About

Maria Sharakhova is an Assistant Professor in the Department of Entomology at Virginia Tech. Her research focuses on mosquito genomics, cytogenetics, and population genomics, particularly in relation to disease vectors such as Aedes aegypti, Aedes albopictus, Culex pipiens complex, and Cx. tarsalis. She has been involved in sequencing, physical mapping, and genome assembly projects for various mosquito species, utilizing advanced genomic technologies like PacBio sequencing, Hi-C scaffolding, and optical mapping to improve genome annotations and understand structural variations. Her work aims to develop genome-based approaches for vector control by studying chromosomal rearrangements, evolution of sex-determining chromosomes, and the genetic basis of traits related to pathogen transmission and insecticide resistance. With a background in cytogenetics and genetics, her contributions include significant advancements in the genetics of disease vectors, providing foundational knowledge for epidemiological and vector control strategies.

Research topics

• Biology
• Ecology
• Sociology
• Evolutionary biology
• Genetics
• Computational biology
• Medicine
• Demography
• Internal medicine
• Zoology

Selected publications

• The Expansion of Dirofilaria repens in the Irtysh Basin of Western Siberia Is Associated with Nine Species of Aedes Mosquitoes

  Insects · 2026-04-07

  articleOpen accessCorresponding

  The northward expansion of Dirofilaria spp. is a current medical and veterinary concern. However, it is unclear how far north the parasite has spread in Western Siberia and what species of mosquito can carry and transmit it. This study examined Dirofilaria spp. infection in Aedes mosquitoes in the taiga zone of the Irtysh Basin. The mosquito species were identified based on morphology, and Dirofilaria spp. were identified using PCR. Of the 13 habitats surveyed, 24 of 2205 mosquito samples were infected with D. repens and 1 with Dirofilaria sp. The highest infection rate (~7.6) was recorded in Tobolsk, Tyumen region, at 58.4° N. Mosquito infection was recorded as far north as 61° N in Khanty-Mansiysk. The presence of the infective L3 stage of the parasite was recorded up to 60° N in Bobrovsky. Nine species of mosquitoes were found to be infected with D. repens: Aedes rossicus, Aedes behningi, Aedes cantans, Aedes communis, Aedes cyprius, Aedes euedes, Aedes excrucians, Aedes flavescens, and Aedes sticticus. Two of these species, Ae. behningi and Ae. communis, were competent vectors of the parasite. Thus, D. repens has successfully adapted to the Aedes mosquito in the taiga zone of Siberia.

  PublisherOA PDFDOI

• Species Composition, Ecological Preferences, and Chromosomal Polymorphism of Malaria Mosquitoes of the Crimean Peninsula and the Black Sea Coast of the Caucasus

  Insects · 2025-04-01

  articleOpen access

  In this study, we sampled malaria mosquito larvae in natural and artificial breeding places to study the geographical distribution, ecological preferences, and chromosomal variability of different species of the genus Anopheles in the territory of the Crimean Peninsula and the Black Sea coast of the Caucasus. Species were diagnosed using a combination of morphological, cytogenetic, and molecular markers. The ecological conditions of the larval habitats, such as dissolved oxygen content in the water, acidity, salinity, and temperature, were measured. Seven species of malaria mosquitoes were identified in the pool of 2229 individual mosquitoes collected at 56 breeding sites, including An. atroparvus, An. claviger, An. daciae (formerly identified as An. messeae s. l.), An. hyrcanus, An. maculipennis s. s., An. plumbeus, and An. melanoon. The previously recorded species of An. algeriensis, An. messeae s. s., An. sacharovi, and An. superpictus were not found in this study. Anopheles maculipennis was dominant in typical anophylogenic water bodies. Anopheles plumbeus, which used to breed mainly in tree holes in coastal forests, has spread to urban settlements along the Black Sea coast and breeds in artificial containers. Chromosomal polymorphism was studied and found in An. atroparvus and An. daciae populations. Differences in the chromosomal composition of An. daciae populations in Crimea and on the Black Sea coast of the Caucasus were revealed. The Crimean population had a low level of polymorphism in autosomal inversions. The data obtained in this study can be used to inform a better control of potential malaria vectors in the Black Sea coastal region.

  PublisherOA PDFDOI

• From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives

  Genome Biology and Evolution · 2025-07-12 · 2 citations

  articleOpen access

  The yellow fever mosquito (Aedes aegypti) is an organism of high medical importance because it is the primary vector for diseases such as yellow fever, Zika, dengue, and chikungunya. Its medical importance has made it a subject of numerous efforts to understand its biology. One such effort was the development of a high-quality reference genome (AaegL5). However, this reference genome was sourced from a highly inbred laboratory strain with unknown geographic origin. Thus, the reference is not representative of a wild mosquito, let alone one from its native range in sub-Saharan Africa. To better understand the genetic architecture of Ae. aegypti and their sister species, we developed two de novo chromosome-scale genomes with sequences sourced from single individuals: one of Ae. aegypti formosus (Aaf) from Burkina Faso and one of Aedes mascarensis (Am) from Mauritius. Both genomes exhibit high contiguity and gene completeness, comparable to AaegL5. While Aaf exhibits a high degree of synteny to AaegL5, it also exhibits several large inversions. We also conducted comparative genomic analyses using our genomes and other publicly available culicid reference genomes to find extensive chromosomal rearrangements between major lineages. The expanded gene families common to Aaf, AaegL5, and Am revealed that while the overarching category of genes that have expanded are similar, the specific genes that have expanded differ. Our findings elucidate novel insights into chromosome evolution at both microevolutionary and macroevolutionary scales. The genomic resources we present are additions to a growing arsenal for biologists in understanding mosquito biology and genome evolution.

  PublisherOA PDFDOI

• The Species-Specific Inversion Polymorphism of the X Chromosome in Anopheles messeae and Anopheles daciae Is Based on the Common Ancestral Variant X1

  Genes · 2025-12-19

  articleOpen access

  Background/Objectives: Chromosomal inversions play an important role in the evolution of insects by forming genetic barriers between closely related species and facilitating local adaptation. Polymorphic inversions in malaria mosquitoes of the Maculipennis subgroup have been studied for over 50 years, yet the evolutionary ancestry of the gene orders remains unknown. In this study, we mapped the genes flanking the breakpoints of two polymorphic X-chromosome inversions in the cryptic species Anopheles messeae and Anopheles daciae of the Maculipennis subgroup. Methods: We used an iterative mapping approach to define the breakpoint regions, selecting flanking markers based on the genome assembly of the reference species, Anopheles atroparvus. To identify the ancestral X chromosomal arrangement in An. messeae and An. daciae, we developed and implemented the genomic inversion calculator (GIC), which uses greedy heuristics to determine the shortest evolutionary scenario of rearrangements. Results: Our knowledge of the relative genomic positions of the inversion breakpoints in An. daciae and An. messeae enabled us to use the An. atroparvus genome as an outgroup and the GIC tool to show that the X0 and X2 arrangements emerged independently along the evolutionary lineages of An. daciae and An. messeae, respectively, based on the X1 arrangement. Conclusions: These results refine the structure and boundaries of the X chromosome rearrangements and reconstruct the sequence of evolutionary events in the cryptic complex An. messeae–An. daciae, demonstrating that the X1 arrangement is ancestral. This study lays the groundwork for analyzing the molecular organization of breakpoints, the mechanisms of inversion formation, and their role in speciation.

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• Protocol for Hi-C-based identification of chromosomal inversions in mosquitoes

  STAR Protocols · 2025-09-23 · 1 citations

  articleOpen access

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  PublisherDOI

• Tomsk school of evolutionary cytogenetics of malaria mosquitoes

  Vestnik Tomskogo gosudarstvennogo universiteta Biologiya · 2025-01-01

  articleOpen accessSenior author

  In this article we provide a brief overview of research in the main areas of evolutionary cytogenetics of malaria mosquitoes initiated in the 1960s at Tomsk State University. The threat of mass malaria in the Soviet Union was eliminated in the 1950s and 1960s. However, malaria mosquitoes were not destroyed and still remain potential or actual carriers of infectious diseases such as malaria and dirofilariasis. A great contribution to the study of the ecology of malaria mosquitoes in our country was made by the outstanding Russian zoologist and ecologist Vladimir Nikolaevich Beklimishev (1890-1962), who wrote the fundamental work "Ecology of the Malaria Mosquito" in 1944. In the 1950s and 1970s, the American zoologist James B. Kitzmiller (1918-1995) was very actively involved in the cytogenetics of malaria mosquitoes in North America. Using interspecific hybridization, he proved the relationship between the mosquito species of North America and Eurasia and the more ancient origin of the Nearctic group. Kitzmiller's works clearly demonstrated the relevance and timeliness of studying the paleoarctic group of mosquitoes using cytogenetic methods. The ideological inspirer of conducting cytogenetic research at Tomsk University was Tatyana Semenovna Pestryakova (1909-1996), who headed the Department of Invertebrate Zoology at TSU from 1964 to 1974 and had previously studied the ecology of Siberian malaria mosquitoes. Work on the study of the chromosomes of malaria mosquitoes of the Maculipennis group began with the support and participation of the head of the Department of Cytology and Genetics of TSU Nadezhda Nikolaevna Kartashova (19071998). The first published works were devoted to the characterization of the karyotype of Anopheles messeae of the Middle Ob region and the cytogenetic identification of sibling species of malaria mosquitoes An. maculipennis and An. messeae. Vladimir Nikolaevich Stegniy (1946-2023), together with Valentina Matveyevna Kabanova, was the first to use the cytogenetic method to describe a new species of mosquito -An. beklemishevi Stegniy & Kabanova, 1976, named in honor of V. N. Beklemishev. Studying the chromosomes of different mosquito species at different stages of development, V.N. Stegniy discovered that the spatial organization of chromosomes changes significantly during ontogenesis and speciation. It turned out that An. messeae has the largest range among the species of the Maculipennis group, covering almost the entire Boreal subregion of the Paleoarctic, and the greatest inversion polymorphism, which is a classic example of adaptive chromosomal polymorphism. The first works formed three main areas of research on the evolutionary cytogenetics of mosquitoes: 1) species composition and phylogenetic relationships of malaria mosquitoes; 2) reorganization of the spatial architecture of the malaria mosquito genome in ontogenesis and evolution; 3) population and ecological genetics of malaria mosquitoes. Reconstruction of the phylogenetic relationships of mosquito species is important for understanding how and when their genomes changed, and how this contributed to adaptation to new habitats and new pathogens, and also allows researchers to determine the geographical routes of migration and the order of speciation. The study established the geographic distribution, reproductive relationships, and chromosomal phylogenetic relationships in the Anopheles maculipennis species group. It turned out that An. beklemishevi is closest to the Eurasian species and separated from them ~20 million years ago. Thus, the common ancestor of An. beklemishevi and other Eurasian species could have migrated from North America to Eurasia when the Bering Land Bridge existed. The main malaria carriers evolved independently of each other in the Maculipennis group. These data make it possible to approach the study of the molecular genetic basis of the ability of mosquitoes of different phylogenetic lineages to effectively transmit malaria. Studies on the evolutionary cytogenetics of malaria mosquitoes, initiated at Tomsk State University in the 1960s, played an important role in the development of this field of science. They made it possible to significantly advance the understanding of the species composition and phylogenetic relationships of malaria carriers and other diseases. Studies of the spatial organization of chromosomes have provided new insights into the regulation of genomic activity during cell differentiation and the mechanisms of genome architecture reorganization in evolution. These achievements provide a basis for further study of the mechanisms of speciation and adaptation of malaria mosquitoes to changing environmental conditions and interactions with pathogens. The article contains 41 References. The authors dedicate this article to the memory of Vladimir Nikolaevich Stegniy, the founder of the scientific school for the study of cytogenetic mechanisms of evolution and adaptation of natural populations of animals and plants at Tomsk State University. The Authors declare no conflict of interest.

  PublisherOA PDFDOI

• Population Structure of the Invasive Asian Tiger Mosquito, <i>Aedes albopictus</i>, in Europe

  Ecology and Evolution · 2025-03-01 · 2 citations

  articleOpen access

  ABSTRACT The Asian tiger mosquito, Aedes albopictus , is currently the most widespread invasive mosquito species in the world. It poses a significant threat to human health, as it is a vector for several arboviruses. We used a SNP chip to genotype 748 Ae. albopictus mosquitoes from 41 localities across Europe, 28 localities in the native range in Asia, and 4 in the Americas. Using multiple algorithms, we examined population genetic structure and differentiation within Europe and across our global dataset to gain insight into the origin of the invasive European populations. We also compared results from our SNP data to those obtained using genotypes from 11 microsatellite loci ( N = 637 mosquitoes from 25 European localities) to explore how sampling effort and the type of genetic marker used may influence conclusions about Ae. albopictus population structure. While some analyses detected more than 20 clusters worldwide, we found mosquitoes could be grouped into 7 distinct genetic clusters, with most European populations originating in East Asia (Japan or China). Interestingly, some populations in Eastern Europe did not share genetic ancestry with any populations from the native range or Americas, indicating that these populations originated from areas not sampled in this study. The SNP and microsatellite datasets found similar patterns of genetic differentiation in Europe, but the microsatellite dataset could not detect the more subtle genetic structure revealed using SNPs. Overall, data from the SNP chip offered a higher resolution for detecting the genetic structure and the potential origins of invasions.

  PublisherOA PDFDOI

• Chromosomal Inversions and Their Potential Impact on the Evolution of Arboviral Vector <i>Aedes aegypti</i>

  Genome Biology and Evolution · 2025-06-07 · 5 citations

  articleOpen accessSenior author

  Chromosomal inversions play a crucial role in evolution and have been found to regulate epidemiologically significant traits in malaria mosquitoes. However, they have not been characterized in Aedes aegypti, the primary vector of arboviruses, due to the poor structure of its polytene chromosomes. The Hi-C proximity ligation approach was used to identify chromosomal inversions in 25 strains of A. aegypti obtained from its worldwide distribution and in one strain of Aedes mascarensis. The study identified 21 multimegabase polymorphic inversions ranging in size from 5 to 55 Mbp. Inversions were more abundant in African than in non-African strains, 15 versus 3 inversions, with the highest number observed in West Africa. All inversions were grouped into two geographic clusters of African or non-African origin, suggesting their association with A. aegypti subspecies. Inversions were unevenly distributed along chromosomal arms, with the highest number found in the 1q and 3p arms homologous to the inversion-rich 2R chromosomal arm in the malaria vector Anopheles gambiae. Direct comparison of inversions between A. aegypti and An. gambiae revealed significant overlap in their genomic locations. This finding may explain the parallel evolution of the two species under similar environmental conditions. Some of the inversions colocalized with chemoreceptor genes and quantitative trait loci associated with pathogen infection, suggesting their potential role in host preference and disease transmission. Our study revealed the large pool of structural variations in the A. aegypti genome and provides the foundation for future studies of their impact on the biology of this important arboviral vector.

  PublisherOA PDFDOI

• Chromosomal rearrangements in mosquitoes: from micro- to macroevolution

  Current Opinion in Insect Science · 2025-06-01 · 2 citations

  reviewOpen access1st authorCorresponding
  PublisherOA PDFDOI

• Species Composition, Ecological Preferences and Chromosomal Polymorphism of Malaria Mosquitoes of the Crimean Peninsula and the Black Sea Coast of the Caucasus

  Preprints.org · 2025-02-04

  preprintOpen access

  Ecological and genetic studies of malaria mosquitoes of the Black Sea coast have not been recently conducted despite increasing human-caused environmental changes in the area. In this study, we investigated the species composition, geographical distribution, ecological preferences, and chromosomal polymorphism of malaria mosquitoes of the Crimean Peninsula and the Black Sea coast of the Caucasus. Species were diagnosed using a combination of morphological, cytogenetic, and molecular markers. The ecological conditions of the larval habitats, such as dissolved oxygen content in the water, acidity, salinity, and temperature, were measured. Seven species of malaria mosquitoes were identified in the pool of 2229 individual mosquitoes collected at 56 breeding sites including An. atroparvus, An. claviger, An. daciae (formely identified as An. messeae s. l.), An. hyrcanus, An. maculipennis s. s., An. plumbeus and An. melanoon. The previously recorded species of An. algeriensis, An. messeae s. s., An. sacharovi, An. superpictus were not found in this study. Anopheles maculipennis was dominant in typical anophylogenic water bodies. Anopheles plumbeus, which used to breed mainly in tree holes in coastal forests, has spread to urban settlements along the Black Sea coast and breeds in artificial containers. Chromosomal polymorphism was studied and found in An. atroparvus and An. daciae populations. Differences in the chromosomal composition of An. daciae populations in Crimea and on the Black Sea coast of the Caucasus were revealed. The Crimean population had a low level of polymorphism in autosomal inversions. The data obtained in this study can be used to inform a better control of potential malaria vectors in the Black Sea coastal region.

  PublisherOA PDFDOI

Recent grants

• NIH Grant R21AI088035

  NIH · $433k · 2013

• Improving the reference genome assembly for the dengue fever vector Aedes aegypti

  NIH · $423k · 2016–2018

• A reference genome assembly for Zika vector Aedes albopictus

  NIH · $428k · 2017–2020

Frequent coauthors

• Igor V. Sharakhov

  150 shared

• Sergey Koren

  National Human Genome Research Institute

  46 shared

• Adam M. Phillippy

  National Human Genome Research Institute

  42 shared

• Zhijian Tu

  Wenzhou Medical University

  40 shared

• Andrey A. Yurchenko

  38 shared

• Atashi Sharma

  Virginia Tech

  31 shared

• Gleb N. Artemov

  National Research Tomsk State University

  26 shared

• Reem A. Masri

  Virginia Tech

  25 shared

Labs

• Maria Sharakhova LabPI

Education

• PhD, Genetics

  Institute of Cytology and Genetics

• Ms, Genetics

  Tomsk State University

  1987