1
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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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2
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Liang J, Bondarenko SM, Sharakhov IV, Sharakhova MV. Obtaining Polytene, Meiotic, and Mitotic Chromosomes from Mosquitoes for Cytogenetic Analysis. Cold Spring Harb Protoc 2022; 2022:591-598. [PMID: 35960616 DOI: 10.1101/pdb.prot107872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chromosome visualization is a key step for developing cytogenetic maps and idiograms, analyzing inversion polymorphisms, and identifying mosquito species. Three types of chromosomes-polytene, mitotic, and meiotic-are used in cytogenetic studies of mosquitoes. Here, we describe a detailed method for obtaining high-quality polytene chromosome preparations from the salivary glands of larvae and the ovaries of females for Anopheles mosquitoes. We also describe how to obtain mitotic chromosomes from imaginal discs of fourth-instar larvae and meiotic chromosomes from the testes of male pupae for all mosquitoes. These chromosomes can be used for fluorescence in situ hybridization (FISH), a fundamental technique in cytogenetic research that is used for physical genome mapping, detecting chromosomal rearrangements, and studying chromosome organization.
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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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3
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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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4
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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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5
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Dreyer SM, Morin KJ, Magaña M, Pott M, Leiva D, Achee NL, Grieco JP, Vaughan JA. Oral susceptibility to ivermectin is over fifty times greater in a wild population of Anopheles albimanus mosquitoes from Belize than the STECLA laboratory reference strain of this mosquito. Malar J 2022; 21:72. [PMID: 35246147 PMCID: PMC8896111 DOI: 10.1186/s12936-022-04092-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
Background The STECLA strain of Anopheles albimanus has been in continuous colony for many years and is the reference strain on which genomic studies for the species are based. Recently, the STECLA strain was demonstrated to be much less susceptible to ivermectin ingested in a blood meal (4-day LC50 of 1468 ng/ml) than all other Anopheles species tested to-date (LC50 values range from 7 to 56 ng/ml). The ability of An. albimanus to survive ingestion of ivermectin at concentrations far beyond that typically found in the blood of ivermectin-treated people or livestock (i.e., 30–70 ng/ml) could invalidate the use of ivermectin as a malaria vector control strategy in areas where An. albimanus is a primary vector. Methods To investigate this, host-seeking An. albimanus were captured in northern Belize and used in membrane feeding bioassays of ivermectin, employing the same methods as described earlier with the STECLA strain. Results Field-collected An. albimanus in Belize were 55 times more susceptible to ingested ivermectin than were the STECLA reference strain. Oral susceptibility to ivermectin in wild An. albimanus from Belize (4-day LC50 of 26 ng/ml) was equivalent to that of other Anopheles species tested. Conclusions Contrary to initial assessments using a highly inbred strain of mosquito, laboratory studies using a field population indicate that ivermectin treatment of livestock could reduce An. albimanus populations in areas of Central America and the Caribbean where malaria transmission may occur. Toxicity screening of ivermectin and other systemic parasiticides for malaria control should examine wild populations of the vector species being targeted.
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Affiliation(s)
| | | | - Marla Magaña
- Belize Vector and Ecology Center, Orange Walk Town, Belize
| | - Marie Pott
- Belize Vector and Ecology Center, Orange Walk Town, Belize
| | - Donovan Leiva
- Belize Vector and Ecology Center, Orange Walk Town, Belize
| | - Nicole L Achee
- Belize Vector and Ecology Center, Orange Walk Town, Belize.,University of Notre Dame, South Bend, IN, 46556, USA
| | - John P Grieco
- Belize Vector and Ecology Center, Orange Walk Town, Belize.,University of Notre Dame, South Bend, IN, 46556, USA
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6
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Rafael MS, Bridi LC, Sharakhov IV, Marinotti O, Sharakhova MV, Timoshevskiy V, Guimarães-Marques GM, Santos VS, da Silva CGN, Astolfi-Filho S, Tadei WP. Physical Mapping of the Anopheles ( Nyssorhynchus) darlingi Genomic Scaffolds. INSECTS 2021; 12:insects12020164. [PMID: 33671870 PMCID: PMC7918962 DOI: 10.3390/insects12020164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022]
Abstract
The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping is a useful tool for anchoring genome assemblies to mosquito chromosomes.
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Affiliation(s)
- Míriam Silva Rafael
- Coordenação de Sociedade Ambiente e Saúde, Laboratório de Vetores de Malária e Dengue, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Manaus, AM 69060-001, Brazil;
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiv, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM 69060-001, Brazil; (L.C.B.); (G.M.G.-M.); (V.S.S.)
- Correspondence: ; Tel.: +55-092-3643-3066
| | - Leticia Cegatti Bridi
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiv, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM 69060-001, Brazil; (L.C.B.); (G.M.G.-M.); (V.S.S.)
| | - Igor V. Sharakhov
- Department of Entomology and Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (I.V.S.); (M.V.S.); (V.T.)
- Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Genetics and Cell Biology, Tomsk State University, 634050 Tomsk, Russia
| | | | - Maria V. Sharakhova
- Department of Entomology and Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (I.V.S.); (M.V.S.); (V.T.)
- Laboratory of Evolutionary Genomics of Insects, the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Vladimir Timoshevskiy
- Department of Entomology and Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (I.V.S.); (M.V.S.); (V.T.)
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Giselle Moura Guimarães-Marques
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiv, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM 69060-001, Brazil; (L.C.B.); (G.M.G.-M.); (V.S.S.)
| | - Valéria Silva Santos
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiv, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM 69060-001, Brazil; (L.C.B.); (G.M.G.-M.); (V.S.S.)
| | - Carlos Gustavo Nunes da Silva
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas, Av. Rodrigo Otávio, 6.200. Coroado l, Manaus, AM 69080-900, Brazil;
| | - Spartaco Astolfi-Filho
- Laboratorio de Tecnologias de DNA, Divisão de Biotecnologia, Centro de Apoio Multidisciplinar, Universi dade Federal do Amazonas, Av. Rodrigo Otávio, 6.200. Coroado l, Manaus, AM 69080-900, Brazil;
| | - Wanderli Pedro Tadei
- Coordenação de Sociedade Ambiente e Saúde, Laboratório de Vetores de Malária e Dengue, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2936, Manaus, AM 69060-001, Brazil;
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiv, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM 69060-001, Brazil; (L.C.B.); (G.M.G.-M.); (V.S.S.)
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Masri RA, Karagodin DA, Sharma A, Sharakhova MV. A Gene-Based Method for Cytogenetic Mapping of Repeat-Rich Mosquito Genomes. INSECTS 2021; 12:138. [PMID: 33561960 PMCID: PMC7916018 DOI: 10.3390/insects12020138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 11/30/2022]
Abstract
Long-read sequencing technologies have opened up new avenues of research on the mosquito genome biology, enabling scientists to better understand the remarkable abilities of vectors for transmitting pathogens. Although new genome mapping technologies such as Hi-C scaffolding and optical mapping may significantly improve the quality of genomes, only cytogenetic mapping, with the help of fluorescence in situ hybridization (FISH), connects genomic scaffolds to a particular chromosome and chromosome band. This mapping approach is important for creating and validating chromosome-scale genome assemblies for mosquitoes with repeat-rich genomes, which can potentially be misassembled. In this study, we describe a new gene-based physical mapping approach that was optimized using the newly assembled Aedes albopictus genome, which is enriched with transposable elements. To avoid amplification of the repetitive DNA, 15 protein-coding gene transcripts were used for the probe design. Instead of using genomic DNA, complementary DNA was utilized as a template for development of the PCR-amplified probes for FISH. All probes were successfully amplified and mapped to specific chromosome bands. The genome-unique probes allowed to perform unambiguous mapping of genomic scaffolds to chromosome regions. The method described in detail here can be used for physical genome mapping in other insects.
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Affiliation(s)
- Reem A. Masri
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Dmitriy A. Karagodin
- Laboratory of Evolutionary Genomics of Insects, The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Atashi Sharma
- Department of Biochemistry and the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Maria V. Sharakhova
- Department of Entomology and the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
- Laboratory of Evolutionary Genomics of Insects, The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia;
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8
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Lezcano ÓM, Sánchez-Polo M, Ruiz JL, Gómez-Díaz E. Chromatin Structure and Function in Mosquitoes. Front Genet 2020; 11:602949. [PMID: 33365050 PMCID: PMC7750206 DOI: 10.3389/fgene.2020.602949] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/29/2020] [Indexed: 12/27/2022] Open
Abstract
The principles and function of chromatin and nuclear architecture have been extensively studied in model organisms, such as Drosophila melanogaster. However, little is known about the role of these epigenetic processes in transcriptional regulation in other insects including mosquitoes, which are major disease vectors and a worldwide threat for human health. Some of these life-threatening diseases are malaria, which is caused by protozoan parasites of the genus Plasmodium and transmitted by Anopheles mosquitoes; dengue fever, which is caused by an arbovirus mainly transmitted by Aedes aegypti; and West Nile fever, which is caused by an arbovirus transmitted by Culex spp. In this contribution, we review what is known about chromatin-associated mechanisms and the 3D genome structure in various mosquito vectors, including Anopheles, Aedes, and Culex spp. We also discuss the similarities between epigenetic mechanisms in mosquitoes and the model organism Drosophila melanogaster, and advocate that the field could benefit from the cross-application of state-of-the-art functional genomic technologies that are well-developed in the fruit fly. Uncovering the mosquito regulatory genome can lead to the discovery of unique regulatory networks associated with the parasitic life-style of these insects. It is also critical to understand the molecular interactions between the vectors and the pathogens that they transmit, which could hold the key to major breakthroughs on the fight against mosquito-borne diseases. Finally, it is clear that epigenetic mechanisms controlling mosquito environmental plasticity and evolvability are also of utmost importance, particularly in the current context of globalization and climate change.
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Affiliation(s)
| | | | - José L. Ruiz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, Granada, Spain
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9
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Luo M, Finet C, Cong H, Wei HY, Chung H. The evolution of insect metallothioneins. Proc Biol Sci 2020; 287:20202189. [PMID: 33109013 DOI: 10.1098/rspb.2020.2189] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Metallothioneins (MTs) are a family of cysteine-rich metal-binding proteins that are important in the chelating and detoxification of toxic heavy metals. Until now, the short length and the low sequence complexity of MTs have hindered the inference of robust phylogenies, hampering the study of their evolution. To address this longstanding question, we applied an iterative BLAST search pipeline that allowed us to build a unique dataset of more than 300 MT sequences in insects. By combining phylogenetics and synteny analysis, we reconstructed the evolutionary history of MTs in insects. We show that the MT content in insects has been shaped by lineage-specific tandem duplications from a single ancestral MT. Strikingly, we also uncovered a sixth MT, MtnF, in the model organism Drosophila melanogaster. MtnF evolves faster than other MTs and is characterized by a non-canonical length and higher cysteine content. Our methodological framework not only paves the way for future studies on heavy metal detoxification but can also allow us to identify other previously unidentified genes and other low complexity genomic features.
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Affiliation(s)
- Mei Luo
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA.,College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Cédric Finet
- Yale-NUS College, 16 College Avenue West, Singapore 138527, Republic of Singapore
| | - Haosu Cong
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Hong-Yi Wei
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, People's Republic of China
| | - Henry Chung
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
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10
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The Beginning of the End: A Chromosomal Assembly of the New World Malaria Mosquito Ends with a Novel Telomere. G3-GENES GENOMES GENETICS 2020; 10:3811-3819. [PMID: 32883756 PMCID: PMC7534423 DOI: 10.1534/g3.120.401654] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved. Here we produce a de novo assembly of the New World malaria mosquito, Anopheles albimanus by integrating Oxford Nanopore sequencing, Illumina, Hi-C and optical mapping. This 172.6 Mbps female assembly, which we call AalbS3, is obtained by scaffolding polished large contigs (contig N50 = 13.7 Mbps) into three chromosomes. All chromosome arms end with telomeric repeats, which is the first in mosquito assemblies and represents a significant step toward the completion of a genome assembly. These telomeres consist of tandem repeats of a novel 30-32 bp Telomeric Repeat Unit (TRU) and are confirmed by analyzing the termini of long reads and through both chromosomal in situ hybridization and a Bal31 sensitivity assay. The AalbS3 assembly included previously uncharacterized centromeric and rDNA clusters and more than doubled the content of transposable elements and other repetitive sequences. This telomere-to-telomere assembly, although still containing gaps, represents a significant step toward resolving biologically important but previously hidden genomic components. The comparison of different scaffolding methods will also inform future efforts to obtain reference-quality genomes for other mosquito species.
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11
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Compton A, Sharakhov IV, Tu Z. Recent advances and future perspectives in vector-omics. CURRENT OPINION IN INSECT SCIENCE 2020; 40:94-103. [PMID: 32650287 PMCID: PMC8041138 DOI: 10.1016/j.cois.2020.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/07/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
We have reviewed recent progress and the remaining challenges in vector-omics. We have highlighted several technologies and applications that facilitate novel biological insights beyond achieving a reference-quality genome assembly. Among other topics, we have discussed the applications of chromatin conformation capture, chromatin accessibility assays, optical mapping, full-length RNA sequencing, single cell RNA analysis, proteomics, and population genomics. We anticipate that we will witness a great expansion in vector-omics research not only in its application in a broad range of species, but also its ability to uncover novel genetic elements and tackle previously inaccessible regions of the genome. It is our hope that the continued innovation in device portability, cost reduction, and informatics support will in the foreseeable future bring vector-omics to every vector laboratory and field station in the world, which will have an unparalleled impact on basic research and the control of vector-borne infectious diseases.
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Affiliation(s)
- Austin Compton
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24061, United States
| | - Igor V Sharakhov
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24061, United States; Department of Entomology, Virginia Tech, Blacksburg, VA 24061, United States; The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States; Department of Genetics and Cell Biology, Tomsk State University, Tomsk 634050, Russia
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States; Department of Entomology, Virginia Tech, Blacksburg, VA 24061, United States; The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA 24061, United States.
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12
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Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJMF, Feron R, Bérard S, George P, Hahn MW, Howell PI, Kamali M, Koren S, Lawson D, Maslen G, Peery A, Phillippy AM, Sharakhova MV, Tannier E, Unger MF, Zhang SV, Alekseyev MA, Besansky NJ, Chauve C, Emrich SJ, Sharakhov IV. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. BMC Biol 2020; 18:1. [PMID: 31898513 PMCID: PMC6939337 DOI: 10.1186/s12915-019-0728-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/26/2019] [Indexed: 11/18/2022] Open
Abstract
Background New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. Results We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. Conclusions Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.
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Affiliation(s)
- Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
| | - Sergey Aganezov
- Department of Computer Science, Princeton University, Princeton, NJ, 08450, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
| | | | - Jiyoung Lee
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Maarten J M F Reijnders
- 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
| | - Sèverine Bérard
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Phillip George
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Matthew W Hahn
- Departments of Biology and Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Paul I Howell
- Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Maryam Kamali
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Department of Medical Entomology and Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel Lawson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Gareth Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Ashley Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia, 634050
| | - Eric Tannier
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, Unité Mixte de Recherche 5558 Centre National de la Recherche Scientifique, 69622, Villeurbanne, France.,Institut national de recherche en informatique et en automatique, Montbonnot, 38334, Grenoble, Rhône-Alpes, France
| | - Maria F Unger
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN, 46556, USA
| | - Simo V Zhang
- Departments of Biology and Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Max A Alekseyev
- Department of Mathematics and Computational Biology Institute, George Washington University, Ashburn, VA, 20147, USA
| | - Nora J Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN, 46556, USA
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Scott J Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Igor V Sharakhov
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA. .,Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA. .,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia, 634050.
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13
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Mackenzie-Impoinvil L, Weedall GD, Lol JC, Pinto J, Vizcaino L, Dzuris N, Riveron J, Padilla N, Wondji C, Lenhart A. Contrasting patterns of gene expression indicate differing pyrethroid resistance mechanisms across the range of the New World malaria vector Anopheles albimanus. PLoS One 2019; 14:e0210586. [PMID: 30699158 PMCID: PMC6353143 DOI: 10.1371/journal.pone.0210586] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/25/2018] [Indexed: 11/18/2022] Open
Abstract
Decades of unmanaged insecticide use and routine exposure to agrochemicals have left many populations of malaria vectors in the Americas resistant to multiple classes of insecticides, including pyrethroids. The molecular basis of pyrethroid resistance is relatively uncharacterised in American malaria vectors, preventing the design of suitable resistance management strategies. Using whole transcriptome sequencing, we characterized the mechanisms of pyrethroid resistance in Anopheles albimanus from Peru and Guatemala. An. albimanus were phenotyped as either deltamethrin or alpha-cypermethrin resistant. RNA from 1) resistant, 2) unexposed, and 3) a susceptible laboratory strain of An. albimanus was sequenced and analyzed using RNA-Seq. Expression profiles of the three groups were compared based on the current annotation of the An. albimanus reference genome. Several candidate genes associated with pyrethroid resistance in other malaria vectors were found to be overexpressed in resistant An. albimanus. In addition, gene ontology terms related to serine-type endopeptidase activity, extracellular activity and chitin metabolic process were also commonly overexpressed in the field caught resistant and unexposed samples from both Peru and Guatemala when compared to the susceptible strain. The cytochrome P450 CYP9K1 was overexpressed 14x in deltamethrin and 8x in alpha-cypermethrin-resistant samples from Peru and 2x in deltamethrin-resistant samples from Guatemala, relative to the susceptible laboratory strain. CYP6P5 was overexpressed 68x in deltamethrin-resistant samples from Peru but not in deltamethrin-resistant samples from Guatemala. When comparing overexpressed genes between deltamethrin-resistant and alpha-cypermethrin-resistant samples from Peru, a single P450 gene, CYP4C26, was overexpressed 9.8x (p<0.05) in alpha-cypermethrin-resistant samples. In Peruvian deltamethrin-resistant samples, the knockdown resistance mutation (kdr) variant alleles at position 1014 were rare, with approximately 5% frequency, but in the alpha-cypermethrin-resistant samples, the frequency of these alleles was approximately 15-30%. Functional validation of the candidate genes and the kdr mutation as a resistance marker for alpha-cypermethrin will confirm the role of these mechanisms in conferring pyrethroid resistance.
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Affiliation(s)
- Lucy Mackenzie-Impoinvil
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Gareth D. Weedall
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, United Kingdom
| | - Juan C. Lol
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala
| | - Jesús Pinto
- Instituto Nacional de Salud Lima, Lima, Peru
| | - Lucrecia Vizcaino
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Nicole Dzuris
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jacob Riveron
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
| | - Norma Padilla
- Centro de Estudios en Salud, Universidad del Valle de Guatemala, Guatemala
| | - Charles Wondji
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Centre for Research in Infectious Diseases (CRID), Yaoundé, Cameroon
| | - Audrey Lenhart
- Entomology Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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14
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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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15
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Sharakhova MV, Artemov GN, Timoshevskiy VA, Sharakhov IV. Physical Genome Mapping Using Fluorescence In Situ Hybridization with Mosquito Chromosomes. Methods Mol Biol 2019; 1858:177-194. [PMID: 30414118 DOI: 10.1007/978-1-4939-8775-7_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The development of genomic resources and tools is an important step in designing novel approaches to genetic control of mosquitoes. Physical genome maps enhance the quality of the genome assemblies, improve gene annotation, and provide a better framework for comparative and population genomics studies in mosquitoes. In this chapter, we describe protocols for an important procedure in physical genome mapping-fluorescence in situ hybridization (FISH). We provide details on (1) dissection of salivary glands, ovaries, and imaginal discs for obtaining high-quality polytene or mitotic chromosome preparations; (2) DNA-labeling procedures and extraction of repetitive DNA fractions; and (3) approaches to FISH on polytene and mitotic chromosomes.
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Affiliation(s)
- Maria V Sharakhova
- Department of Entomology and Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.
| | - Gleb N Artemov
- Department of Entomology and Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Vladimir A Timoshevskiy
- Department of Entomology and Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Igor V Sharakhov
- Department of Entomology and Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
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16
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Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 2018; 563:501-507. [PMID: 30429615 PMCID: PMC6421076 DOI: 10.1038/s41586-018-0692-z] [Citation(s) in RCA: 330] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 10/05/2018] [Indexed: 11/10/2022]
Abstract
Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector. An improved, fully re-annotated Aedes aegypti genome assembly (AaegL5) provides insights into the sex-determining M locus, chemosensory systems that help mosquitoes to hunt humans and loci involved in insecticide resistance and will help to generate intervention strategies to fight this deadly disease vector.
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Affiliation(s)
- Benjamin J Matthews
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA. .,Howard Hughes Medical Institute, New York, NY, USA. .,Kavli Neural Systems Institute, New York, NY, USA.
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA
| | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Igor Antoshechkin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - William J Glassford
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Margaret Herre
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.,Kavli Neural Systems Institute, New York, NY, USA
| | - Seth N Redmond
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Noah H Rose
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Gareth D Weedall
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK.,Liverpool John Moores University, Liverpool, UK
| | - Yang Wu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China.,Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Sanjit S Batra
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA
| | - Carlos A Brito-Sierra
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Steven D Buckingham
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | - Corey L Campbell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Saki Chan
- Bionano Genomics, San Diego, CA, USA
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin R Evans
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Thanyalak Fansiri
- Vector Biology and Control Section, Department of Entomology, Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Igor Filipović
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Albin Fontaine
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Unité de Parasitologie et Entomologie, Département des Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France.,Aix Marseille Université, IRD, AP-HM, SSA, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), IHU - Méditerranée Infection, Marseille, France
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | | | - Vinita S Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew K Jones
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Raissa G G Kay
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | - Gareth J Lycett
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | | | - Michael R Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Arina D Omer
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA
| | - Frederick A Partridge
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | | | - Aviva Presser Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Bioengineering, Rice University, Houston, TX, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Vidya Ramasamy
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Gordana Rašić
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sourav Roy
- Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Karla Saavedra-Rodriguez
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Shruti Sharan
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - Atashi Sharma
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA
| | | | - Joe Turner
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | | | - Zhilei Zhao
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Omar S Akbari
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, USA
| | - William C Black
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Han Cao
- Bionano Genomics, San Diego, CA, USA
| | - Alistair C Darby
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Catherine A Hill
- Department of Entomology, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Alexander S Raikhel
- Department of Entomology, Center for Disease Vector Research and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - David B Sattelle
- Centre for Respiratory Biology, UCL Respiratory, University College London, London, UK
| | - Igor V Sharakhov
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | | | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Computer Science, Rice University, Houston, TX, USA.,Center for Theoretical and Biological Physics, Rice University, Houston, TX, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard S Mann
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2000, Paris, France
| | - Jeffrey R Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Maria V Sharakhova
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Department of Entomology, Virginia Tech, Blacksburg, VA, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Zhijian Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | | | | | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology and Infectious Disease, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Adam M Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leslie B Vosshall
- Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA.,Kavli Neural Systems Institute, New York, NY, USA
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17
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The Development of Cytogenetic Maps for Malaria Mosquitoes. INSECTS 2018; 9:insects9030121. [PMID: 30227611 PMCID: PMC6164047 DOI: 10.3390/insects9030121] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/13/2018] [Accepted: 09/13/2018] [Indexed: 11/20/2022]
Abstract
Anopheline mosquitoes are important vectors of human malaria. Next-generation sequencing opens new opportunities for studies of mosquito genomes to uncover the genetic basis of a Plasmodium transmission. Physical mapping of genome sequences to polytene chromosomes significantly improves reference assemblies. High-resolution cytogenetic maps are essential for anchoring genome sequences to chromosomes as well as for studying breakpoints of chromosome rearrangements and chromatin protein localization. Here we describe a detailed pipeline for the development of high-resolution cytogenetic maps using polytene chromosomes of malaria mosquitoes. We apply this workflow to the refinement of the cytogenetic map developed for Anopheles beklemishevi.
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18
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Artemov GN, Velichevskaya AI, Bondarenko SM, Karagyan GH, Aghayan SA, Arakelyan MS, Stegniy VN, Sharakhov IV, Sharakhova MV. A standard photomap of the ovarian nurse cell chromosomes for the dominant malaria vector in Europe and Middle East Anopheles sacharovi. Malar J 2018; 17:276. [PMID: 30060747 PMCID: PMC6065146 DOI: 10.1186/s12936-018-2428-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/25/2018] [Indexed: 08/10/2023] Open
Abstract
Background Anopheles sacharovi is a dominant malaria vector species in South Europe and the Middle East which has a highly plastic behaviour at both adult and larval stages. Such plasticity has prevented this species from eradication by several anti-vector campaigns. The development of new genome-based strategies for vector control will benefit from genome sequencing and physical chromosome mapping of this mosquito. Although a cytogenetic photomap for chromosomes from salivary glands of An. sacharovi has been developed, no cytogenetic map suitable for physical genome mapping is available. Methods Mosquitoes for this study were collected at adult stage in animal shelters in Armenia. Polytene chromosome preparations were prepared from ovarian nurse cells. Fluorescent in situ hybridization (FISH) was performed using PCR amplified probes. Results This study constructed a high-quality standard photomap for polytene chromosomes from ovarian nurse cells of An. sacharovi. Following the previous nomenclature, chromosomes were sub-divided into 39 numbered and 119 lettered sub-divisions. Chromosomal landmarks for the chromosome recognition were described. Using FISH, 4 PCR-amplified genic probes were mapped to the chromosomes. The positions of the probes demonstrated gene order reshuffling between An. sacharovi and Anopheles atroparvus which has not been seen cytologically. In addition, this study described specific chromosomal landmarks that can be used for the cytotaxonomic diagnostics of An. sacharovi based on the banding pattern of its polytene chromosomes. Conclusions This study constructed a high-quality standard photomap for ovarian nurse cell chromosomes of An. sacharovi and validated its utility for physical genome mapping. Based on the map, cytotaxonomic features for identification of An. sacharovi have been described. The cytogenetic map constructed in this study will assist in creating a chromosome-based genome assembly for this mosquito and in developing cytotaxonomic tools for identification of other species from the Maculipennis group.
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Affiliation(s)
- Gleb N Artemov
- Laboratory of Ecology, Genetics and Environment Protection, Tomsk State University, Tomsk, Russia
| | - Alena I Velichevskaya
- Laboratory of Ecology, Genetics and Environment Protection, Tomsk State University, Tomsk, Russia
| | - Semen M Bondarenko
- Laboratory of Ecology, Genetics and Environment Protection, Tomsk State University, Tomsk, Russia
| | - Gayane H Karagyan
- Scientific Center of Zoology and Hydroecology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Sargis A Aghayan
- Scientific Center of Zoology and Hydroecology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia.,Chair of Zoology, Yerevan State University, Yerevan, Armenia
| | | | - Vladimir N Stegniy
- Laboratory of Ecology, Genetics and Environment Protection, Tomsk State University, Tomsk, Russia
| | - Igor V Sharakhov
- Laboratory of Ecology, Genetics and Environment Protection, Tomsk State University, Tomsk, Russia. .,Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.
| | - Maria V Sharakhova
- Laboratory of Ecology, Genetics and Environment Protection, Tomsk State University, Tomsk, Russia. .,Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.
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19
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Anselmetti Y, Duchemin W, Tannier E, Chauve C, Bérard S. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes. BMC Genomics 2018; 19:96. [PMID: 29764366 PMCID: PMC5954271 DOI: 10.1186/s12864-018-4466-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. Results We present a computational method, ADseq, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADseq provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADseq to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. Conclusions We demonstrate the method’s ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression. Electronic supplementary material The online version of this article (10.1186/s12864-018-4466-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoann Anselmetti
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France
| | - Wandrille Duchemin
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France.,INRIA Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France
| | - Eric Tannier
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, 43 Boulevard du 11 novembre 1918, Villeurbanne cedex, 69622, France.,INRIA Grenoble - Rhône-Alpes, 655 Avenue de l'Europe, Montbonnot-Saint-Martin, 38330, France
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, V5A1S6, BC, Canada
| | - Sèverine Bérard
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.
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20
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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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21
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Artemov GN, Gordeev MI, Kokhanenko AA, Moskaev AV, Velichevskaya AI, Stegniy VN, Sharakhov IV, Sharakhova MV. A standard photomap of ovarian nurse cell chromosomes and inversion polymorphism in Anopheles beklemishevi. Parasit Vectors 2018; 11:211. [PMID: 29587834 PMCID: PMC5870207 DOI: 10.1186/s13071-018-2657-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/17/2018] [Indexed: 11/23/2022] Open
Abstract
Background Anopheles beklemishevi is a member of the Maculipennis group of malaria mosquitoes that has the most northern distribution among other members of the group. Although a cytogenetic map for the larval salivary gland chromosomes of this species has been developed, a high-quality standard cytogenetic photomap that enables genomics and population genetics studies of this mosquito at the adult stage is still lacking. Methods In this study, a cytogenetic map for the polytene chromosomes of An. beklemishevi from ovarian nurse cells was developed using high-resolution digital imaging from field collected mosquitoes. PCR-amplified DNA probes for fluorescence in situ hybridization (FISH) were designed based on the genome of An. atroparvus. The DNA probe obtained by microdissection procedures from the breakpoint region was labelled in a DOP-PCR reaction. Population analysis was performed on 371 specimens collected in 18 locations. Results We report the development of a high-quality standard photomap for the polytene chromosomes from ovarian nurse cells of An. beklemishevi. To confirm the suitability of the map for physical mapping, several PCR-amplified probes were mapped to the chromosomes of An. beklemishevi using FISH. In addition, we identified and mapped DNA probes to flanking regions of the breakpoints of two inversions on chromosome X of this species. Inversion polymorphism was determined in 13 geographically distant populations of An. beklemishevi. Four polymorphic inversions were detected. The positions of common chromosomal inversions were indicated on the map. Conclusions The study constructed a standard photomap for ovarian nurse cell chromosomes of An. beklemishevi and tested its suitability for physical genome mapping and population studies. Cytogenetic analysis determined inversion polymorphism in natural populations of An. beklemishevi related to this species’ adaptation. Electronic supplementary material The online version of this article (10.1186/s13071-018-2657-3) 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, Tomsk, Russia
| | - Mikhail I Gordeev
- Department of General Biology and Ecology, Moscow Regional State University, Moscow, Russia
| | - Alina A Kokhanenko
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Anton V Moskaev
- Department of General Biology and Ecology, Moscow Regional State University, Moscow, Russia
| | - Alena I Velichevskaya
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Vladimir N Stegniy
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Igor V Sharakhov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia. .,Virginia Tech, Department of Entomology, Fralin Life Science Institute, Blacksburg, VA, USA.
| | - Maria V Sharakhova
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia. .,Virginia Tech, Department of Entomology, Fralin Life Science Institute, Blacksburg, VA, USA.
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22
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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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23
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Wei Y, Cheng B, Zhu G, Shen D, Liang J, Wang C, Wang J, Tang J, Cao J, Sharakhov IV, Xia A. Comparative physical genome mapping of malaria vectors Anopheles sinensis and Anopheles gambiae. Malar J 2017; 16:235. [PMID: 28583133 PMCID: PMC5460330 DOI: 10.1186/s12936-017-1888-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/31/2017] [Indexed: 11/29/2022] Open
Abstract
Background Anopheles sinensis is a dominant natural vector of Plasmodium vivax in China, Taiwan, Japan, and Korea. Recent genome sequencing of An. sinensis provides important insights into the genomic basis of vectorial capacity. However, the lack of a physical genome map with chromosome assignment and orientation of sequencing scaffolds hinders comparative analyses with other genomes to infer evolutionary changes relevant to the vector capacity. Results Here, a physical genome map for An. sinensis was constructed by assigning 52 scaffolds onto the chromosomes using fluorescence in situ hybridization (FISH). This chromosome-based genome assembly composes approximately 36% of the total An. sinensis genome. Comparisons of 3955 orthologous genes between An. sinensis and Anopheles gambiae identified 361 conserved synteny blocks and 267 inversions fixed between these two lineages. The rate of gene order reshuffling on the X chromosome is approximately 3.2 times higher than that on the autosomes. Conclusions The physical map will facilitate detailed genomic analysis of An. sinensis and contribute to understanding of the patterns and mechanisms of large-scale genome rearrangements in anopheline mosquitoes. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-1888-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yun Wei
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Biao Cheng
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Guoding Zhu
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, China
| | - Danyu Shen
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Jiangtao Liang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Cong Wang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Jing Wang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Jianxia Tang
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, China
| | - Jun Cao
- Key Laboratory of National Health and Family Planning Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, China
| | - Igor V Sharakhov
- Department of Entomology, Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA.,Laboratory for Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia
| | - Ai Xia
- Department of Entomology, Nanjing Agricultural University, Nanjing, China.
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