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Boddé M, Makunin A, Ayala D, Bouafou L, Diabaté A, Ekpo UF, Kientega M, Le Goff G, Makanga BK, Ngangue MF, Omitola OO, Rahola N, Tripet F, Durbin R, Lawniczak MKN. High-resolution species assignment of Anopheles mosquitoes using k-mer distances on targeted sequences. eLife 2022; 11:e78775. [PMID: 36222650 PMCID: PMC9648975 DOI: 10.7554/elife.78775] [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: 03/18/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
The ANOSPP amplicon panel is a genus-wide targeted sequencing panel to facilitate large-scale monitoring of Anopheles species diversity. Combining information from the 62 nuclear amplicons present in the ANOSPP panel allows for a more senstive and specific species assignment than single gene (e.g. COI) barcoding, which is desirable in the light of permeable species boundaries. Here, we present NNoVAE, a method using Nearest Neighbours (NN) and Variational Autoencoders (VAE), which we apply to k-mers resulting from the ANOSPP amplicon sequences in order to hierarchically assign species identity. The NN step assigns a sample to a species-group by comparing the k-mers arising from each haplotype's amplicon sequence to a reference database. The VAE step is required to distinguish between closely related species, and also has sufficient resolution to reveal population structure within species. In tests on independent samples with over 80% amplicon coverage, NNoVAE correctly classifies to species level 98% of samples within the An. gambiae complex and 89% of samples outside the complex. We apply NNoVAE to over two thousand new samples from Burkina Faso and Gabon, identifying unexpected species in Gabon. NNoVAE presents an approach that may be of value to other targeted sequencing panels, and is a method that will be used to survey Anopheles species diversity and Plasmodium transmission patterns through space and time on a large scale, with plans to analyse half a million mosquitoes in the next five years.
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Affiliation(s)
- Marilou Boddé
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | - Diego Ayala
- Institut de Recherche pour le Développement, MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellier,France
| | - Lemonde Bouafou
- Institut de Recherche pour le Développement, MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellier,France
| | - Abdoulaye Diabaté
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l'OuestBobo-DioulassoBurkina Faso
| | | | - Mahamadi Kientega
- Institut de Recherche en Sciences de la Santé, Direction Régionale de l'OuestBobo-DioulassoBurkina Faso
| | - Gilbert Le Goff
- Institut de Recherche pour le Développement, MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellier,France
| | | | - Marc F Ngangue
- Centre International de Recherches Medicales de FrancevilleFrancevilleGabon
| | | | - Nil Rahola
- Institut de Recherche pour le Développement, MIVEGEC, Univ. Montpellier, CNRS, IRDMontpellier,France
| | - Frederic Tripet
- Centre for Applied Entomology and Parasitology, Keele UniversityNewcastleUnited Kingdom
| | - Richard Durbin
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger InstituteHinxtonUnited Kingdom
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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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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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4
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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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5
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Fouet C, Kamdem C, Gamez S, White BJ. Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group. Evol Appl 2017; 10:897-906. [PMID: 29151881 PMCID: PMC5680430 DOI: 10.1111/eva.12492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 01/16/2023] Open
Abstract
Ongoing speciation in the most important African malaria vectors gives rise to cryptic populations, which differ remarkably in their behavior, ecology, and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is crucial for effective disease control because heterogeneity within vector species contributes to variability in malaria cases and allow fractions of populations to escape control efforts. To examine population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group-a large taxonomic group that diverged ~3 Myr ago. Using 4,343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high-FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA, and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.
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Affiliation(s)
- Caroline Fouet
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Colince Kamdem
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Stephanie Gamez
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Bradley J. White
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
- Center for Disease Vector ResearchInstitute for Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
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6
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Ayala D, Acevedo P, Pombi M, Dia I, Boccolini D, Costantini C, Simard F, Fontenille D. Chromosome inversions and ecological plasticity in the main African malaria mosquitoes. Evolution 2017; 71:686-701. [PMID: 28071788 DOI: 10.1111/evo.13176] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/22/2016] [Indexed: 01/30/2023]
Abstract
Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes.
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Affiliation(s)
- Diego Ayala
- UMR 224 MIVEGEC/ESV, IRD, Montpellier, 34394, France.,CIRMF, BP 769, Franceville, Gabon
| | - Pelayo Acevedo
- SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC), CSIC-UCLM-JCCM, Ciudad Real, 13005, Spain
| | - Marco Pombi
- Sezione di Parassitologia, Dipartimento di Scienze di Sanità Pubblica, Università di Roma "La Sapienza,", Rome, 00185, Italy
| | - Ibrahima Dia
- Medical Entomology Unit, Institut Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Daniela Boccolini
- Department MIPI, Unit Vector-Borne Diseases and International Health, Istituto Superiore di Sanità, Rome, 00161, Italy
| | | | | | - Didier Fontenille
- UMR 224 MIVEGEC/ESV, IRD, Montpellier, 34394, France.,Current Address: Institut Pasteur du Cambodge, BP 983, Phnom Penh, Cambodia
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The Physical Genome Mapping of Anopheles albimanus Corrected Scaffold Misassemblies and Identified Interarm Rearrangements in Genus Anopheles. G3-GENES GENOMES GENETICS 2017; 7:155-164. [PMID: 27821634 PMCID: PMC5217105 DOI: 10.1534/g3.116.034959] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The genome of the Neotropical malaria vector Anopheles albimanus was sequenced as part of the 16 Anopheles Genomes Project published in 2015. The draft assembly of this species consisted of 204 scaffolds with an N50 scaffold size of 18.1 Mb and a total assembly size of 170.5 Mb. It was among the smallest genomes with the longest scaffolds in the 16 Anopheles species cluster, making An. albimanus the logical choice for anchoring the genome assembly to chromosomes. In this study, we developed a high-resolution cytogenetic photomap with completely straightened polytene chromosomes from the salivary glands of the mosquito larvae. Based on this photomap, we constructed a chromosome-based genome assembly using fluorescent in situ hybridization of PCR-amplified DNA probes. Our physical mapping, assisted by an ortholog-based bioinformatics approach, identified and corrected nine misassemblies in five large genomic scaffolds. Misassemblies mostly occurred in junctions between contigs. Our comparative analysis of scaffolds with the An. gambiae genome detected multiple genetic exchanges between pericentromeric regions of chromosomal arms caused by partial-arm translocations. The final map consists of 40 ordered genomic scaffolds and corrected fragments of misassembled scaffolds. The An. albimanus physical map comprises 98.2% of the total genome assembly and represents the most complete genome map among mosquito species. This study demonstrates that physical mapping is a powerful tool for correcting errors in draft genome assemblies and for creating chromosome-anchored reference genomes.
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Adler PH, Yadamsuren O, Procunier WS. Chromosomal Translocations in Black Flies (Diptera: Simuliidae)-Facilitators of Adaptive Radiation? PLoS One 2016; 11:e0158272. [PMID: 27348428 PMCID: PMC4922673 DOI: 10.1371/journal.pone.0158272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 06/13/2016] [Indexed: 01/03/2023] Open
Abstract
A macrogenomic investigation of a Holarctic clade of black flies-the Simulium cholodkovskii lineage-provided a platform to explore the implications of a unique, synapomorphic whole-arm interchange in the evolution of black flies. Nearly 60 structural rearrangements were discovered in the polytene complement of the lineage, including 15 common to all 138 analyzed individuals, relative to the central sequence for the entire subgenus Simulium. Three species were represented, of which two Palearctic entities (Simulium cholodkovskii and S. decimatum) were sympatric; an absence of hybrids confirmed their reproductive isolation. A third (Nearctic) entity had nonhomologous sex chromosomes, relative to the other species, and is considered a separate species, for which the name Simulium nigricoxum is revalidated. A cytophylogeny is inferred and indicates that the two Palearctic taxa are sister species and these, in turn, are the sister group of the Nearctic species. The rise of the S. cholodkovskii lineage encompassed complex chromosomal and genomic restructuring phenomena associated with speciation in black flies, viz. expression of one and the same rearrangement as polymorphic, fixed, or sex linked in different species; taxon-specific differentiation of sex chromosomes; and reciprocal translocation of chromosome arms. The translocation is hypothesized to have occurred early in male spermatogonia, with the translocated chromosomal complement being transmitted to the X- and Y-bearing sperm during spermatogenesis, resulting in alternate disjunction of viable F1 translocation heterozygotes and the eventual formation of more viable and selectable F2 translocation homozygous progeny. Of 11 or 12 independently derived whole-arm interchanges known in the family Simuliidae, at least six are associated with subsequent speciation events, suggesting a facilitating role of translocations in adaptive radiations. The findings are discussed in the context of potential structural and functional interactions for future genomic research.
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Affiliation(s)
- Peter H. Adler
- Department of Agricultural and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Oyunchuluun Yadamsuren
- Department of Biology, Mongolian National University of Education, Ulaanbaatar, Mongolia
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9
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Artemov GN, Sharakhova MV, Naumenko AN, Karagodin DA, Baricheva EM, Stegniy VN, Sharakhov IV. A standard photomap of ovarian nurse cell chromosomes in the European malaria vector Anopheles atroparvus. MEDICAL AND VETERINARY ENTOMOLOGY 2015; 29:230-237. [PMID: 25776224 PMCID: PMC4515173 DOI: 10.1111/mve.12113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/20/2014] [Accepted: 06/04/2014] [Indexed: 06/04/2023]
Abstract
Anopheles atroparvus (Diptera: Culicidae) is one of the main malaria vectors of the Maculipennis group in Europe. Cytogenetic analysis based on salivary gland chromosomes has been used in taxonomic and population genetic studies of mosquitoes from this group. However, a high-resolution cytogenetic map that could be used in physical genome mapping in An. atroparvus is still lacking. In the present study, a high-quality photomap of the polytene chromosomes from ovarian nurse cells of An. atroparvus was developed. Using fluorescent in situ hybridization, 10 genes from the five largest genomic supercontigs on the polytene chromosome were localized and 28% of the genome was anchored to the cytogenetic map. The study established chromosome arm homology between An. atroparvus and the major African malaria vector Anopheles gambiae, suggesting a whole-arm translocation between autosomes of these two species. The standard photomap constructed for ovarian nurse cell chromosomes of An. atroparvus will be useful for routine physical mapping. This map will assist in the development of a fine-scale chromosome-based genome assembly for this species and will also facilitate comparative and evolutionary genomics studies in the genus Anopheles.
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Affiliation(s)
- Gleb N. Artemov
- Tomsk State University, Institute of Biology and Biophysics, Tomsk, Russia
| | - Maria V. Sharakhova
- Tomsk State University, Institute of Biology and Biophysics, Tomsk, Russia
- Virginia Tech, Department of Entomology, Fralin Life Science Institute, Blacksburg, VA, USA
| | - Anastasia N. Naumenko
- Virginia Tech, Department of Entomology, Fralin Life Science Institute, Blacksburg, VA, USA
| | | | | | | | - Igor V. Sharakhov
- Virginia Tech, Department of Entomology, Fralin Life Science Institute, Blacksburg, VA, USA
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10
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Sharakhova MV, Antonio-Nkondjio C, Xia A, Ndo C, Awono-Ambene P, Simard F, Sharakhov IV. Polymorphic chromosomal inversions in Anopheles moucheti, a major malaria vector in Central Africa. MEDICAL AND VETERINARY ENTOMOLOGY 2014; 28:337-340. [PMID: 24192050 PMCID: PMC4010561 DOI: 10.1111/mve.12037] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/29/2013] [Accepted: 09/09/2013] [Indexed: 06/02/2023]
Abstract
Anopheles moucheti Evans (Diptera: Culicidae) is a major vector of malaria in forested areas of Central Africa. However, few genetic tools are available for this species. The present study represents the first attempt to characterize chromosomes in An. moucheti females collected in Cameroon. Ovarian nurse cells contained polytene chromosomes, which were suitable for standard cytogenetic applications. The presence of three polymorphic chromosomal inversions in An. moucheti was revealed. Two of these inversions were located on the 2R chromosome arm. The homology between the 2R chromosome arms of An. moucheti and Anopheles gambiae Giles was established by fluorescent in situ hybridization of six An. gambiae genic sequences. Mapping of the probes on chromosomes of An. moucheti detected substantial gene order reshuffling between the two species. The presence of polytene chromosomes and polymorphic inversions in An. moucheti provides a new basis for further population genetic, taxonomic and ecological studies of this neglected malaria vector.
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Affiliation(s)
- Maria V. Sharakhova
- Department of Entomology, 203 Fralin Life Science Institute, MC 0346, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Ai Xia
- Department of Entomology, 203 Fralin Life Science Institute, MC 0346, Virginia Tech, Blacksburg, VA 24061, USA
| | - Cyrille Ndo
- Malaria Research Laboratory, OCEAC, PO Box 288, Yaoundé, Cameroon
- MIVEGEC (UMR IRD224-CNRS5290-UM1-UM2), Institut de Recherche pour le Développement (IRD), BP 64501, 34394, Montpellier, Cedex 5, France
- Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, Cameroon
| | | | - Frederic Simard
- MIVEGEC (UMR IRD224-CNRS5290-UM1-UM2), Institut de Recherche pour le Développement (IRD), BP 64501, 34394, Montpellier, Cedex 5, France
| | - Igor V. Sharakhov
- Department of Entomology, 203 Fralin Life Science Institute, MC 0346, Virginia Tech, Blacksburg, VA 24061, USA
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11
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Kamali M, Marek PE, Peery A, Antonio-Nkondjio C, Ndo C, Tu Z, Simard F, Sharakhov IV. Multigene phylogenetics reveals temporal diversification of major African malaria vectors. PLoS One 2014; 9:e93580. [PMID: 24705448 PMCID: PMC3976319 DOI: 10.1371/journal.pone.0093580] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/05/2014] [Indexed: 12/21/2022] Open
Abstract
The major vectors of malaria in sub-Saharan Africa belong to subgenus Cellia. Yet, phylogenetic relationships and temporal diversification among African mosquito species have not been unambiguously determined. Knowledge about vector evolutionary history is crucial for correct interpretation of genetic changes identified through comparative genomics analyses. In this study, we estimated a molecular phylogeny using 49 gene sequences for the African malaria vectors An. gambiae, An. funestus, An. nili, the Asian malaria mosquito An. stephensi, and the outgroup species Culex quinquefasciatus and Aedes aegypti. To infer the phylogeny, we identified orthologous sequences uniformly distributed approximately every 5 Mb in the five chromosomal arms. The sequences were aligned and the phylogenetic trees were inferred using maximum likelihood and neighbor-joining methods. Bayesian molecular dating using a relaxed log normal model was used to infer divergence times. Trees from individual genes agreed with each other, placing An. nili as a basal clade that diversified from the studied malaria mosquito species 47.6 million years ago (mya). Other African malaria vectors originated more recently, and independently acquired traits related to vectorial capacity. The lineage leading to An. gambiae diverged 30.4 mya, while the African vector An. funestus and the Asian vector An. stephensi were the most closely related sister taxa that split 20.8 mya. These results were supported by consistently high bootstrap values in concatenated phylogenetic trees generated individually for each chromosomal arm. Genome-wide multigene phylogenetic analysis is a useful approach for discerning historic relationships among malaria vectors, providing a framework for the correct interpretation of genomic changes across species, and comprehending the evolutionary origins of this ubiquitous and deadly insect-borne disease.
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Affiliation(s)
- Maryam Kamali
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Paul E Marek
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Ashley Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | | | - Cyrille Ndo
- Malaria Research Laboratory, OCEAC, Yaounde, Cameroon; MIVEGEC (UMR IRD224-CNRS5290-UM1-UM2), Institut de Recherche pour le Développement (IRD), Montpellier, France; Faculty of Medicine and Pharmaceutical Sciences, University of Douala, Douala, Cameroon
| | - Zhijian Tu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Frederic Simard
- MIVEGEC (UMR IRD224-CNRS5290-UM1-UM2), Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Igor V Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
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