches assist with the development of chromosome-scale genome assemblies that are useful tools for studying mosquito biology and for designing novel vector control strategies. Fluorescence in situ hybridization is a powerful technique for localizing specific DNA sequences within the linear chromosome structure and within the spatial organization of the cell nucleus. Here, we introduce protocols used in our laboratories for chromosome visualization and their application in mosquitoes.
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Affiliation(s)
- Jiangtao Liang
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, USA
| | - Simon M Bondarenko
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, USA.,Department of Genetics and Cell Biology, Tomsk State University, Tomsk 634050, Russia
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, USA.,Department of Genetics and Cell Biology, Tomsk State University, Tomsk 634050, Russia
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, USA .,Laboratory of Evolutionary Genomics of Insects, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
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Gloria-Soria A. Special Collection: Highlights of Medical, Urban and Veterinary Entomology. Highlights in Medical Entomology, 2021. JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:1853-1860. [PMID: 36197947 DOI: 10.1093/jme/tjac063] [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: 03/14/2022] [Indexed: 06/16/2023]
Abstract
Life remained far from normal as we completed the first year of the Covid-19 pandemic and entered a second year. Despite the challenges faced worldwide, together we continue to move the field of Medical Entomology forward. Here, I reflect on parallels between control of Covid-19 and vector-borne disease control, discuss the advantages and caveats of using new genotyping technologies for the study of invasive species, and proceed to highlight papers that were published between 2020 and 2021 with a focus on those related to mosquito surveillance and population genetics of mosquito vectors.
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Affiliation(s)
- A Gloria-Soria
- Department of Environmental Sciences, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, 123 Huntington Street, New Haven, CT 06511, USA
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511, USA
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8
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Nebbak A, Almeras L, Parola P, Bitam I. Mosquito Vectors (Diptera: Culicidae) and Mosquito-Borne Diseases in North Africa. INSECTS 2022; 13:962. [PMID: 36292910 PMCID: PMC9604161 DOI: 10.3390/insects13100962] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Mosquitoes (Diptera: Culicidae) are of significant public health importance because of their ability to transmit major diseases to humans and animals, and are considered as the world's most deadly arthropods. In recent decades, climate change and globalization have promoted mosquito-borne diseases' (MBDs) geographic expansion to new areas, such as North African countries, where some of these MBDs were unusual or even unknown. In this review, we summarize the latest data on mosquito vector species distribution and MBDs affecting both human and animals in North Africa, in order to better understand the risks associated with the introduction of new invasive mosquito species such as Aedes albopictus. Currently, 26 mosquito species confirmed as pathogen vectors occur in North Africa, including Aedes (five species), Culex (eight species), Culiseta (one species) and Anopheles (12 species). These 26 species are involved in the circulation of seven MBDs in North Africa, including two parasitic infections (malaria and filariasis) and five viral infections (WNV, RVF, DENV, SINV and USUV). No bacterial diseases have been reported so far in this area. This review may guide research studies to fill the data gaps, as well as helping with developing effective vector surveillance and controlling strategies by concerned institutions in different involved countries, leading to cooperative and coordinate vector control measures.
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Affiliation(s)
- Amira Nebbak
- Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques (CRAPC), BP 384, Zone Industrielle, Bou-Ismail 42004, Algeria
| | - Lionel Almeras
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Philippe Parola
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Idir Bitam
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France
- École Supérieure en Sciences de l’Aliment et des Industries Agroalimentaire d’Alger, Oued Smar 16059, Algeria
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9
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Kojin BB, Compton A, Adelman ZN, Tu Z. Selective targeting of biting females to control mosquito-borne infectious diseases. Trends Parasitol 2022; 38:791-804. [PMID: 35952630 PMCID: PMC9372635 DOI: 10.1016/j.pt.2022.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 10/18/2022]
Abstract
Mosquitoes are vectors for a number of infectious diseases. Only females feed on blood to provision for their embryos and, in doing so, transmit pathogens to the associated vertebrate hosts. Therefore, sex is an important phenotype in the context of genetic control programs, both for sex separation in the rearing facilities to avoid releasing biting females and for ways to distort the sex ratio towards nonbiting males. We review recent progress in the fundamental knowledge of sex determination and sex chromosomes in mosquitoes and discuss new methods to achieve sex separation and sex ratio distortion to help control mosquito-borne infectious diseases. We conclude by suggesting a few critical areas for future research.
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Affiliation(s)
- Bianca B Kojin
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, TX, USA
| | - Austin Compton
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA; Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Zach N Adelman
- Department of Entomology and Agrilife Research, Texas A&M University, College Station, TX, USA.
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA; Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA.
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10
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Vitale M, Leo C, Courty T, Kranjc N, Connolly JB, Morselli G, Bamikole C, Haghighat-Khah RE, Bernardini F, Fuchs S. Comprehensive characterization of a transgene insertion in a highly repetitive, centromeric region of Anopheles mosquitoes. Pathog Glob Health 2022; 117:273-283. [PMID: 35861105 PMCID: PMC10081084 DOI: 10.1080/20477724.2022.2100192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The availability of the genomic sequence of the malaria mosquito Anopheles gambiae has in recent years sparked the development of transgenic technologies with the potential to be used as novel vector control tools. These technologies rely on genome editing that confer traits able to affect vectorial capacity. This can be achieved by either reducing the mosquito population or by making mosquitoes refractory to the parasite infection. For any genetically modified organism that is regarded for release, molecular characterization of the transgene and flanking sites are essential for their safety assessment and post-release monitoring. Despite great advancements, Whole-Genome Sequencing data are still subject to limitations due to the presence of repetitive and unannotated DNA sequences. Faced with this challenge, we describe a number of techniques that were used to identify the genomic location of a transgene in the male bias mosquito strain Ag(PMB)1 considered for potential field application. While the initial inverse PCR identified the most likely insertion site on Chromosome 3 R 36D, reassessment of the data showed a high repetitiveness in those sequences and multiple genomic locations as potential insertion sites of the transgene. Here we used a combination of DNA sequencing analysis and in-situ hybridization to clearly identify the integration of the transgene in a poorly annotated centromeric region of Chromosome 2 R 19D. This study emphasizes the need for accuracy in sequencing data for the genome of organisms of medical importance such as Anopheles mosquitoes and other tools available that can support genomic locations of transgenes.
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Affiliation(s)
- Matteo Vitale
- Department of Life Sciences, Imperial College London, London, UK
| | - Chiara Leo
- Polo d'Innovazione di Genomica, Genetica, e Biologia, Siena, Italy
| | - Thomas Courty
- Department of Infectious Diseases, King's College London, London, UK
| | - Nace Kranjc
- Department of Life Sciences, Imperial College London, London, UK
| | - John B Connolly
- Department of Life Sciences, Imperial College London, London, UK
| | - Giulia Morselli
- Department of Life Sciences, Imperial College London, London, UK
| | - Christopher Bamikole
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | | | | | - Silke Fuchs
- Department of Life Sciences, Imperial College London, London, UK
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Goel M, Schneeberger K. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics 2022; 38:2922-2926. [PMID: 35561173 PMCID: PMC9113368 DOI: 10.1093/bioinformatics/btac196] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Third-generation genome sequencing technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of multiple assembled genomes of individual species and demands new tools for visualizing their structural properties. Here, we present plotsr, an efficient tool to visualize structural similarities and rearrangements between genomes. It can be used to compare genomes on chromosome level or to zoom in on any selected region. In addition, plotsr can augment the visualization with regional identifiers (e.g. genes or genomic markers) or histogram tracks for continuous features (e.g. GC content or polymorphism density). AVAILABILITY AND IMPLEMENTATION plotsr is implemented as a python package and uses the standard matplotlib library for plotting. It is freely available under the MIT license at GitHub (https://github.com/schneebergerlab/plotsr) and bioconda (https://anaconda.org/bioconda/plotsr). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Manish Goel
- Faculty of Biology, LMU Munich, Planegg-Martinsried 82152, Germany
- Department of Genetics, Faculty of Biology, LMU Munich, Germany
| | - Korbinian Schneeberger
- Faculty of Biology, LMU Munich, Planegg-Martinsried 82152, Germany
- Department of Genetics, Faculty of Biology, LMU Munich, Germany
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12
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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13
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Lukyanchikova V, Nuriddinov M, Belokopytova P, Taskina A, Liang J, Reijnders MJMF, Ruzzante L, Feron R, Waterhouse RM, Wu Y, Mao C, Tu Z, Sharakhov IV, Fishman V. Anopheles mosquitoes reveal new principles of 3D genome organization in insects. Nat Commun 2022; 13:1960. [PMID: 35413948 PMCID: PMC9005712 DOI: 10.1038/s41467-022-29599-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. Evolutionary analysis reveals conservation of chromatin architecture within synteny blocks for tens of millions of years and enrichment of synteny breakpoints in regions with increased genomic insulation. However, in-depth analysis shows a confounding effect of gene density on both insulation and distribution of synteny breakpoints, suggesting limited causal relationship between breakpoints and regions with increased genomic insulation. At the level of individual loci, we identify specific, extremely long-ranged looping interactions, conserved for ~100 million years. We demonstrate that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin.
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Affiliation(s)
- Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Miroslav Nuriddinov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Polina Belokopytova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Alena Taskina
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Jiangtao Liang
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Yang Wu
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Department of Pathogen Biology, School of Public Health, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Chunhong Mao
- Biocomplexity Institute & Initiative, University of Virginia, Charlottesville, VA, 22911, USA
| | - Zhijian Tu
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
- Department of Genetics and Cell Biology, Tomsk State University, Tomsk, Russia.
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
- AIRI, Moscow, Russia.
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14
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Zamyatin A, Avdeyev P, Liang J, Sharma A, Chen C, Lukyanchikova V, Alexeev N, Tu Z, Alekseyev MA, Sharakhov IV. Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis. Gigascience 2021; 10:giab017. [PMID: 33718948 PMCID: PMC7957348 DOI: 10.1093/gigascience/giab017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/01/2021] [Accepted: 01/23/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Anopheles coluzzii and Anopheles arabiensis belong to the Anopheles gambiae complex and are among the major malaria vectors in sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species. FINDINGS In this study, we produced de novo chromosome-level genome assemblies for A. coluzzii and A. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 and 256.8 Mb of the total assemblies for A. coluzzii and A. arabiensis, respectively. Each assembly consists of 3 chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in A. coluzzii and A. arabiensis. CONCLUSION The new chromosome-level assemblies will facilitate functional and population genomic studies in A. coluzzii and A. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.
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Affiliation(s)
- Anton Zamyatin
- Computer Technologies Laboratory, ITMO University, Kronverkskiy Prospekt 49-A, Saint Petersburg 197101, Russia
| | - Pavel Avdeyev
- Department of Mathematics, The George Washington University, 801 22nd Street NW, Washington, DC 20052, USA
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Jiangtao Liang
- Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
| | - Atashi Sharma
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Chujia Chen
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Varvara Lukyanchikova
- Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
- Institute of Cytology and Genetics the Siberian Division of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikita Alexeev
- Computer Technologies Laboratory, ITMO University, Kronverkskiy Prospekt 49-A, Saint Petersburg 197101, Russia
| | - Zhijian Tu
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Max A Alekseyev
- Department of Mathematics, The George Washington University, 801 22nd Street NW, Washington, DC 20052, USA
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, 800 22nd Street NW, Washington, DC 20052, USA
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
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