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Soboleva ES, Kirilenko KM, Fedorova VS, Kokhanenko AA, Artemov GN, Sharakhov IV. Two Nested Inversions in the X Chromosome Differentiate the Dominant Malaria Vectors in Europe, Anopheles atroparvus and Anopheles messeae. INSECTS 2024; 15:312. [PMID: 38786868 PMCID: PMC11122324 DOI: 10.3390/insects15050312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
The Maculipennis subgroup of malaria mosquitoes includes both dominant malaria vectors and non-vectors in Eurasia. Understanding the genetic factors, particularly chromosomal inversions, that differentiate Anopheles species can provide valuable insights for vector control strategies. Although autosomal inversions between the species in this subgroup have been characterized based on the chromosomal banding patterns, the number and positions of rearrangements in the X chromosome remain unclear due to the divergent banding patterns. Here, we identified two large X chromosomal inversions, approximately 13 Mb and 10 Mb in size, using fluorescence in situ hybridization. The inversion breakpoint regions were mapped by hybridizing 53 gene markers with polytene chromosomes of An. messeae. The DNA probes were designed based on gene sequences from the annotated An. atroparvus genome. The two nested inversions resulted in five syntenic blocks. Only two small syntenic blocks, which encompass 181 annotated genes in the An. atroparvus genome, changed their position and orientation in the X chromosome. The analysis of the An. atroparvus genome revealed an enrichment of gene ontology terms associated with immune system and mating behavior in the rearranged syntenic blocks. Additionally, the enrichment of DNA transposons was found in sequences homologous to three of the four breakpoint regions. This study demonstrates the successful application of the physical genome mapping approach to identify rearrangements that differentiate species in insects with polytene chromosomes.
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Affiliation(s)
- Evgenia S. Soboleva
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Kirill M. Kirilenko
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Valentina S. Fedorova
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Alina A. Kokhanenko
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Gleb N. Artemov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
| | - Igor V. Sharakhov
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
- Department of Entomology, the Fralin Life Sciences Institute, Virginia Polytechnic Institute and State University, 360 West Campus Drive, Blacksburg, VA 24061, USA
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Olatunji G, Kokori E, Kwape JM, Olatunji D, Anthony CS, Ogieuhi IJ, Damian JU, Abraham IC, Igwe SC, Alabi O, Aderinto N. Anopheles stephensi and the impending challenge to malaria eradication in Africa. New Microbes New Infect 2024; 58:101232. [PMID: 38425456 PMCID: PMC10901900 DOI: 10.1016/j.nmni.2024.101232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Gbolahan Olatunji
- Department of Medicine and Surgery, University of Ilorin, Ilorin, Nigeria
| | - Emmanuel Kokori
- Department of Medicine and Surgery, University of Ilorin, Ilorin, Nigeria
| | | | - Doyin Olatunji
- Department of Health Sciences, Western Illinois University, USA
| | | | | | | | | | | | | | - Nicholas Aderinto
- Department of Medicine and Surgery, Ladoke, Akintola University Teaching Hospital, Ogbomoso, Nigeria
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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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Alencar RM, Sepulveda CCP, Martinez-Villegas L, Bahia AC, Santana RA, de Souza IB, D'Elia GMA, Duarte APM, de Lacerda MVG, Monteiro WM, Secundino NFC, Pimenta PFP, Koerich LB. Unravelling the genome of the brackish water malaria vector Anopheles aquasalis. Sci Rep 2023; 13:20472. [PMID: 37993652 PMCID: PMC10665375 DOI: 10.1038/s41598-023-47830-1] [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: 02/09/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
Malaria is a severe public health problem in several developing tropical and subtropical countries. Anopheles aquasalis is the primary coastal malaria vector in Central and South America and the Caribbean Islands, and it has the peculiar feature of living in water with large changes in salinity. Recent research has recognised An. aquasalis as an important model for studying the interactions of murine and human Plasmodium parasites. This study presents the complete genome of An. aquasalis and offers insights into its evolution and physiology. The genome is similar in size and gene content to other Neotropical anophelines, with 162 Mb and 12,446 protein-coding genes. There are 1387 single-copy orthologs at the Diptera level (eg. An. gambiae, An. darlingi and Drosophila melanogaster). An. aquasalis diverged from An. darlingi, the primary malaria vector in inland South America, nearly 20 million years ago. Proteins related to ion transport and metabolism belong to the most abundant gene families with 660 genes. We identified gene families relevant to osmosis control (e.g., aquaporins, vacuolar-ATPases, Na+/K+-ATPases, and carbonic anhydrases). Evolutionary analysis suggests that all osmotic regulation genes are under strong purifying selection. We also observed low copy number variation in insecticide resistance and immunity-related genes for all known classical pathways. The data provided by this study offers candidate genes for further studies of parasite-vector interactions and for studies on how anophelines of brackish water deal with the high fluctuation in water salinity. We also established data and insights supporting An. aquasalis as an emerging Neotropical malaria vector model for genetic and molecular studies.
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Affiliation(s)
- Rodrigo Maciel Alencar
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Cesar Camilo Prado Sepulveda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Luis Martinez-Villegas
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
| | - Ana Cristina Bahia
- Laboratório de Bioquímica de Insetos e Parasitos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, CEP 21.941-170, Brazil
| | - Rosa Amélia Santana
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisa Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas, CEP 69.027-070, Brazil
| | - Igor Belém de Souza
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Gigliola Mayara Ayres D'Elia
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Ana Paula Marques Duarte
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Marcus Vinicius Guimarães de Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisa Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas, CEP 69.027-070, Brazil
- University of Texas Medical Branch, Galveston, United States of America
| | - Wuelton Marcelo Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Nágila Francinete Costa Secundino
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
| | - Paulo Filemon Paolucci Pimenta
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil.
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil.
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil.
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil.
| | - Leonardo Barbosa Koerich
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 31.270-901, Brazil.
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Ghosh C, Kumar N, Kushwah RBS, M. S, Joshi SG, Ramanjini CK, Alalamath T, Srinivasan S, Subramani S, Kumar S, Swain S. Enrichment of phenotype among biological forms of Anopheles stephensi Liston through establishment of isofemale lines. Parasit Vectors 2023; 16:79. [PMID: 36855157 PMCID: PMC9976541 DOI: 10.1186/s13071-023-05696-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Vector management programs rely on knowledge of the biology and genetic make-up of mosquitoes. Anopheles stephensi is a major invasive urban malaria vector, distributed throughout the Indian subcontinent and Middle East, and has recently been expanding its range in Africa. With the existence of three biological forms, distinctly identifiable based on the number of ridges on eggs and varying vectorial competence, An. stephensi is a perfect species for developing isofemale lines, which can be tested for insecticide susceptibility and vectorial competence of various biological forms. METHODS We describe key steps involved in establishment and validation of isofemale lines. Isofemale colonies were further used for the characterization of insecticide susceptibility and differential vector competence. The results were statistically evaluated through descriptive and inferential statistics using Vassar Stat and Prism GraphPad software packages. RESULTS Through a meticulous selection process, we overcame an initial inbreeding depression and found no significant morphometric differences in wings and egg size between the parental and respective isofemale lines in later generations. IndCh and IndInt strains showed variations in resistance to different insecticides belonging to all four major classes. We observed a significant change in vectorial competence between the respective isofemale and parental lines. CONCLUSIONS Isofemale lines can be a valuable resource for characterizing and enhancing several genotypic and phenotypic traits. This is the first detailed report of the establishment of two isofemale lines of type and intermediate biological forms in Anopheles stephensi. The work encompasses characterization of fitness traits among two lines through a transgenerational study. Furthermore, isofemale colonies were established and used to characterize insecticide susceptibility and vector competence. The study provides valuable insights into differential susceptibility status of the parental and isofemale lines to different insecticides belonging to the same class. Corroborating an earlier hypothesis, we demonstrate the high vector competence of the type form relative to the intermediate form using homozygous lines. Using these lines, it is now possible to study host-parasite interactions and identify factors that might be responsible for altered susceptibility and increased vector competence in An. stephensi biological forms that would also pave the way for developing better vector management strategies.
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Affiliation(s)
- Chaitali Ghosh
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society, Centre at inStem-GKVK Campus, Bellary Road, Bangalore, 560065 India
| | - Naveen Kumar
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society, Centre at inStem-GKVK Campus, Bellary Road, Bangalore, 560065 India
| | - Raja Babu Singh Kushwah
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society, Centre at inStem-GKVK Campus, Bellary Road, Bangalore, 560065 India ,grid.264756.40000 0004 4687 2082Present Address: Department of Entomology, Texas A&M University, College Station, TX 7845 USA
| | - Soumya M.
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society, Centre at inStem-GKVK Campus, Bellary Road, Bangalore, 560065 India
| | - Soumya Gopal Joshi
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society, Centre at inStem-GKVK Campus, Bellary Road, Bangalore, 560065 India
| | - Chethan Kumar Ramanjini
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society, Centre at inStem-GKVK Campus, Bellary Road, Bangalore, 560065 India
| | - Tejashwini Alalamath
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Phase I, Bangalore, 560100 India
| | - Subhashini Srinivasan
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City, Phase I, Bangalore, 560100 India
| | - Suresh Subramani
- grid.266100.30000 0001 2107 4242University of California San Diego, La Jolla, CA 92093 USA
| | - Sampath Kumar
- Tata Institute for Genetics and Society, Centre at inStem-GKVK Campus, Bellary Road, Bangalore, 560065, India.
| | - Sunita Swain
- Tata Institute for Genetics and Society, Centre at inStem-GKVK Campus, Bellary Road, Bangalore, 560065, India.
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Venkataraman K, Shai N, Lakhiani P, Zylka S, Zhao J, Herre M, Zeng J, Neal LA, Molina H, Zhao L, Vosshall LB. Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought. eLife 2023; 12:e80489. [PMID: 36744865 PMCID: PMC10076016 DOI: 10.7554/elife.80489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 01/29/2023] [Indexed: 02/07/2023] Open
Abstract
Female Aedes aegypti mosquitoes impose a severe global public health burden as vectors of multiple viral pathogens. Under optimal environmental conditions, Aedes aegypti females have access to human hosts that provide blood proteins for egg development, conspecific males that provide sperm for fertilization, and freshwater that serves as an egg-laying substrate suitable for offspring survival. As global temperatures rise, Aedes aegypti females are faced with climate challenges like intense droughts and intermittent precipitation, which create unpredictable, suboptimal conditions for egg-laying. Here, we show that under drought-like conditions simulated in the laboratory, females retain mature eggs in their ovaries for extended periods, while maintaining the viability of these eggs until they can be laid in freshwater. Using transcriptomic and proteomic profiling of Aedes aegypti ovaries, we identify two previously uncharacterized genes named tweedledee and tweedledum, each encoding a small, secreted protein that both show ovary-enriched, temporally-restricted expression during egg retention. These genes are mosquito-specific, linked within a syntenic locus, and rapidly evolving under positive selection, raising the possibility that they serve an adaptive function. CRISPR-Cas9 deletion of both tweedledee and tweedledum demonstrates that they are specifically required for extended retention of viable eggs. These results highlight an elegant example of taxon-restricted genes at the heart of an important adaptation that equips Aedes aegypti females with 'insurance' to flexibly extend their reproductive schedule without losing reproductive capacity, thus allowing this species to exploit unpredictable habitats in a changing world.
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Affiliation(s)
- Krithika Venkataraman
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Nadav Shai
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Priyanka Lakhiani
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
- Laboratory of Evolutionary Genetics and Genomics, Rockefeller UniversityNew YorkUnited States
| | - Sarah Zylka
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Jieqing Zhao
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Margaret Herre
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
- Kavli Neural Systems InstituteNew YorkUnited States
| | - Joshua Zeng
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Lauren A Neal
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Henrik Molina
- Proteomics Resource Center, Rockefeller UniversityNew YorkUnited States
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, Rockefeller UniversityNew YorkUnited States
| | - Leslie B Vosshall
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Kavli Neural Systems InstituteNew YorkUnited States
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7
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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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8
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Surendran SN, Kesavan L, Jayadas TTP, Sivabalakrishnan K, Tharsan A, Liyanagedara N, Eswaramohan T, Raveendran S, Singh OP, Ramasamy R. Morphological and odorant-binding protein 1 gene intron 1 sequence variations in Anopheles stephensi from Jaffna city in northern Sri Lanka. MEDICAL AND VETERINARY ENTOMOLOGY 2022; 36:496-502. [PMID: 35838413 DOI: 10.1111/mve.12595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Three Anopheles stephensi biotypes have historically been differentiated through variations in the mode numbers of egg ridges and adult spiracular indices. Anopheles stephensi odorant-binding protein 1 gene (AsteObp1) sequences in Iran and Afghanistan have been recently interpreted to suggest that the three biotypes are sibling species. AsteObp1 intron 1 sequences, mode numbers of egg ridges and spiracular indices of An. stephensi in Jaffna city in Sri Lanka were therefore investigated in field-collected mosquitoes and short-term laboratory colonies established from them. AsteObp1 intron 1 sequences revealed the region to be polymorphic with four unique sequences, ASJF1-4, present in both short-term laboratory colonies and field-collected An. stephensi. The spiracular index did not relate to the mode number of egg ridges in Jaffna An. stephensi. The results suggested that numbers of egg ridges, spiracular indices and AsteObp1 intron 1 sequences were not useful for differentiating An. stephensi biotypes in Jaffna. It is proposed that the observed differences between An. stephensi mosquitoes in Jaffna now result from normal population variance in the context of rapidly changing bionomics in India and northern Sri Lanka.
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Affiliation(s)
| | - Laxshi Kesavan
- Department of Zoology, University of Jaffna, Jaffna, Sri Lanka
| | | | | | | | | | | | | | - Om P Singh
- National Institute of Malaria Research, Dwarka, New Delhi, India
| | - Ranjan Ramasamy
- Department of Zoology, University of Jaffna, Jaffna, Sri Lanka
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9
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Srinivasan S, Ghosh C, Das S, Thakare A, Singh S, Ganesh A, Mahawar H, Jaisimha A, Krishna M, Chattopadhyay A, Borah R, Singh V, M S, Kumar N, Kumar S, Swain S, Subramani S. Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance. Sci Rep 2022; 12:19079. [PMID: 36351999 PMCID: PMC9646898 DOI: 10.1038/s41598-022-23780-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. Anopheles stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, were reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in the IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a tumor necrosis factor-alpha (TNF-alpha) like gene, which is the homolog of the Eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of Wengen (Wgn) and Grindelwald (Grnd) genes, which are known to be the receptors for Eiger in Drosophila. We have identified all the genes in IndInt required for Eiger-mediated signaling by analogy to the TNF-alpha system, suggesting the presence of a functionally-active Eiger signaling pathway in IndInt. Comparative genomics of the three type-forms with that of IndInt, reveals structurally disruptive mutations in Eiger gene in all three strains of the type-form, suggesting compromised innate immunity in the type-form as the likely cause of high vectorial capacity in these strains. This is the first report of the presence of a homolog of Eiger in malaria vectors, known to be involved in cell death in Drosophila, within an inversion region in IndInt syntenic to an inversion associated with Plasmodium resistance in An. gambiae.
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Affiliation(s)
- Subhashini Srinivasan
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Chaitali Ghosh
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society (TIGS), Center at inStem, Bellary Road, GKVK Campus, Bengaluru, 560065 India
| | - Shrestha Das
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Aditi Thakare
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Siddharth Singh
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Apoorva Ganesh
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Harsh Mahawar
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Aadhya Jaisimha
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Mohanapriya Krishna
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Aritra Chattopadhyay
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Rishima Borah
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Vikrant Singh
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bengaluru, 560100 India
| | - Soumya M
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society (TIGS), Center at inStem, Bellary Road, GKVK Campus, Bengaluru, 560065 India
| | - Naveen Kumar
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society (TIGS), Center at inStem, Bellary Road, GKVK Campus, Bengaluru, 560065 India
| | - Sampath Kumar
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society (TIGS), Center at inStem, Bellary Road, GKVK Campus, Bengaluru, 560065 India
| | - Sunita Swain
- grid.508203.c0000 0004 9410 4854Tata Institute for Genetics and Society (TIGS), Center at inStem, Bellary Road, GKVK Campus, Bengaluru, 560065 India
| | - Suresh Subramani
- grid.266100.30000 0001 2107 4242TIGS, University of California San Diego, La Jolla, CA 92093 USA
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10
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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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11
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Pathak AK, Shiau JC, Franke-Fayard B, Shollenberger LM, Harn DA, Kyle DE, Murdock CC. Streamlining sporozoite isolation from mosquitoes by leveraging the dynamics of migration to the salivary glands. Malar J 2022; 21:264. [PMID: 36100902 PMCID: PMC9472382 DOI: 10.1186/s12936-022-04270-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/12/2022] [Indexed: 12/05/2022] Open
Abstract
Background Sporozoites isolated from the salivary glands of Plasmodium-infected mosquitoes are a prerequisite for several basic and pre-clinical applications. Although salivary glands are pooled to maximize sporozoite recovery, insufficient yields pose logistical and analytical hurdles; thus, predicting yields prior to isolation would be valuable. Preceding oocyst densities in the midgut is an obvious candidate. However, it is unclear whether current understanding of its relationship with sporozoite densities can be used to maximize yields, or whether it can capture the potential density-dependence in rates of sporozoite invasion of the salivary glands. Methods This study presents a retrospective analysis of Anopheles stephensi mosquitoes infected with two strains of the rodent-specific Plasmodium berghei. Mean oocyst densities were estimated in the midguts earlier in the infection (11–15 days post-blood meal), with sporozoites pooled from the salivary glands later in the infection (17–29 days). Generalized linear mixed effects models were used to determine if (1) mean oocyst densities can predict sporozoite yields from pooled salivary glands, (2) whether these densities can capture differences in rates of sporozoite invasion of salivary glands, and (3), if the interaction between oocyst densities and time could be leveraged to boost overall yields. Results The non-linear effect of mean oocyst densities confirmed the role of density-dependent constraints in limiting yields beyond certain oocyst densities. Irrespective of oocyst densities however, the continued invasion of salivary glands by the sporozoites boosted recoveries over time (17–29 days post-blood meal) for either parasite strain. Conclusions Sporozoite invasion of the salivary glands over time can be leveraged to maximize yields for P. berghei. In general, however, invasion of the salivary glands over time is a critical fitness determinant for all Plasmodium species (extrinsic incubation period, EIP). Thus, delaying sporozoite collection could, in principle, substantially reduce dissection effort for any parasite within the genus, with the results also alluding to the potential for changes in sporozoites densities over time to modify infectivity for the next host. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04270-y.
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12
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Singh OP, Mishra S, Sharma G, Sindhania A, Kaur T, Sreehari U, Das MK, Kapoor N, Gupta B. Evaluation of intron-1 of odorant-binding protein-1 of Anopheles stephensi as a marker for the identification of biological forms or putative sibling species. PLoS One 2022; 17:e0270760. [PMID: 35862377 PMCID: PMC9302840 DOI: 10.1371/journal.pone.0270760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Anopheles stephensi, an invasive malaria vector, has been reported to have three biological forms identifiable mainly based on the number of ridges present on the egg's floats. Recently, the first intron of the odorant-binding protein-1 (AsteObp1) has been introduced as a molecular marker for the identification of these forms, and based on this marker, the presence of three putative sibling species (designated as species A, B and C) has been proposed. However, there is no data on the association of proposed markers with biological form or putative species on field populations. METHODS Field collected and laboratory-reared An. stephensi were characterized for biological forms based on the number of ridges on the egg's float. DNA sequencing of the partial AsteObp1 gene of An. stephensi individuals were performed by Sanger's method, either directly or after cloning with a plasmid vector. Additionally, AsteObp1 sequences of various laboratory lines of An. stephensi were retrieved from a public sequence database. RESULTS AsteObp1 intron-1 in Indian An. stephensi populations are highly polymorphic with the presence of more than 13 haplotypes exhibiting nucleotides as well as length-polymorphism (90-to-121 bp). No specific haplotype or a group of closely related haplotypes of intron-1 was found associated with any biological form identified morphologically. High heterozygosity for this marker with a low inbreeding coefficient in field and laboratory populations indicates that this marker is not suitable for the delimitation of putative sibling species, at least in Indian populations. CONCLUSIONS AsteObp1 cannot serve as a marker for identifying biological forms of An. stephensi or putative sibling species in Indian populations.
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Affiliation(s)
- Om P. Singh
- National Institute of Malaria Research, Dwarka, New Delhi, India
- * E-mail: ,
| | - Shobhna Mishra
- National Institute of Malaria Research, Dwarka, New Delhi, India
| | - Gunjan Sharma
- National Institute of Malaria Research, Dwarka, New Delhi, India
| | - Ankita Sindhania
- National Institute of Malaria Research, Dwarka, New Delhi, India
| | - Taranjeet Kaur
- National Institute of Malaria Research, Dwarka, New Delhi, India
| | - U. Sreehari
- National Institute of Malaria Research, Field Unit, Bengaluru, India
| | - Manoj K. Das
- National Institute of Malaria Research, Field Unit, Ranchi, India
| | - Neera Kapoor
- School of Sciences, Indira Gandhi National Open University, Maidangarhi, New Delhi, India
| | - Bhavna Gupta
- Vector Control Research Centre, Field Station, Madurai, India
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13
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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: 2] [Impact Index Per Article: 1.0] [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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14
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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] [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. Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehensively characterize chromatin architecture and its evolutionary dynamics in five Anopheles species.
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15
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The genome trilogy of Anopheles stephensi, an urban malaria vector, reveals structure of a locus associated with adaptation to environmental heterogeneity. Sci Rep 2022; 12:3610. [PMID: 35246568 PMCID: PMC8897464 DOI: 10.1038/s41598-022-07462-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 02/15/2022] [Indexed: 12/31/2022] Open
Abstract
Anopheles stephensi is the most menacing malaria vector to watch for in newly urbanising parts of the world. Its fitness is reported to be a direct consequence of the vector adapting to laying eggs in over-head water tanks with street-side water puddles polluted by oil and sewage. Large frequent inversions in the genome of malaria vectors are implicated in adaptation. We report the genome assembly of a strain of An. stephensi of the type-form, collected from a construction site from Chennai (IndCh) in 2016. The genome reported here with a L50 of 4, completes the trilogy of high-resolution genomes of strains with respect to a 16.5 Mbp 2Rb genotype in An. stephensi known to be associated with adaptation to environmental heterogeneity. Unlike the reported genomes of two other strains, STE2 (2R+b/2Rb) and UCI (2Rb/2Rb), IndCh is found to be homozygous for the standard form (2R+b/2R+b). Comparative genome analysis revealed base-level details of the breakpoints and allowed extraction of 22,650 segregating SNPs for typing this inversion in populations. Whole genome sequencing of 82 individual mosquitoes from diverse geographical locations reveal that one third of both wild and laboratory populations maintain the heterozygous genotype of 2Rb. The large number of SNPs can be tailored to 1740 exonic SNPs enabling genotyping directly from transcriptome sequencing. The genome trilogy approach accelerated the study of fine structure and typing of an important inversion in An. stephensi, putting the genome resources for this understudied species on par with the extensively studied malaria vector, Anopheles gambiae. We argue that the IndCh genome is relevant for field translation work compared to those reported earlier by showing that individuals from diverse geographical locations cluster with IndCh, pointing to significant convergence resulting from travel and commerce between cities, perhaps, contributing to the survival of the fittest strain.
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Bottino-Rojas V, Ferreira-Almeida I, Nunes RD, Feng X, Pham TB, Kelsey A, Carballar-Lejarazú R, Gantz V, Oliveira PL, James AA. Beyond the eye: Kynurenine pathway impairment causes midgut homeostasis dysfunction and survival and reproductive costs in blood-feeding mosquitoes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 142:103720. [PMID: 34999199 PMCID: PMC11055609 DOI: 10.1016/j.ibmb.2022.103720] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Insect ommochrome biosynthesis pathways metabolize tryptophan to generate eye-color pigments and wild-type alleles of pathway genes are useful phenotypic markers in transgenesis studies. Pleiotropic effects of mutations in some genes exert a load on both survival and reproductive success in blood-feeding species. Here, we investigated the challenges imposed on mosquitoes by the increase of tryptophan metabolites resulting from blood meal digestion and the impact of disruptions of the ommochrome biosynthesis pathway. Female mosquitoes with spontaneous and induced mutations in the orthologs of the genes encoding kynurenine hydroxylase in Aedes aegypti, Anopheles stephensi and Culex quinquefasciatus exhibited impaired survival and reproductive phenotypes that varied in type and severity among the species. A compromised midgut permeability barrier function was also observed in An. stephensi. Surprisingly, mutant mosquitoes displayed an increase in microbiota compared to controls that was not accompanied by a general induction of immune genes. Antibiotic treatment rescued some deleterious traits implicating a role for the kynurenine pathway (KP) in midgut homeostasis. Supplemental xanthurenic acid, a KP end-product, rescued lethality and limited microbiota proliferation in Ae. aegypti. These data implicate the KP in the regulation of the host/microbiota interface. These pleiotropic effects on mosquito physiology are important in the development of genetic strategies targeting vector mosquitoes.
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Affiliation(s)
- Vanessa Bottino-Rojas
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, USA
| | - Igor Ferreira-Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodrigo D Nunes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Xuechun Feng
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Thai Binh Pham
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, USA
| | - Adam Kelsey
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, USA
| | | | - Valentino Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Pedro L Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil.
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, USA; Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA.
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17
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Ruzzante L, Feron R, Reijnders MJMF, Thiébaut A, Waterhouse RM. Functional constraints on insect immune system components govern their evolutionary trajectories. Mol Biol Evol 2021; 39:6459179. [PMID: 34893861 PMCID: PMC8788225 DOI: 10.1093/molbev/msab352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Roles of constraints in shaping evolutionary outcomes are often considered in the contexts of developmental biology and population genetics, in terms of capacities to generate new variants and how selection limits or promotes consequent phenotypic changes. Comparative genomics also recognizes the role of constraints, in terms of shaping evolution of gene and genome architectures, sequence evolutionary rates, and gene gains or losses, as well as on molecular phenotypes. Characterizing patterns of genomic change where putative functions and interactions of system components are relatively well described offers opportunities to explore whether genes with similar roles exhibit similar evolutionary trajectories. Using insect immunity as our test case system, we hypothesize that characterizing gene evolutionary histories can define distinct dynamics associated with different functional roles. We develop metrics that quantify gene evolutionary histories, employ these to characterize evolutionary features of immune gene repertoires, and explore relationships between gene family evolutionary profiles and their roles in immunity to understand how different constraints may relate to distinct dynamics. We identified three main axes of evolutionary trajectories characterized by gene duplication and synteny, maintenance/stability and sequence conservation, and loss and sequence divergence, highlighting similar and contrasting patterns across these axes amongst subsets of immune genes. Our results suggest that where and how genes participate in immune responses limit the range of possible evolutionary scenarios they exhibit. The test case study system of insect immunity highlights the potential of applying comparative genomics approaches to characterize how functional constraints on different components of biological systems govern their evolutionary trajectories.
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Affiliation(s)
- Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Antonin Thiébaut
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
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18
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Couper LI, Farner JE, Caldwell JM, Childs ML, Harris MJ, Kirk DG, Nova N, Shocket M, Skinner EB, Uricchio LH, Exposito-Alonso M, Mordecai EA. How will mosquitoes adapt to climate warming? eLife 2021; 10:69630. [PMID: 34402424 PMCID: PMC8370766 DOI: 10.7554/elife.69630] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/13/2021] [Indexed: 12/14/2022] Open
Abstract
The potential for adaptive evolution to enable species persistence under a changing climate is one of the most important questions for understanding impacts of future climate change. Climate adaptation may be particularly likely for short-lived ectotherms, including many pest, pathogen, and vector species. For these taxa, estimating climate adaptive potential is critical for accurate predictive modeling and public health preparedness. Here, we demonstrate how a simple theoretical framework used in conservation biology-evolutionary rescue models-can be used to investigate the potential for climate adaptation in these taxa, using mosquito thermal adaptation as a focal case. Synthesizing current evidence, we find that short mosquito generation times, high population growth rates, and strong temperature-imposed selection favor thermal adaptation. However, knowledge gaps about the extent of phenotypic and genotypic variation in thermal tolerance within mosquito populations, the environmental sensitivity of selection, and the role of phenotypic plasticity constrain our ability to make more precise estimates. We describe how common garden and selection experiments can be used to fill these data gaps. Lastly, we investigate the consequences of mosquito climate adaptation on disease transmission using Aedes aegypti-transmitted dengue virus in Northern Brazil as a case study. The approach outlined here can be applied to any disease vector or pest species and type of environmental change.
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Affiliation(s)
- Lisa I Couper
- Department of Biology, Stanford University, Stanford, United States
| | | | - Jamie M Caldwell
- Department of Biology, Stanford University, Stanford, United States.,Department of Biology, University of Hawaii at Manoa, Honolulu, United States
| | - Marissa L Childs
- Emmett Interdisciplinary Program in Environment and Resources, Stanford University, Stanford, United States
| | - Mallory J Harris
- Department of Biology, Stanford University, Stanford, United States
| | - Devin G Kirk
- Department of Biology, Stanford University, Stanford, United States.,Department of Zoology, University of Toronto, Toronto, Canada
| | - Nicole Nova
- Department of Biology, Stanford University, Stanford, United States
| | - Marta Shocket
- Department of Biology, Stanford University, Stanford, United States.,Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, United States
| | - Eloise B Skinner
- Department of Biology, Stanford University, Stanford, United States.,Environmental Futures Research Institute, Griffith University, Brisbane, Australia
| | - Lawrence H Uricchio
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
| | - Moises Exposito-Alonso
- Department of Biology, Stanford University, Stanford, United States.,Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Erin A Mordecai
- Department of Biology, Stanford University, Stanford, United States
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19
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Speth Z, Kaur G, Mazolewski D, Sisomphou R, Siao DDC, Pooraiiouby R, Vasquez-Gross H, Petereit J, Gulia-Nuss M, Mathew D, Nuss AB. Characterization of Anopheles stephensi Odorant Receptor 8, an Abundant Component of the Mouthpart Chemosensory Transcriptome. INSECTS 2021; 12:593. [PMID: 34208911 PMCID: PMC8304465 DOI: 10.3390/insects12070593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/22/2021] [Accepted: 06/26/2021] [Indexed: 01/25/2023]
Abstract
Several mosquito species within the genus Anopheles are vectors for human malaria, and the spread of this disease is driven by the propensity of certain species to feed preferentially on humans. The study of olfaction in mosquitoes is important to understand dynamics of host-seeking and host-selection; however, the majority of these studies focus on Anopheles gambiae or An. coluzzii, both vectors of malaria in Sub-Saharan Africa. Other malaria vectors may recognize different chemical cues from potential hosts; therefore, in this study, we investigated An. stephensi, the south Asian malaria mosquito. We specifically focused on the mouthparts (primarily the maxillary palp and labella) that have been much less investigated compared to the antennae but are also important for host-seeking. To provide a broad view of chemoreceptor expression, RNAseq was used to examine the transcriptomes from the mouthparts of host-seeking females, blood-fed females, and males. Notably, AsOr8 had a high transcript abundance in all transcriptomes and was, therefore, cloned and expressed in the Drosophila empty neuron system. This permitted characterization with a panel of odorants that were selected, in part, for their presence in the human odor profile. The responsiveness of AsOr8 to odorants was highly similar to An. gambiae Or8 (AgOr8), except for sulcatone, which was detected by AsOr8 but not AgOr8. Subtle differences in the receptor sensitivity to specific odorants may provide clues to species- or strain-specific approaches to host-seeking and host selection. Further exploration of the profile of An. stephensi chemosensory proteins may yield a better understanding of how different malaria vectors navigate host-finding and host-choice.
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Affiliation(s)
- Zachary Speth
- Cell and Molecular Biology Graduate Program, University of Nevada, Reno, NV 89557, USA; (Z.S.); (G.K.); (D.M.)
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Gurlaz Kaur
- Cell and Molecular Biology Graduate Program, University of Nevada, Reno, NV 89557, USA; (Z.S.); (G.K.); (D.M.)
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Devin Mazolewski
- Cell and Molecular Biology Graduate Program, University of Nevada, Reno, NV 89557, USA; (Z.S.); (G.K.); (D.M.)
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Rayden Sisomphou
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Danielle Denise C. Siao
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Rana Pooraiiouby
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
| | - Hans Vasquez-Gross
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA; (H.V.-G.); (J.P.)
| | - Juli Petereit
- Nevada Bioinformatics Center, University of Nevada, Reno, NV 89557, USA; (H.V.-G.); (J.P.)
| | - Monika Gulia-Nuss
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA;
| | - Dennis Mathew
- Department of Biology, University of Nevada, Reno, NV 89557, USA;
| | - Andrew B. Nuss
- Department of Agriculture, Veterinary and Rangeland Sciences, University of Nevada, Reno, NV 89557, USA; (R.S.); (D.D.C.S.); (R.P.)
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV 89557, USA;
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20
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Billingsley PF, George KI, Eappen AG, Harrell RA, Alford R, Li T, Chakravarty S, Sim BKL, Hoffman SL, O'Brochta DA. Transient knockdown of Anopheles stephensi LRIM1 using RNAi increases Plasmodium falciparum sporozoite salivary gland infections. Malar J 2021; 20:284. [PMID: 34174879 PMCID: PMC8235909 DOI: 10.1186/s12936-021-03818-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium falciparum (Pf) sporozoites (PfSPZ) can be administered as a highly protective vaccine conferring the highest protection seen to date. Sanaria® PfSPZ vaccines are produced using aseptically reared Anopheles stephensi mosquitoes. The bionomics of sporogonic development of P. falciparum in A. stephensi to fully mature salivary gland PfSPZ is thought to be modulated by several components of the mosquito innate immune system. In order to increase salivary gland PfSPZ infections in A. stephensi and thereby increase vaccine production efficiency, a gene knock down approach was used to investigate the activity of the immune deficiency (IMD) signaling pathway downstream effector leucine-rich repeat immune molecule 1 (LRIM1), an antagonist to Plasmodium development. METHODS Expression of LRIM1 in A. stephensi was reduced following injection of double stranded (ds) RNA into mosquitoes. By combining the Gal4/UAS bipartite system with in vivo expression of short hairpin (sh) RNA coding for LRIM1 reduced expression of LRIM1 was targeted in the midgut, fat body, and salivary glands. RT-qPCR was used to demonstrate fold-changes in gene expression in three transgenic crosses and the effects on P. falciparum infections determined in mosquitoes showing the greatest reduction in LRIM1 expression. RESULTS LRIM1 expression could be reduced, but not completely silenced, by expression of LRIM1 dsRNA. Infections of P. falciparum oocysts and PfSPZ were consistently and significantly higher in transgenic mosquitoes than wild type controls, with increases in PfSPZ ranging from 2.5- to tenfold. CONCLUSIONS Plasmodium falciparum infections in A. stephensi can be increased following reduced expression of LRIM1. These data provide the springboard for more precise knockout of LRIM1 for the eventual incorporation of immune-compromised A. stephensi into manufacturing of Sanaria's PfSPZ products.
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Affiliation(s)
- Peter F Billingsley
- Sanaria Inc, Suite A209, 9800 Medical Center Drive, Rockville, MD, 20850, USA.
| | - Kasim I George
- Institute for Bioscience and Biotechnology Research and Department of Entomology, University of Maryland, Gudelsky Drive, Rockville, MD, 20850, USA
- Qiagen Inc, 19300 Germantown Road, Germantown, MD, 20874, USA
| | - Abraham G Eappen
- Sanaria Inc, Suite A209, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Robert A Harrell
- Institute for Bioscience and Biotechnology Research and Department of Entomology, University of Maryland, Gudelsky Drive, Rockville, MD, 20850, USA
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Robert Alford
- Institute for Bioscience and Biotechnology Research and Department of Entomology, University of Maryland, Gudelsky Drive, Rockville, MD, 20850, USA
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Tao Li
- Sanaria Inc, Suite A209, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Sumana Chakravarty
- Sanaria Inc, Suite A209, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - B Kim Lee Sim
- Sanaria Inc, Suite A209, 9800 Medical Center Drive, Rockville, MD, 20850, USA
- Protein Potential, Suite A209, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Stephen L Hoffman
- Sanaria Inc, Suite A209, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - David A O'Brochta
- Institute for Bioscience and Biotechnology Research and Department of Entomology, University of Maryland, Gudelsky Drive, Rockville, MD, 20850, USA
- Foundation for the National Institutes of Health, 11400 Rockville Pike, Suite 600, North Bethesda, MD, 20852, USA
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21
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Mishra S, Sharma G, Das MK, Pande V, Singh OP. Intragenomic sequence variations in the second internal transcribed spacer (ITS2) ribosomal DNA of the malaria vector Anopheles stephensi. PLoS One 2021; 16:e0253173. [PMID: 34125861 PMCID: PMC8202910 DOI: 10.1371/journal.pone.0253173] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/28/2021] [Indexed: 11/18/2022] Open
Abstract
Second Internal Transcribed Spacer (ITS2) ribosomal DNA (rDNA) sequence is a widely used molecular marker for species-identification or -delimitation due to observed concerted evolution which is believed to homogenize rDNA copies in an interbreeding population. However, intra-specific differences in ITS2 of Anopheles stephensi have been reported. This study reports the presence of intragenomic sequence variation in the ITS2-rDNA of An. stephensi and hypothesizes that observed intra-specific differences in this species may have resulted due to ambiguous DNA sequence-chromatogram resulting from intragenomic heterogeneity. Anopheles stephensi collected from different parts of India were sequenced for complete ITS2 and the variable region of 28S-rDNA (d1-d3 domains). Intragenomic variations were found in ITS2 region of all An. stephensi sequenced, but no such variation was observed in d1 to d3 domains of 28S-rDNA. Cloning and sequencing of ITS2 through the d3 domain of the 28S region of rDNA from representative samples from northern, central, and southern India confirmed the presence of intragenomic variation in ITS2 due to transitions at three loci and two bp indel in a di-nucleotide microsatellite locus. Multiple haplotypes were observed in ITS2 raised from such variations. Due to the absence of detectable intragenomic sequence variation in the d1 to d3 domain of 28S rDNA of An. stephensi, this region can serve as an ideal reference sequence for taxonomic and phylogenetic studies. The presence of intragenomic variation in rDNA should be carefully examined before using this as a molecular marker for species delimitation or phylogenetic analyses.
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Affiliation(s)
- Shobhna Mishra
- National Institute of Malaria Research, New Delhi, India
| | - Gunjan Sharma
- National Institute of Malaria Research, New Delhi, India
| | - Manoj K. Das
- Field Unit, National Institute of Malaria Research, Itki, Ranchi, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Om P. Singh
- National Institute of Malaria Research, New Delhi, India
- * E-mail: ,
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22
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Sun J, Dong Y, Wang C, Xiao S, Jiao Z, Gao C. Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis. PeerJ 2021; 9:e11216. [PMID: 33959417 PMCID: PMC8053381 DOI: 10.7717/peerj.11216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/15/2021] [Indexed: 12/25/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of newly discovered non-coding RNAs that are typically derived from a genome's exonic, intronic, and intergenic regions. Recent studies of circRNAs in animals and plants have shown that circRNAs are vital in response to various abiotic and biotic stresses. Powdery mildew disease (PM) is a serious fungal disease threatening the melon industry. We performed whole transcriptome sequencing using the leaves of a PM-resistant (M1) and a PM-susceptible (B29) melon to identify circRNAs and determine their molecular functions. A total of 303 circRNAs were identified and >50% circRNAs were derived from exonic regions. Expression levels were significantly altered in 17 and 23 circRNAs after PM infections in B29 and M1, respectively. Melon circRNAs may participate in the response to biotic stimuli, oxidation reduction, metabolic processes, and the regulation of gene expression based on the functional annotation of circRNA parental genes. Furthermore, 27 circRNAs were predicted to be potential targets or 'sponges' for 18 microRNAs (miRNAs). Our results are the first to identify and characterize circRNA functions in melon and may contribute to a better understanding of the role and regulatory mechanisms of circRNAs in resisting PM.
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Affiliation(s)
- Jianlei Sun
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Improvement Center for Vegetable, Vegetable Science Observation and Experiment Station in Huang huai District of Ministry of Agriculture (Shandong), Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yumei Dong
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Improvement Center for Vegetable, Vegetable Science Observation and Experiment Station in Huang huai District of Ministry of Agriculture (Shandong), Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chongqi Wang
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Improvement Center for Vegetable, Vegetable Science Observation and Experiment Station in Huang huai District of Ministry of Agriculture (Shandong), Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shouhua Xiao
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Improvement Center for Vegetable, Vegetable Science Observation and Experiment Station in Huang huai District of Ministry of Agriculture (Shandong), Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zigao Jiao
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Improvement Center for Vegetable, Vegetable Science Observation and Experiment Station in Huang huai District of Ministry of Agriculture (Shandong), Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chao Gao
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Improvement Center for Vegetable, Vegetable Science Observation and Experiment Station in Huang huai District of Ministry of Agriculture (Shandong), Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Jinan, China
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23
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Chakraborty M, Ramaiah A, Adolfi A, Halas P, Kaduskar B, Ngo LT, Jayaprasad S, Paul K, Whadgar S, Srinivasan S, Subramani S, Bier E, James AA, Emerson JJ. Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biol 2021; 19:28. [PMID: 33568145 PMCID: PMC7876825 DOI: 10.1186/s12915-021-00963-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vector's genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution. RESULTS To access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element (TE) families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y chromosome in any mosquito. By tracking full-length mRNA for > 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively throughout male development and adulthood, suggesting an important role. CONCLUSION Collectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate the development of genetic control strategies of malaria transmission.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Arunachalam Ramaiah
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Adriana Adolfi
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Paige Halas
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Bhagyashree Kaduskar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Luna Thanh Ngo
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Suvratha Jayaprasad
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Kiran Paul
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Saurabh Whadgar
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Subhashini Srinivasan
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Suresh Subramani
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093-0322, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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24
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Plasmodium's journey through the Anopheles mosquito: A comprehensive review. Biochimie 2020; 181:176-190. [PMID: 33346039 DOI: 10.1016/j.biochi.2020.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
The malaria parasite has an extraordinary ability to evade the immune system due to which the development of a malaria vaccine is a challenging task. Extensive research on malarial infection in the human host particularly during the liver stage has resulted in the discovery of potential candidate vaccines including RTS,S/AS01 and R21. However, complete elimination of malaria would require a holistic multi-component approach. In line with this, under the World Health Organization's PATH Malaria Vaccine Initiative (MVI), the research focus has shifted towards the sexual stages of malaria in the mosquito host. Last two decades of scientific research obtained seminal information regarding the sexual/mosquito stages of the malaria. This updated and comprehensive review would provide the basis for consolidated understanding of cellular, biochemical, molecular and immunological aspects of parasite transmission right from the sexual stage commitment in the human host to the sporozoite delivery back into subsequent vertebrate host by the female Anopheles mosquito.
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25
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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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26
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Chida AR, Ravi S, Jayaprasad S, Paul K, Saha J, Suresh C, Whadgar S, Kumar N, Rao K R, Ghosh C, Choudhary B, Subramani S, Srinivasan S. A Near-Chromosome Level Genome Assembly of Anopheles stephensi. Front Genet 2020; 11:565626. [PMID: 33312190 PMCID: PMC7703621 DOI: 10.3389/fgene.2020.565626] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/28/2020] [Indexed: 12/31/2022] Open
Abstract
Malaria remains a major healthcare risk to growing economies like India, and a chromosome-level reference genome of Anopheles stephensi is critical for successful vector management and understanding of vector evolution using comparative genomics. We report chromosome-level assemblies of an Indian strain, STE2, and a Pakistani strain SDA-500 by combining draft genomes of the two strains using a homology-based iterative approach. The resulting assembly IndV3/PakV3 with L50 of 9/12 and N50 6.3/6.9 Mb had scaffolds long enough for building 90% of the euchromatic regions of the three chromosomes, IndV3s/PakV3s, using low-resolution physical markers and enabled the generation of the next version of genome assemblies, IndV4/PakV4, using HiC data. We have validated these assemblies using contact maps against publicly available HiC raw data from two strains including STE2 and another lab strain of An. stephensi from UCI and compare the quality of the assemblies with other assemblies made available as preprints since the submission of the manuscript. We show that the IndV3s and IndV4 assemblies are sensitive in identifying a homozygous 2Rb inversion in the UCI strain and a 2Rb polymorphism in the STE2 strain. Multiple tandem copies of CYP6a14, 4c1, and 4c21 genes, implicated in insecticide resistance, lie within this inversion locus. Comparison of assembled genomes suggests a variation of 1 in 81 positions between the UCI and STE2 lab strains, 1 in 82 between SDA-500 and UCI strain, and 1 in 113 between SDA-500 and STE2 strains of An. stephensi, which are closer than 1 in 68 variations among individuals from two other lab strains sequenced and reported here. Based on the developmental transcriptome and orthology of all the 54 olfactory receptors (ORs) to those of other Anopheles species, we identify an OR with the potential for host recognition in the genus Anopheles. A comparative analysis of An. stephensi genomes with the completed genomes of a few other Anopheles species suggests limited inter-chromosomal gene flow and loss of synteny within chromosomal arms even among the closely related species.
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Affiliation(s)
- Afiya Razia Chida
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Samathmika Ravi
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | | | - Kiran Paul
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Jaysmita Saha
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Chinjusha Suresh
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Saurabh Whadgar
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Naveen Kumar
- Tata Institute for Genetics and Society Center at inStem, Bangalore, India
| | - Raksha Rao K
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Chaitali Ghosh
- Tata Institute for Genetics and Society Center at inStem, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Suresh Subramani
- Tata Institute for Genetics and Society Center at inStem, Bangalore, India
| | - Subhashini Srinivasan
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
- Tata Institute for Genetics and Society Center at inStem, Bangalore, India
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Romanenko SA, Fedorova YE, Serdyukova NA, Zaccaroni M, Stanyon R, Graphodatsky AS. Evolutionary rearrangements of X chromosomes in voles (Arvicolinae, Rodentia). Sci Rep 2020; 10:13235. [PMID: 32764633 PMCID: PMC7413345 DOI: 10.1038/s41598-020-70226-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/20/2020] [Indexed: 11/09/2022] Open
Abstract
Euchromatic segments of the X chromosomes of placental mammals are the most conservative elements of the karyotype, only rarely subjected to either inter- or intrachromosomal rearrangements. Here, using microdissection-derived set of region-specific probes of Terricola savii we detailed the evolutionary rearrangements found in X chromosomes in 20 vole species (Arvicolinae, Rodentia). We show that the evolution of X chromosomes in this taxon was accompanied by multiple para- and pericentric inversions and centromere shifts. The contribution of intrachromosomal rearrangements to the karyotype evolution of Arvicolinae species was approximately equivalent in both the separate autosomal conserved segments and the X chromosomes. Intrachromosmal rearrangements and structural reorganization of the X chromosomes was likely accompanied by an accumulation, distribution, and evolution of repeated sequences.
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Affiliation(s)
| | - Yulia E Fedorova
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | - Marco Zaccaroni
- Department of Biology, University of Florence, Florence, Italy
| | - Roscoe Stanyon
- Department of Biology, University of Florence, Florence, Italy
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28
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Wang ZL, Zhu YQ, Yan Q, Yan WY, Zheng HJ, Zeng ZJ. A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome. Front Genet 2020; 11:279. [PMID: 32292419 PMCID: PMC7119468 DOI: 10.3389/fgene.2020.00279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
Apis cerana is one of the main honeybee species in artificial farming, which is widely distributed in Asian countries. The genome of A. cerana has been sequenced by several different research groups using second generation sequencing technologies. However, it is still necessary to obtain more complete and accurate genome sequences. Here we present a chromosome-scale assembly of the A. cerana genome using single-molecule real-time (SMRT) Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated assembly is 215.67 Mb in size with a contig N50 of 4.49 Mb, representing an 212-fold improvement over the previous Illumina-based version. Hi-C scaffolding resulted in 16 pseudochromosomes occupying 97.85% of the assembled genome sequences. A total of 10,741 protein-coding genes were predicted and 9,627 genes were annotated. Besides, 314 new genes were identified compared to the previous version. The improved high-quality A. cerana reference genome will provide precise sequence information for biological research of A. cerana.
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Affiliation(s)
- Zi-Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Yong-Qiang Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Qing Yan
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Wei-Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Zhi-Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
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29
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Sharma A, Kinney NA, Timoshevskiy VA, Sharakhova MV, Sharakhov IV. Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex. Genes (Basel) 2020; 11:E327. [PMID: 32204543 PMCID: PMC7140835 DOI: 10.3390/genes11030327] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
Heterochromatin is identified as a potential factor driving diversification of species. To understand the magnitude of heterochromatin variation within the Anopheles gambiae complex of malaria mosquitoes, we analyzed metaphase chromosomes in An. arabiensis, An. coluzzii, An. gambiae, An. merus, and An. quadriannulatus. Using fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA), a highly repetitive fraction of DNA, and heterochromatic Bacterial Artificial Chromosome (BAC) clones, we established the correspondence of pericentric heterochromatin between the metaphase and polytene X chromosomes of An. gambiae. We then developed chromosome idiograms and demonstrated that the X chromosomes exhibit qualitative differences in their pattern of heterochromatic bands and position of satellite DNA (satDNA) repeats among the sibling species with postzygotic isolation, An. arabiensis, An. merus, An. quadriannulatus, and An. coluzzii or An. gambiae. The identified differences in the size and structure of the X chromosome heterochromatin point to a possible role of repetitive DNA in speciation of mosquitoes. We found that An. coluzzii and An. gambiae, incipient species with prezygotic isolation, share variations in the relative positions of the satDNA repeats and the proximal heterochromatin band on the X chromosomes. This previously unknown genetic polymorphism in malaria mosquitoes may be caused by a differential amplification of DNA repeats or an inversion in the sex chromosome heterochromatin.
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Affiliation(s)
- Atashi Sharma
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
| | - Nicholas A. Kinney
- Genomics Bioinformatics and Computational Biology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA;
| | - Vladimir A. Timoshevskiy
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
| | - Maria V. Sharakhova
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
- 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
- Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, 634050 Tomsk, Russia
| | - Igor V. Sharakhov
- Department of Entomology, Virginia Polytechnic and State University, Blacksburg, VA 24061, USA; (A.S.); (V.A.T.); (M.V.S.)
- Genomics Bioinformatics and Computational Biology, Virginia Polytechnic 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
- Department of Cytology and Genetics, Tomsk State University, 634050 Tomsk, Russia
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30
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Carballar-Lejarazú R, Kelsey A, Pham TB, Bennett EP, James AA. Digital droplet PCR and IDAA for the detection of CRISPR indel edits in the malaria species Anopheles stephensi. Biotechniques 2020; 68:172-179. [PMID: 32040336 PMCID: PMC7177198 DOI: 10.2144/btn-2019-0103] [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] [Indexed: 01/19/2023] Open
Abstract
CRISPR/Cas9 technology is a powerful tool for the design of gene-drive systems to control and/or modify mosquito vector populations; however, CRISPR/Cas9-mediated nonhomologous end joining mutations can have an important impact on generating alleles resistant to the drive and thus on drive efficiency. We demonstrate and compare the insertions or deletions (indels) detection capabilities of two techniques in the malaria vector mosquito Anopheles stephensi: Indel Detection by Amplicon Analysis (IDAA™) and Droplet Digital™ PCR (ddPCR™). Both techniques showed accuracy and reproducibility for indel frequencies across mosquito samples containing different ratios of indels of various sizes. Moreover, these techniques have advantages that make them potentially better suited for high-throughput nonhomologous end joining analysis in cage trials and contained field testing of gene-drive mosquitoes. Mosquito DNA was extracted with the Promega Wizard® Genomic DNA Purification Kit protocol and quantified with Qubit® 3.0 following manufacturer protocols. PCR products for IDAA and ddPCR were generated with primers spanning 150–500 bp around the target site. IDAA amplicons were sent directly to COBO Technologies for analysis. ddPCR amplicons were analyzed using the Bio-Rad QX200™ ddPCR system.
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Affiliation(s)
- Rebeca Carballar-Lejarazú
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA 92697-4025, USA
| | - Adam Kelsey
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA 92697-4025, USA
| | - Thai Binh Pham
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA 92697-4025, USA
| | - Eric P Bennett
- Department of Odontology, Copenhagen Center for Glycomics, Faculty of Health Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA 92697-4025, USA.,Department of Molecular Biology & Biochemistry, University of California, Irvine, CA 92697-3900, USA
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31
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Mitri C, Bischoff E, Eiglmeier K, Holm I, Dieme C, Brito-Fravallo E, Raz A, Zakeri S, Nejad MIK, Djadid ND, Vernick KD, Riehle MM. Gene copy number and function of the APL1 immune factor changed during Anopheles evolution. Parasit Vectors 2020; 13:18. [PMID: 31931885 PMCID: PMC6958605 DOI: 10.1186/s13071-019-3868-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 12/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background The recent reference genome assembly and annotation of the Asian malaria vector Anopheles stephensi detected only one gene encoding the leucine-rich repeat immune factor APL1, while in the Anopheles gambiae and sibling Anopheles coluzzii, APL1 factors are encoded by a family of three paralogs. The phylogeny and biological function of the unique APL1 gene in An. stephensi have not yet been specifically examined. Methods The APL1 locus was manually annotated to confirm the computationally predicted single APL1 gene in An. stephensi. APL1 evolution within Anopheles was explored by phylogenomic analysis. The single or paralogous APL1 genes were silenced in An. stephensi and An. coluzzii, respectively, followed by mosquito survival analysis, experimental infection with Plasmodium and expression analysis. Results APL1 is present as a single ancestral gene in most Anopheles including An. stephensi but has expanded to three paralogs in an African lineage that includes only the Anopheles gambiae species complex and Anopheles christyi. Silencing of the unique APL1 copy in An. stephensi results in significant mosquito mortality. Elevated mortality of APL1-depleted An. stephensi is rescued by antibiotic treatment, suggesting that pathology due to bacteria is the cause of mortality, and indicating that the unique APL1 gene is essential for host survival. Successful Plasmodium development in An. stephensi depends upon APL1 activity for protection from high host mortality due to bacteria. In contrast, silencing of all three APL1 paralogs in An. coluzzii does not result in elevated mortality, either with or without Plasmodium infection. Expression of the single An. stephensi APL1 gene is regulated by both the Imd and Toll immune pathways, while the two signaling pathways regulate different APL1 paralogs in the expanded APL1 locus. Conclusions APL1 underwent loss and gain of functions concomitant with expansion from a single ancestral gene to three paralogs in one lineage of African Anopheles. We infer that activity of the unique APL1 gene promotes longevity in An. stephensi by conferring protection from or tolerance to an effect of bacterial pathology. The evolution of an expanded APL1 gene family could be a factor contributing to the exceptional levels of malaria transmission mediated by human-feeding members of the An. gambiae species complex in Africa.![]()
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Affiliation(s)
- Christian Mitri
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Emmanuel Bischoff
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Karin Eiglmeier
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Inge Holm
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Constentin Dieme
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France.,Wadsworth Center, New York State Department of Health, Slingerlands, NY, USA
| | - Emma Brito-Fravallo
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France
| | - Abbasali Raz
- Malaria and Vector Research Group, Biotechnology Research Center, Institut Pasteur of Iran, Tehran, Iran
| | - Sedigheh Zakeri
- Malaria and Vector Research Group, Biotechnology Research Center, Institut Pasteur of Iran, Tehran, Iran
| | - Mahdokht I K Nejad
- Malaria and Vector Research Group, Biotechnology Research Center, Institut Pasteur of Iran, Tehran, Iran
| | - Navid D Djadid
- Malaria and Vector Research Group, Biotechnology Research Center, Institut Pasteur of Iran, Tehran, Iran
| | - Kenneth D Vernick
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France. .,CNRS Unit of Evolutionary Genomics, Modeling and Health (UMR2000), Institut Pasteur, Paris, France.
| | - Michelle M Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, USA.
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32
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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: 44] [Impact Index Per Article: 11.0] [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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Experimental population modification of the malaria vector mosquito, Anopheles stephensi. PLoS Genet 2019; 15:e1008440. [PMID: 31856182 PMCID: PMC6922335 DOI: 10.1371/journal.pgen.1008440] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
Small laboratory cage trials of non-drive and gene-drive strains of the Asian malaria vector mosquito, Anopheles stephensi, were used to investigate release ratios and other strain properties for their impact on transgene spread during simulated population modification. We evaluated the effects of transgenes on survival, male contributions to next-generation populations, female reproductive success and the impact of accumulation of gene drive-resistant genomic target sites resulting from nonhomologous end-joining (NHEJ) mutagenesis during Cas9, guide RNA-mediated cleavage. Experiments with a non-drive, autosomally-linked malaria-resistance gene cassette showed ‘full introduction’ (100% of the insects have at least one copy of the transgene) within 8 weeks (≤ 3 generations) following weekly releases of 10:1 transgenic:wild-type males in an overlapping generation trial design. Male release ratios of 1:1 resulted in cages where mosquitoes with at least one copy of the transgene fluctuated around 50%. In comparison, two of three cages in which the malaria-resistance genes were linked to a gene-drive system in an overlapping generation, single 1:1 release reached full introduction in 6–8 generations with a third cage at ~80% within the same time. Release ratios of 0.1:1 failed to establish the transgenes. A non-overlapping generation, single-release trial of the same gene-drive strain resulted in two of three cages reaching 100% introduction within 6–12 generations following a 1:1 transgenic:wild-type male release. Two of three cages with 0.33:1 transgenic:wild-type male single releases achieved full introduction in 13–16 generations. All populations exhibiting full introduction went extinct within three generations due to a significant load on females having disruptions of both copies of the target gene, kynurenine hydroxylase. While repeated releases of high-ratio (10:1) non-drive constructs could achieve full introduction, results from the 1:1 release ratios across all experimental designs favor the use of gene drive, both for efficiency and anticipated cost of the control programs. The experimental introduction of manipulated genes into insect species has a long history in basic genetics. Recent advances in genome editing technologies have spurred considerable effort to exploit these methodologies to provide genetic solutions to some of the worst medical and agricultural problems caused by insects. Insect population suppression and population modification approaches have been proposed to control transmission of vector-borne diseases, including malaria. We used small cage trials to explore the efficacy of non-drive and gene-drive releases to deliver anti-malarial effector genes to a vector mosquito, Anopheles stephensi. We show that both approaches can work to introduce genes to high percentages, but as expected, the gene-drive approaches were more efficient in that they needed only a single release with a much lower number of released insects. The gene-drive females in our studies exhibited a significant load that resulted in some cage populations going to extinction. Furthermore, the accumulation of drive-resistant target genes prevented full introduction of the transgenes in those cages that did not go extinct. While none of the strains evaluated here are proposed for open release, these laboratory cage trials reveal features that can be used to improve next-generation gene-drive strains for population modification.
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34
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Li F, Zhao X, Li M, He K, Huang C, Zhou Y, Li Z, Walters JR. Insect genomes: progress and challenges. INSECT MOLECULAR BIOLOGY 2019; 28:739-758. [PMID: 31120160 DOI: 10.1111/imb.12599] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/22/2019] [Accepted: 05/14/2019] [Indexed: 05/24/2023]
Abstract
In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.
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Affiliation(s)
- F Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - X Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - M Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - K He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - C Huang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Y Zhou
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Z Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - J R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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35
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Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites. Nat Commun 2019; 10:4964. [PMID: 31673027 PMCID: PMC6823429 DOI: 10.1038/s41467-019-12936-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/09/2019] [Indexed: 02/08/2023] Open
Abstract
Plasmodium sporozoites are transmitted from infected mosquitoes to mammals, and must navigate the host skin and vasculature to infect the liver. This journey requires distinct proteomes. Here, we report the dynamic transcriptomes and proteomes of both oocyst sporozoites and salivary gland sporozoites in both rodent-infectious Plasmodium yoelii parasites and human-infectious Plasmodium falciparum parasites. The data robustly define mRNAs and proteins that are upregulated in oocyst sporozoites (UOS) or upregulated in infectious sporozoites (UIS) within the salivary glands, including many that are essential for sporozoite functions in the vector and host. Moreover, we find that malaria parasites use two overlapping, extensive, and independent programs of translational repression across sporozoite maturation to temporally regulate protein expression. Together with gene-specific validation experiments, these data indicate that two waves of translational repression are implemented and relieved at different times during sporozoite maturation, migration and infection, thus promoting their successful development and vector-to-host transition. Here, the authors report transcriptomes and proteomes of oocyst sporozoite and salivary gland sporozoite stages in rodent-infectious Plasmodium yoelii parasites and human infectious Plasmodium falciparum parasites and define two waves of translational repression during sporozoite maturation.
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36
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Imrie L, Le Bihan T, O'Toole Á, Hickner PV, Dunn WA, Weise B, Rund SSC. Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics. PLoS One 2019; 14:e0220225. [PMID: 31356616 PMCID: PMC6663012 DOI: 10.1371/journal.pone.0220225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
The malaria mosquito, Anopheles stephensi, and other mosquitoes modulate their biology to match the time-of-day. In the present work, we used a non-hypothesis driven approach (untargeted proteomics) to identify proteins in mosquito tissue, and then quantified the relative abundance of the identified proteins from An. stephensi bodies. Using these quantified protein levels, we then analyzed the data for proteins that were only detectable at certain times-of-the day, highlighting the need to consider time-of-day in experimental design. Further, we extended our time-of-day analysis to look for proteins which cycle in a rhythmic 24-hour ("circadian") manner, identifying 31 rhythmic proteins. Finally, to maximize the utility of our data, we performed a proteogenomic analysis to improve the genome annotation of An. stephensi. We compare peptides that were detected using mass spectrometry but are 'missing' from the An. stephensi predicted proteome, to reference proteomes from 38 other primarily human disease vector species. We found 239 such peptide matches and reveal that genome annotation can be improved using proteogenomic analysis from taxonomically diverse reference proteomes. Examination of 'missing' peptides revealed reading frame errors, errors in gene-calling, overlapping gene models, and suspected gaps in the genome assembly.
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Affiliation(s)
- Lisa Imrie
- SynthSys–Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thierry Le Bihan
- SynthSys–Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Rapid Novor, Kitchener, Ontario, Canada
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul V. Hickner
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - W. Augustine Dunn
- Boston Children's Hospital, Boston, Massachusetts, United States of America
| | - Benjamin Weise
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Samuel S. C. Rund
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
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37
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Qi Y, Wu Y, Saunders R, Chen XG, Mao C, Biedler JK, Tu ZJ. Guy1, a Y-linked embryonic signal, regulates dosage compensation in Anopheles stephensi by increasing X gene expression. eLife 2019; 8:43570. [PMID: 30888319 PMCID: PMC6440743 DOI: 10.7554/elife.43570] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/16/2019] [Indexed: 12/22/2022] Open
Abstract
We previously showed that Guy1, a primary signal expressed from the Y chromosome, is a strong candidate for a male-determining factor that confers female-specific lethality in Anopheles stephensi (Criscione et al., 2016). Here, we present evidence that Guy1 increases X gene expression in Guy1-transgenic females from two independent lines, providing a mechanism underlying the Guy1-conferred female lethality. The median level gene expression (MGE) of X-linked genes is significantly higher than autosomal genes in Guy1-transgenic females while there is no significant difference in MGE between X and autosomal genes in wild-type females. Furthermore, Guy1 significantly upregulates at least 40% of the 996 genes across the X chromosome in transgenic females. Guy1-conferred female-specific lethality is remarkably stable and completely penetrant. These findings indicate that Guy1 regulates dosage compensation in An. stephensi and components of dosage compensation may be explored to develop novel strategies to control mosquito-borne diseases.
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Affiliation(s)
- Yumin Qi
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Yang Wu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangdong, China
| | - Randy Saunders
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Xiao-Guang Chen
- Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Chunhong Mao
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, United States
| | - James Kite Biedler
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Zhijian Jake Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
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38
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Khamsehnejad MI, Djadid ND, Raz A. Identification, Molecular Characterization, and In Silico Structural Analysis of Carboxypeptidase B2 of Anopheles stephensi. JOURNAL OF MEDICAL ENTOMOLOGY 2019; 56:72-85. [PMID: 30124910 DOI: 10.1093/jme/tjy127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 06/08/2023]
Abstract
Malaria is a vector-borne infectious disease that is considered a priority of the World Health Organization due to its enormous impacts on global health. Plasmodium spp. (Haemosporida: Plasmodiidae), Anopheles spp. (Diptera: Culicidae), and a suitable host are the key elements for malaria transmission. To disrupt the parasitic life cycle of malaria or prevent its transmission, these three key elements should be targeted by effective control strategies. Development of vaccines that interrupt malaria transmission is one of the solutions that has been recommended to the countries that aim to eliminate malaria. With respect to the important role of Anopheles stephensi in malaria transmission and involvement of Anopheles carboxypeptidase B1 in sexual parasite development, we characterized the second member of cpb gene family (cpbAs2) of An. Stephensi to provide some basic information and evaluate significance of cpbAs2's role in complementing sexual plasmodium development role of cpbAs1. The cpbAs2 mRNA sequence was characterized by 3' and 5' RACE and the structural features of its coded protein were studied by in silico modeling. The coding sequence and gene structure of cpbAs2 were determined empirically and compared with the in silico predictions from the An. stephensi genome sequencing project. Furthermore, homology modeling revealed that its structure is very similar to the structurally important domains of procarboxypeptidase B2 in humans. This study provides basic molecular and structural information about another member of the cpb gene family of An. stephensi. The reported results are informative and necessary for evaluation of the role of this gene in sexual parasite development by future studies.
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Affiliation(s)
- Mahdokht Ilbeigi Khamsehnejad
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran (PII), Pasteur Avenue, Tehran, Iran
| | - Navid Dinparast Djadid
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran (PII), Pasteur Avenue, Tehran, Iran
| | - Abbasali Raz
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran (PII), Pasteur Avenue, Tehran, Iran
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39
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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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40
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Abstract
The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build "omics" resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address. This chapter details the use of the Benchmarking Universal Single-Copy Orthologue (BUSCO) assessment tool to estimate the completeness of transcriptomes, genome assemblies, and annotated gene sets in terms of their expected gene content.
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41
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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: 6] [Impact Index Per Article: 1.2] [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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42
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Swearingen KE, Eng JK, Shteynberg D, Vigdorovich V, Springer TA, Mendoza L, Sather DN, Deutsch EW, Kappe SHI, Moritz RL. A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry. J Proteome Res 2018; 18:652-663. [PMID: 30523691 DOI: 10.1021/acs.jproteome.8b00638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thrombospondin type 1 repeats (TSRs), small adhesive protein domains with a wide range of functions, are usually modified with O-linked fucose, which may be extended to O-fucose-β1,3-glucose. Collision-induced dissociation (CID) spectra of O-fucosylated peptides cannot be sequenced by standard tandem mass spectrometry (MS/MS) sequence database search engines because O-linked glycans are highly labile in the gas phase and are effectively absent from the CID peptide fragment spectra, resulting in a large mass error. Electron transfer dissociation (ETD) preserves O-linked glycans on peptide fragments, but only a subset of tryptic peptides with low m/ z can be reliably sequenced from ETD spectra compared to CID. Accordingly, studies to date that have used MS to identify O-fucosylated TSRs have required manual interpretation of CID mass spectra even when ETD was also employed. In order to facilitate high-throughput, automatic identification of O-fucosylated peptides from CID spectra, we re-engineered the MS/MS sequence database search engine Comet and the MS data analysis suite Trans-Proteomic Pipeline to enable automated sequencing of peptides exhibiting the neutral losses characteristic of labile O-linked glycans. We used our approach to reanalyze published proteomics data from Plasmodium parasites and identified multiple glycoforms of TSR-containing proteins.
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Affiliation(s)
| | - Jimmy K Eng
- Proteomics Resource , University of Washington , Seattle , Washington 98195 , United States
| | - David Shteynberg
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research , Seattle Children's Research Institute , Seattle , Washington 98101 , United States
| | - Timothy A Springer
- Harvard Medical School and Boston Children's Hospital , Boston , Massachusetts 02115 , United States
| | - Luis Mendoza
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - D Noah Sather
- Center for Global Infectious Disease Research , Seattle Children's Research Institute , Seattle , Washington 98101 , United States
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research , Seattle Children's Research Institute , Seattle , Washington 98101 , United States
| | - Robert L Moritz
- Institute for Systems Biology , Seattle , Washington 98109 , United States
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Pathak AK, Shiau JC, Thomas MB, Murdock CC. Cryogenically preserved RBCs support gametocytogenesis of Plasmodium falciparum in vitro and gametogenesis in mosquitoes. Malar J 2018; 17:457. [PMID: 30522507 PMCID: PMC6282341 DOI: 10.1186/s12936-018-2612-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/01/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The malaria Eradication Research Agenda (malERA) has identified human-to-mosquito transmission of Plasmodium falciparum as a major target for eradication. The cornerstone for identifying and evaluating transmission in the laboratory is standard membrane feeding assays (SMFAs) where mature gametocytes of P. falciparum generated in vitro are offered to mosquitoes as part of a blood-meal. However, propagation of "infectious" gametocytes requires 10-12 days with considerable physico-chemical demands imposed on host RBCs and thus, "fresh" RBCs that are ≤ 1-week old post-collection are generally recommended. However, in addition to the costs, physico-chemical characteristics unique to RBC donors may confound reproducibility and interpretation of SMFAs. Cryogenic storage of RBCs ("cryo-preserved RBCs") is accepted by European and US FDAs as an alternative to refrigeration (4 °C) for preserving RBC "quality" and while cryo-preserved RBCs have been used for in vitro cultures of other Plasmodia and the asexual stages of P. falciparum, none of the studies required RBCs to support parasite development for > 4 days. RESULTS Using the standard laboratory strain, P. falciparum NF54, 11 SMFAs were performed with RBCs from four separate donors to demonstrate that RBCs cryo-preserved in the gaseous phase of liquid nitrogen (- 196 °C) supported gametocytogenesis in vitro and subsequent gametogenesis in Anopheles stephensi mosquitoes. Overall levels of sporogony in the mosquito, as measured by oocyst and sporozoite prevalence, as well as oocyst burden, from each of the four donors thawed after varying intervals of cryopreservation (1, 4, 8, and 12 weeks) were comparable to using ≤ 1-week old refrigerated RBCs. Lastly, the potential for cryo-preserved RBCs to serve as a suitable alternative substrate is demonstrated for a Cambodian isolate of P. falciparum across two independent SMFAs. CONCLUSIONS Basic guidelines are presented for integrating cryo-preserved RBCs into an existing laboratory/insectary framework for P. falciparum SMFAs with significant potential for reducing running costs while achieving greater reliability. Lastly, scenarios are discussed where cryo-preserved RBCs may be especially useful in enhancing the understanding and/or providing novel insights into the patterns and processes underlying human-to-mosquito transmission.
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Affiliation(s)
- Ashutosh K Pathak
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA.
| | - Justine C Shiau
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
| | - Matthew B Thomas
- Center for Infectious Disease Dynamics and the Department of Entomology, Pennsylvania State University, State College, PA, 16803, USA
| | - Courtney C Murdock
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, 30602, USA
- Center for Tropical Emerging Global Diseases, University of Georgia, Athens, GA, 30602, USA
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, 30602, USA
- Riverbasin Center, University of Georgia, Athens, GA, 30602, USA
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Arredondo SA, Swearingen KE, Martinson T, Steel R, Dankwa DA, Harupa A, Camargo N, Betz W, Vigdorovich V, Oliver BG, Kangwanrangsan N, Ishino T, Sather N, Mikolajczak S, Vaughan AM, Torii M, Moritz RL, Kappe SHI. The Micronemal Plasmodium Proteins P36 and P52 Act in Concert to Establish the Replication-Permissive Compartment Within Infected Hepatocytes. Front Cell Infect Microbiol 2018; 8:413. [PMID: 30547015 PMCID: PMC6280682 DOI: 10.3389/fcimb.2018.00413] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/08/2018] [Indexed: 12/15/2022] Open
Abstract
Within the liver, Plasmodium sporozoites traverse cells searching for a "suitable" hepatocyte, invading these cells through a process that results in the formation of a parasitophorous vacuole (PV), within which the parasite undergoes intracellular replication as a liver stage. It was previously established that two members of the Plasmodium s48/45 protein family, P36 and P52, are essential for productive invasion of host hepatocytes by sporozoites as their simultaneous deletion results in growth-arrested parasites that lack a PV. Recent studies point toward a pathway of entry possibly involving the interaction of P36 with hepatocyte receptors EphA2, CD81, and SR-B1. However, the relationship between P36 and P52 during sporozoite invasion remains unknown. Here we show that parasites with a single P52 or P36 gene deletion each lack a PV after hepatocyte invasion, thereby pheno-copying the lack of a PV observed for the P52/P36 dual gene deletion parasite line. This indicates that both proteins are equally important in the establishment of a PV and act in the same pathway. We created a Plasmodium yoelii P36mCherry tagged parasite line that allowed us to visualize the subcellular localization of P36 and found that it partially co-localizes with P52 in the sporozoite secretory microneme organelles. Furthermore, through co-immunoprecipitation studies in vivo, we determined that P36 and P52 form a protein complex in sporozoites, indicating a concerted function for both proteins within the PV formation pathway. However, upon sporozoite stimulation, only P36 was released as a secreted protein while P52 was not. Our results support a model in which the putatively glycosylphosphatidylinositol (GPI)-anchored P52 may serve as a scaffold to facilitate the interaction of secreted P36 with the host cell during sporozoite invasion of hepatocytes.
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Affiliation(s)
- Silvia A. Arredondo
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | | | - Thomas Martinson
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Ryan Steel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Dorender A. Dankwa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Anke Harupa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Nelly Camargo
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - William Betz
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Brian G. Oliver
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Niwat Kangwanrangsan
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tomoko Ishino
- Department of Molecular Parasitology, Proteo-Science Center, Ehime University, Shitsukawa, Toon, Japan
| | - Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Sebastian Mikolajczak
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Motomi Torii
- Department of Molecular Parasitology, Proteo-Science Center, Ehime University, Shitsukawa, Toon, Japan
| | | | - Stefan H. I. Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
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45
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Firooziyan S, Dinparast Djadid N, Gholizadeh S. Speculation on the possibility for introducing Anopheles stephensi as a species complex: preliminary evidence based on odorant binding protein 1 intron I sequence. Malar J 2018; 17:366. [PMID: 30326917 PMCID: PMC6191895 DOI: 10.1186/s12936-018-2523-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 10/09/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Anopheles stephensi is considered an important malaria vector in Iran, Asia, and recently in the Horn of Africa. Recently, Ansteobp1 intron I sequence has been introduced a new molecular marker for identification of its biological forms including, mysorensis, intermediate and type, using insectary colony specimens. METHODS In the current study, new marker ability in molecular identification of biological forms has been evaluated with An. stephensi specimens collected from Iran and Afghanistan malarious provinces. Following DNA extraction and PCR amplification, sequence analysis and constructed phylogenetic tree revealed that type and intermediate forms are distributed in Iran. RESULTS The specimens collected from Afghanistan identified as intermediate and mysorensis forms. Therefore, intermediate form is sympatric species in both countries. Based on the results of Ansteobp1 intron I sequences, An. stephensi could be suggested as new Anopheles complex species including An. stephensi sibling A (type form), An. stephensi sibling B (intermediate form) and An. stephensi sibling C (mysorensis form). This is the first report on the presence of An. stephensi biological forms in Afghanistan. CONCLUSIONS Iran is going to eliminate malaria transmission from the country, precise species identification, especially in complex species will be helpful in the prevention of malaria resurgence in the country, mainly because of common fauna of Anopheles species and through border malaria and population movement within Afghanistan, Pakistan, and Iran.
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Affiliation(s)
- Samira Firooziyan
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, P.O. Box: 5756115198, Iran.,Medical Entomology Department, School of Public Health, Urmia University of Medical Sciences, Urmia, Iran
| | - Navid Dinparast Djadid
- Malaria and Vector Research Group, National Insectarium, Pasteur Institute of Iran, Tehran, Iran
| | - Saber Gholizadeh
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, P.O. Box: 5756115198, Iran. .,Medical Entomology Department, School of Public Health, Urmia University of Medical Sciences, Urmia, Iran.
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46
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Reid W, Pilitt K, Alford R, Cervantes-Medina A, Yu H, Aluvihare C, Harrell R, O'Brochta DA. An Anopheles stephensi Promoter-Trap: Augmenting Genome Annotation and Functional Genomics. G3 (BETHESDA, MD.) 2018; 8:3119-3130. [PMID: 30135106 PMCID: PMC6169391 DOI: 10.1534/g3.118.200347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022]
Abstract
The piggyBac transposon was modified to generate gene trap constructs, which were then incorporated into the genome of the Asian malaria vector, Anopheles stephensi and remobilized through genetic crosses using a piggyBac transposase expressing line. A total of 620 remobilization events were documented, and 73 were further characterized at the DNA level to identify patterns in insertion site preferences, remobilization frequencies, and remobilization patterns. Overall, the use of the tetameric AmCyan reporter as the fusion peptide displayed a preference for insertion into the 5'-end of transcripts. Notably 183 - 44882 bp upstream of the An. stephensi v1.0 ab initio gene models, which demonstrated that the promoter regions for the genes of An. stephensi are further upstream of the 5'-proximal regions of the genes in the ab inito models than may be otherwise predicted. RNA-Seq transcript coverage supported the insertion of the splice acceptor gene trap element into 5'-UTR introns for nearly half of all insertions identified. The use of a gene trap element that prefers insertion into the 5'-end of genes supports the use of this technology for the random generation of knock-out mutants, as well as the experimental confirmation of 5'-UTR introns in An. stephensi.
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Affiliation(s)
- William Reid
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Kristina Pilitt
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Robert Alford
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Adriana Cervantes-Medina
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Hao Yu
- Department of Plant Protection, Henan Institute of Science and Technology, East Street Huan-Lan, Xinxiang City, Henan Province 453003, CHINA
| | - Channa Aluvihare
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - Rob Harrell
- Insect Transformation Facility, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
| | - David A O'Brochta
- Institute for Bioscience and Biotechnology Research, University of Maryland College Park, 9600 Gudelsky Drive, Rockville, MD 20850-3467
- Department of Entomology, University of Maryland College Park, 4112 Plant Sciences Building, College Park, MD 20742-4454
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Soghigian J, Andreadis TG, Molaei G. Population genomics of Culiseta melanura, the principal vector of Eastern equine encephalitis virus in the United States. PLoS Negl Trop Dis 2018; 12:e0006698. [PMID: 30118494 PMCID: PMC6114928 DOI: 10.1371/journal.pntd.0006698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/29/2018] [Accepted: 07/17/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Eastern Equine Encephalitis (EEE) (Togaviridae, Alphavirus) is a highly pathogenic mosquito-borne arbovirus that circulates in an enzootic cycle involving Culiseta melanura mosquitoes and wild Passeriformes birds in freshwater swamp habitats. Recently, the northeastern United States has experienced an intensification of virus activity with increased human involvement and northward expansion into new regions. In addition to its principal role in enzootic transmission of EEE virus among avian hosts, recent studies on the blood-feeding behavior of Cs. melanura throughout its geographic range suggest that this mosquito may also be involved in epizootic / epidemic transmission to equines and humans in certain locales. Variations in blood feeding behavior may be a function of host availability, environmental factors, and/or underlying genetic differences among regional populations. Despite the importance of Cs. melanura in transmission and maintenance of EEE virus, the genetics of this species remains largely unexplored. METHODOLOGY AND PRINCIPLE FINDINGS To investigate the occurrence of genetic variation in Cs. melanura, the genome of this mosquito vector was sequenced resulting in a draft genome assembly of 1.28 gigabases with a contig N50 of 93.36 kilobases. Populations of Cs. melanura from 10 EEE virus foci in the eastern North America were genotyped with double-digest RAD-seq. Following alignment of reads to the reference genome, variant calling, and filtering, 40,384 SNPs were retained for downstream analyses. Subsequent analyses revealed genetic differentiation between northern and southern populations of this mosquito species. Moreover, limited fine-scale population structure was detected throughout northeastern North America, suggesting local differentiation of populations but also a history of ancestral polymorphism or contemporary gene flow. Additionally, a genetically distinct cluster was identified predominantly at two northern sites. CONCLUSION AND SIGNIFICANCE This study elucidates the first evidence of fine-scale population structure in Cs. melanura throughout its eastern range and detects evidence of gene flow between populations in northeastern North America. This investigation provides the groundwork for examining the consequences of genetic variations in the populations of this mosquito species that could influence vector-host interactions and the risk of human and equine infection with EEE virus.
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Affiliation(s)
- John Soghigian
- Department of Environmental Sciences, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
| | - Theodore G. Andreadis
- Department of Environmental Sciences, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Goudarz Molaei
- Department of Environmental Sciences, Center for Vector Biology & Zoonotic Diseases, The Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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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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49
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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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50
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Xiang L, Cai C, Cheng J, Wang L, Wu C, Shi Y, Luo J, He L, Deng Y, Zhang X, Yuan Y, Cai Y. Identification of circularRNAs and their targets in Gossypium under Verticillium wilt stress based on RNA-seq. PeerJ 2018; 6:e4500. [PMID: 29576969 PMCID: PMC5858604 DOI: 10.7717/peerj.4500] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/23/2018] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt response have not been identified up to now. In this study, two CSSLs (chromosome segment substitution lines) of G.barbadense introgressed into G. hirsutum, CSSL-1 and CSSL-4 (a resistant line and a susceptible line to Verticillium wilt, respectively), were inoculated with V. dahliae for RNA-seq library construction and circRNA analysis. A total of 686 novel circRNAs were identified. CSSL-1 and CSSL-4 had similar numbers of circRNAs and shared many circRNAs in common. However, CSSL-4 differentially expressed approximately twice as many circRNAs as CSSL-1, and the differential expression levels of the common circRNAs were generally higher in CSSL-1 than in CSSL-4. Moreover, two C-RRI comparisons, C-RRI-vs-C-RRM and C-RRI-vs-C-RSI, possessed a large proportion (approximately 50%) of the commonly and differentially expressed circRNAs. These results indicate that the differentially expressed circRNAs may play roles in the Verticillium wilt response in cotton. A total of 280 differentially expressed circRNAs were identified. A Gene Ontology analysis showed that most of the ‘stimulus response’ term source genes were NBS family genes, of which most were the source genes from the differentially expressed circRNAs, indicating that NBS genes may play a role in Verticillium wilt resistance and might be regulated by circRNAs in the disease-resistance process in cotton.
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Affiliation(s)
- Liuxin Xiang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China.,School of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Chaowei Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China
| | - Jieru Cheng
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China
| | - Lu Wang
- School of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Chaofeng Wu
- School of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, China
| | - Jingzhi Luo
- School of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Lin He
- School of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yushan Deng
- School of Bioinformatics, School of Software Engineering, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Xiao Zhang
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Cotton Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Anyang, Henan, China
| | - Yingfan Cai
- State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng, Henan, China
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