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1. The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes

Author

Ryazansky, Sergei S., Chen, Chujia, Potters, Mark, Naumenko, Anastasia N., Lukyanchikova, Varvara, Masri, Reem A., Brusentsov, Ilya I., Karagodin, Dmitriy A., Yurchenko, Andrey A., dos Anjos, Vitor L., Haba, Yuki, Rose, Noah H., Hoffman, Jinna, Guo, Rong, Menna, Theresa, Kelley, Melissa, Ferrill, Emily, Schultz, Karen E., Qi, Yumin, Sharma, Atashi, Deschamps, Stéphane, Llaca, Victor, Mao, Chunhong, Murphy, Terence D., Baricheva, Elina M., Emrich, Scott, Fritz, Megan L., Benoit, Joshua B., Sharakhov, Igor V., McBride, Carolyn S., Tu, Zhijian, and Sharakhova, Maria V.

Published
2024
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3. Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group

Author

Yurchenko, Andrey A., Naumenko, Anastasia N., Artemov, Gleb N., Karagodin, Dmitry A., Hodge, James M., Velichevskaya, Alena I., Kokhanenko, Alina A., Bondarenko, Semen M., Abai, Mohammad R., Kamali, Maryam, Gordeev, Mikhail I., Moskaev, Anton V., Caputo, Beniamino, Aghayan, Sargis A., Baricheva, Elina M., Stegniy, Vladimir N., Sharakhova, Maria V., and Sharakhov, Igor V.

Published
2023
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4. Improved reference genome of the arboviral vector Aedes albopictus

Author

Palatini, Umberto, Masri, Reem A, Cosme, Luciano V, Koren, Sergey, Thibaud-Nissen, Françoise, Biedler, James K, Krsticevic, Flavia, Johnston, J Spencer, Halbach, Rebecca, Crawford, Jacob E, Antoshechkin, Igor, Failloux, Anna-Bella, Pischedda, Elisa, Marconcini, Michele, Ghurye, Jay, Rhie, Arang, Sharma, Atashi, Karagodin, Dmitry A, Jenrette, Jeremy, Gamez, Stephanie, Miesen, Pascal, Masterson, Patrick, Caccone, Adalgisa, Sharakhova, Maria V, Tu, Zhijian, Papathanos, Philippos A, Van Rij, Ronald P, Akbari, Omar S, Powell, Jeffrey, Phillippy, Adam M, and Bonizzoni, Mariangela

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Prevention, Infectious Diseases, Emerging Infectious Diseases, Rare Diseases, Human Genome, Vector-Borne Diseases, Biotechnology, Biodefense, 1.1 Normal biological development and functioning, 2.2 Factors relating to the physical environment, 3.2 Interventions to alter physical and biological environmental risks, Infection, Generic health relevance, Good Health and Well Being, Aedes, Animals, Arboviruses, Chromosome Mapping, Chromosomes, Genome, Genome Size, Immunity, Insect Vectors, Mosquito Vectors, RNA, Small Interfering, Transcriptome, Ae, albopictus, miRNAs, piRNA clusters, Viral integrations, Sex locus, Population differentiation, Developmental transcriptome, Ae. albopictus, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albopictus genome is essential to develop new approaches that involve genetic manipulation of mosquitoes.ResultsWe use long-read sequencing methods and modern scaffolding techniques (PacBio, 10X, and Hi-C) to produce AalbF2, a dramatically improved assembly of the Ae. albopictus genome. AalbF2 reveals widespread viral insertions, novel microRNAs and piRNA clusters, the sex-determining locus, and new immunity genes, and enables genome-wide studies of geographically diverse Ae. albopictus populations and analyses of the developmental and stage-dependent network of expression data. Additionally, we build the first physical map for this species with 75% of the assembled genome anchored to the chromosomes.ConclusionThe AalbF2 genome assembly represents the most up-to-date collective knowledge of the Ae. albopictus genome. These resources represent a foundation to improve understanding of the adaptation potential and the epidemiological relevance of this species and foster the development of innovative control measures.

Published
2020

5. Improved reference genome of Aedes aegypti informs arbovirus vector control

Author

Matthews, Benjamin J, Dudchenko, Olga, Kingan, Sarah B, Koren, Sergey, Antoshechkin, Igor, Crawford, Jacob E, Glassford, William J, Herre, Margaret, Redmond, Seth N, Rose, Noah H, Weedall, Gareth D, Wu, Yang, Batra, Sanjit S, Brito-Sierra, Carlos A, Buckingham, Steven D, Campbell, Corey L, Chan, Saki, Cox, Eric, Evans, Benjamin R, Fansiri, Thanyalak, Filipović, Igor, Fontaine, Albin, Gloria-Soria, Andrea, Hall, Richard, Joardar, Vinita S, Jones, Andrew K, Kay, Raissa GG, Kodali, Vamsi K, Lee, Joyce, Lycett, Gareth J, Mitchell, Sara N, Muehling, Jill, Murphy, Michael R, Omer, Arina D, Partridge, Frederick A, Peluso, Paul, Aiden, Aviva Presser, Ramasamy, Vidya, Rašić, Gordana, Roy, Sourav, Saavedra-Rodriguez, Karla, Sharan, Shruti, Sharma, Atashi, Smith, Melissa Laird, Turner, Joe, Weakley, Allison M, Zhao, Zhilei, Akbari, Omar S, Black, William C, Cao, Han, Darby, Alistair C, Hill, Catherine A, Johnston, J Spencer, Murphy, Terence D, Raikhel, Alexander S, Sattelle, David B, Sharakhov, Igor V, White, Bradley J, Zhao, Li, Aiden, Erez Lieberman, Mann, Richard S, Lambrechts, Louis, Powell, Jeffrey R, Sharakhova, Maria V, Tu, Zhijian, Robertson, Hugh M, McBride, Carolyn S, Hastie, Alex R, Korlach, Jonas, Neafsey, Daniel E, Phillippy, Adam M, and Vosshall, Leslie B

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Rare Diseases, Emerging Infectious Diseases, Biodefense, Infectious Diseases, Vector-Borne Diseases, 2.2 Factors relating to the physical environment, 3.2 Interventions to alter physical and biological environmental risks, Infection, Good Health and Well Being, Aedes, Animals, Arbovirus Infections, Arboviruses, DNA Copy Number Variations, Dengue Virus, Female, Genetic Variation, Genetics, Population, Genome, Insect, Genomics, Glutathione Transferase, Insect Control, Insecticide Resistance, Male, Molecular Sequence Annotation, Mosquito Vectors, Multigene Family, Pyrethrins, Reference Standards, Sex Determination Processes, General Science & Technology
Abstract

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.

Published
2018

7. Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes

Author

Hall, Andrew Brantley, Papathanos, Philippos-Aris, Sharma, Atashi, Cheng, Changde, Akbari, Omar S, Assour, Lauren, Bergman, Nicholas H, Cagnetti, Alessia, Crisanti, Andrea, Dottorini, Tania, Fiorentini, Elisa, Galizi, Roberto, Hnath, Jonathan, Jiang, Xiaofang, Koren, Sergey, Nolan, Tony, Radune, Diane, Sharakhova, Maria V, Steele, Aaron, Timoshevskiy, Vladimir A, Windbichler, Nikolai, Zhang, Simo, Hahn, Matthew W, Phillippy, Adam M, Emrich, Scott J, Sharakhov, Igor V, Tu, Zhijian Jake, and Besansky, Nora J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Clinical Sciences, Medical Microbiology, Human Genome, Infectious Diseases, Vector-Borne Diseases, Rare Diseases, Biotechnology, Malaria, 2.2 Factors relating to the physical environment, 1.1 Normal biological development and functioning, Aetiology, Underpinning research, Infection, Good Health and Well Being, Animals, Anopheles, Chromosomes, Insect, Female, Insect Vectors, Male, Phylogeny, Sequence Analysis, DNA, X Chromosome, Y Chromosome, Anopheles gambiae, PacBio, RNA-Seq, tandem repetitive DNA, Y-chromosome
Abstract

Y chromosomes control essential male functions in many species, including sex determination and fertility. However, because of obstacles posed by repeat-rich heterochromatin, knowledge of Y chromosome sequences is limited to a handful of model organisms, constraining our understanding of Y biology across the tree of life. Here, we leverage long single-molecule sequencing to determine the content and structure of the nonrecombining Y chromosome of the primary African malaria mosquito, Anopheles gambiae We find that the An. gambiae Y consists almost entirely of a few massively amplified, tandemly arrayed repeats, some of which can recombine with similar repeats on the X chromosome. Sex-specific genome resequencing in a recent species radiation, the An. gambiae complex, revealed rapid sequence turnover within An. gambiae and among species. Exploiting 52 sex-specific An. gambiae RNA-Seq datasets representing all developmental stages, we identified a small repertoire of Y-linked genes that lack X gametologs and are not Y-linked in any other species except An. gambiae, with the notable exception of YG2, a candidate male-determining gene. YG2 is the only gene conserved and exclusive to the Y in all species examined, yet sequence similarity to YG2 is not detectable in the genome of a more distant mosquito relative, suggesting rapid evolution of Y chromosome genes in this highly dynamic genus of malaria vectors. The extensive characterization of the An. gambiae Y provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.

Published
2016

9. Author Correction: Improved reference genome of the arboviral vector Aedes albopictus

Author

Palatini, Umberto, Masri, Reem A., Cosme, Luciano V., Koren, Sergey, Thibaud-Nissen, Françoise, Biedler, James K., Krsticevic, Flavia, Johnston, J. Spencer, Halbach, Rebecca, Crawford, Jacob E., Antoshechkin, Igor, Failloux, Anna-Bella, Pischedda, Elisa, Marconcini, Michele, Ghurye, Jay, Rhie, Arang, Sharma, Atashi, Karagodin, Dmitry A., Jenrette, Jeremy, Gamez, Stephanie, Miesen, Pascal, Masterson, Patrick, Caccone, Adalgisa, Sharakhova, Maria V., Tu, Zhijian, Papathanos, Philippos A., Van Rij, Ronald P., Akbari, Omar S., Powell, Jeffrey, Phillippy, Adam M., and Bonizzoni, Mariangela

Published
2021
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10. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

Author

Neafsey, Daniel E, Waterhouse, Robert M, Abai, Mohammad R, Aganezov, Sergey S, Alekseyev, Max A, Allen, James E, Amon, James, Arcà, Bruno, Arensburger, Peter, Artemov, Gleb, Assour, Lauren A, Basseri, Hamidreza, Berlin, Aaron, Birren, Bruce W, Blandin, Stephanie A, Brockman, Andrew I, Burkot, Thomas R, Burt, Austin, Chan, Clara S, Chauve, Cedric, Chiu, Joanna C, Christensen, Mikkel, Costantini, Carlo, Davidson, Victoria LM, Deligianni, Elena, Dottorini, Tania, Dritsou, Vicky, Gabriel, Stacey B, Guelbeogo, Wamdaogo M, Hall, Andrew B, Han, Mira V, Hlaing, Thaung, Hughes, Daniel ST, Jenkins, Adam M, Jiang, Xiaofang, Jungreis, Irwin, Kakani, Evdoxia G, Kamali, Maryam, Kemppainen, Petri, Kennedy, Ryan C, Kirmitzoglou, Ioannis K, Koekemoer, Lizette L, Laban, Njoroge, Langridge, Nicholas, Lawniczak, Mara KN, Lirakis, Manolis, Lobo, Neil F, Lowy, Ernesto, MacCallum, Robert M, Mao, Chunhong, Maslen, Gareth, Mbogo, Charles, McCarthy, Jenny, Michel, Kristin, Mitchell, Sara N, Moore, Wendy, Murphy, Katherine A, Naumenko, Anastasia N, Nolan, Tony, Novoa, Eva M, O'Loughlin, Samantha, Oringanje, Chioma, Oshaghi, Mohammad A, Pakpour, Nazzy, Papathanos, Philippos A, Peery, Ashley N, Povelones, Michael, Prakash, Anil, Price, David P, Rajaraman, Ashok, Reimer, Lisa J, Rinker, David C, Rokas, Antonis, Russell, Tanya L, Sagnon, N'Fale, Sharakhova, Maria V, Shea, Terrance, Simão, Felipe A, Simard, Frederic, Slotman, Michel A, Somboon, Pradya, Stegniy, Vladimir, Struchiner, Claudio J, Thomas, Gregg WC, Tojo, Marta, Topalis, Pantelis, Tubio, José MC, Unger, Maria F, Vontas, John, Walton, Catherine, Wilding, Craig S, Willis, Judith H, Wu, Yi-Chieh, Yan, Guiyun, Zdobnov, Evgeny M, Zhou, Xiaofan, Catteruccia, Flaminia, Christophides, George K, Collins, Frank H, and Cornman, Robert S

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Medical Microbiology, Biotechnology, Rare Diseases, Vector-Borne Diseases, Malaria, Infectious Diseases, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Animals, Anopheles, Base Sequence, Chromosomes, Insect, Drosophila, Evolution, Molecular, Genome, Insect, Humans, Insect Vectors, Molecular Sequence Data, Phylogeny, Sequence Alignment, General Science & Technology
Abstract

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Published
2015

11. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Author

Neafsey, Daniel E, Waterhouse, Robert M, Abai, Mohammad R, Aganezov, Sergey S, Alekseyev, Max A, Allen, James E, Amon, James, Arcà, Bruno, Arensburger, Peter, Artemov, Gleb, Assour, Lauren A, Basseri, Hamidreza, Berlin, Aaron, Birren, Bruce W, Blandin, Stephanie A, Brockman, Andrew I, Burkot, Thomas R, Burt, Austin, Chan, Clara S, Chauve, Cedric, Chiu, Joanna C, Christensen, Mikkel, Costantini, Carlo, Davidson, Victoria LM, Deligianni, Elena, Dottorini, Tania, Dritsou, Vicky, Gabriel, Stacey B, Guelbeogo, Wamdaogo M, Hall, Andrew B, Han, Mira V, Hlaing, Thaung, Hughes, Daniel ST, Jenkins, Adam M, Jiang, Xiaofang, Jungreis, Irwin, Kakani, Evdoxia G, Kamali, Maryam, Kemppainen, Petri, Kennedy, Ryan C, Kirmitzoglou, Ioannis K, Koekemoer, Lizette L, Laban, Njoroge, Langridge, Nicholas, Lawniczak, Mara KN, Lirakis, Manolis, Lobo, Neil F, Lowy, Ernesto, MacCallum, Robert M, Mao, Chunhong, Maslen, Gareth, Mbogo, Charles, McCarthy, Jenny, Michel, Kristin, Mitchell, Sara N, Moore, Wendy, Murphy, Katherine A, Naumenko, Anastasia N, Nolan, Tony, Novoa, Eva M, O'Loughlin, Samantha, Oringanje, Chioma, Oshaghi, Mohammad A, Pakpour, Nazzy, Papathanos, Philippos A, Peery, Ashley N, Povelones, Michael, Prakash, Anil, Price, David P, Rajaraman, Ashok, Reimer, Lisa J, Rinker, David C, Rokas, Antonis, Russell, Tanya L, Sagnon, N'Fale, Sharakhova, Maria V, Shea, Terrance, Simão, Felipe A, Simard, Frederic, Slotman, Michel A, Somboon, Pradya, Stegniy, Vladimir, Struchiner, Claudio J, Thomas, Gregg WC, Tojo, Marta, Topalis, Pantelis, Tubio, José MC, Unger, Maria F, Vontas, John, Walton, Catherine, Wilding, Craig S, Willis, Judith H, Wu, Yi-Chieh, Yan, Guiyun, Zdobnov, Evgeny M, Zhou, Xiaofan, Catteruccia, Flaminia, Christophides, George K, Collins, Frank H, and Cornman, Robert S

Subjects
Animals, Humans, Anopheles, Drosophila, Malaria, Sequence Alignment, Insect Vectors, Evolution, Molecular, Phylogeny, Base Sequence, Molecular Sequence Data, Genome, Insect, Chromosomes, Insect, Evolution, Molecular, Genome, Insect, Chromosomes, General Science & Technology
Abstract

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Published
2015

12. Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.

Author

Jiang, Xiaofang, Peery, Ashley, Hall, A Brantley, Sharma, Atashi, Chen, Xiao-Guang, Waterhouse, Robert M, Komissarov, Aleksey, Riehle, Michelle M, Shouche, Yogesh, Sharakhova, Maria V, Lawson, Dan, Pakpour, Nazzy, Arensburger, Peter, Davidson, Victoria LM, Eiglmeier, Karin, Emrich, Scott, George, Phillip, Kennedy, Ryan C, Mane, Shrinivasrao P, Maslen, Gareth, Oringanje, Chioma, Qi, Yumin, Settlage, Robert, Tojo, Marta, Tubio, Jose MC, Unger, Maria F, Wang, Bo, Vernick, Kenneth D, Ribeiro, Jose MC, James, Anthony A, Michel, Kristin, Riehle, Michael A, Luckhart, Shirley, Sharakhov, Igor V, and Tu, Zhijian

Subjects
Animals, Humans, Anopheles, Malaria, Insect Proteins, Cluster Analysis, Chromosome Mapping, Sequence Analysis, DNA, Insect Vectors, Evolution, Molecular, Phylogeny, Synteny, Polymorphism, Single Nucleotide, Urban Population, Genome, Insect, Chromosomes, Insect, Transcriptome, Sequence Analysis, DNA, Evolution, Molecular, Polymorphism, Single Nucleotide, Genome, Insect, Chromosomes, Biotechnology, Vector-Borne Diseases, Rare Diseases, Genetics, Human Genome, Infectious Diseases, 2.2 Factors relating to physical environment, Infection, Bioinformatics, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract

BackgroundAnopheles stephensi is the key vector of malaria throughout the Indian subcontinent and Middle East and an emerging model for molecular and genetic studies of mosquito-parasite interactions. The type form of the species is responsible for the majority of urban malaria transmission across its range.ResultsHere, we report the genome sequence and annotation of the Indian strain of the type form of An. stephensi. The 221 Mb genome assembly represents more than 92% of the entire genome and was produced using a combination of 454, Illumina, and PacBio sequencing. Physical mapping assigned 62% of the genome onto chromosomes, enabling chromosome-based analysis. Comparisons between An. stephensi and An. gambiae reveal that the rate of gene order reshuffling on the X chromosome was three times higher than that on the autosomes. An. stephensi has more heterochromatin in pericentric regions but less repetitive DNA in chromosome arms than An. gambiae. We also identify a number of Y-chromosome contigs and BACs. Interspersed repeats constitute 7.1% of the assembled genome while LTR retrotransposons alone comprise more than 49% of the Y contigs. RNA-seq analyses provide new insights into mosquito innate immunity, development, and sexual dimorphism.ConclusionsThe genome analysis described in this manuscript provides a resource and platform for fundamental and translational research into a major urban malaria vector. Chromosome-based investigations provide unique perspectives on Anopheles chromosome evolution. RNA-seq analysis and studies of immunity genes offer new insights into mosquito biology and mosquito-parasite interactions.

Published
2014

13. Patterns of genetic differentiation imply distinct phylogeographic history of the mosquito species Anopheles messeae and Anopheles daciae in Eurasia

Author

Brusentsov, Ilya I., primary, Gordeev, Mikhail I., additional, Yurchenko, Andrey A., additional, Karagodin, Dimitriy A., additional, Moskaev, Anton V., additional, Hodge, James M., additional, Burlak, Vladimir A., additional, Artemov, Gleb N., additional, Sibataev, Anuarbek K., additional, Becker, Norbert, additional, Sharakhov, Igor V., additional, Baricheva, Elina M., additional, and Sharakhova, Maria V., additional

Published
2023
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14. The Genome Sequence of the Malaria Mosquito Anopheles gamblae

Author

Holt, Robert A., Subramanian, G. Mani, Halpern, Aaron, Sutton, Granger G., Charlab, Rosane, Nusskern, Deborah R., Wincker, Patrick, Clark, Andrew G., Wides, Ron, Salzberg, Steven L., Loftus, Brendan, Yandell, Mark, Majoros, William H., Rusch, Douglas B., Lai, Zhongwu, Kraft, Cheryl L., Abril, Josep F., Anthouard, Veronique, Arensburger, Peter, Atkinson, Peter W., Baden, Holly, de Berardinis, Veronique, Baldwin, Danita, Benes, Vladimir, Biedler, Jim, Blass, Claudia, Bolanos, Randall, Boscus, Didier, Barnstead, Mary, Cai, Shuang, Chatuverdi, Kabir, Christophides, George K., Chrystal, Mathew A., Clamp, Michele, Cravchik, Anibal, Curwen, Val, Dana, Ali, Delcher, Art, Dew, Ian, Evans, Cheryl A., Flanigan, Michael, Grundschober-Freimoser, Anne, Friedli, Lisa, Gu, Zhiping, Guan, Ping, Guigo, Roderic, Hillenmeyer, Maureen E., Hladun, Susanne L., Hogan, James R., Hong, Young S., Hoover, Jeffrey, Jaillon, Olivier, Ke, Zhaoxi, Kodira, Chinnappa, Kokoza, Elena, Koutsos, Anastasios, Letunic, Ivica, Levitsky, Alex, Liang, Yong, Lin, Jhy-Jhu, Lobo, Neil F., Lopez, John R., Malek, Joel A., McIntosh, Tina C., Meister, Stephan, Miller, Jason, Mobarry, Clark, Mongin, Emmanuel, Murphy, Sean D., O'Brochta, David A., Pfannkoch, Cynthia, Qi, Rong, Regier, Megan A., Remington, Karin, Shao, Hongguang, Sharakhova, Maria V., Sitter, Cynthia D., Shetty, Jyoti, Smith, Thomas J., Strong, Renee, Sun, Jingtao, Thomasova, Dana, Ton, Lucas Q., Topalis, Pantelis, Tu, Zhijian, Unger, Maria F., Walenz, Brian, Wang, Aihui, Wang, Jian, Wang, Mei, Wang, Xuelan, Woodford, Kerry J., Wortman, Jennifer R., Wu, Martin, Yao, Alison, Zdobnov, Evgeny M., Zhang, Hongyu, Zhao, Qi, Zhao, Shaying, Zhu, Shiaoping C., Zhimulev, Igor, Coluzzi, Mario, della Torre, Alessandra, Roth, Charles W., Louis, Christos, Kalush, Francis, Mural, Richard J., Myers, Eugene W., Adams, Mark D., Smith, Hamilton O., Broder, Samuel, Gardner, Malcolm J., Fraser, Claire M., Birney, Ewan, Bork, Peer, Brey, Paul T., Venter, J. Craig, Weissenbach, Jean, Kafatos, Fotis C., Collins, Frank H., and Hoffman, Stephen L.

Published
2002

16. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Author

Waterhouse, Robert M., Aganezov, Sergey, Anselmetti, Yoann, Lee, Jiyoung, Ruzzante, Livio, Reijnders, Maarten J. M. F., Feron, Romain, Bérard, Sèverine, George, Phillip, Hahn, Matthew W., Howell, Paul I., Kamali, Maryam, Koren, Sergey, Lawson, Daniel, Maslen, Gareth, Peery, Ashley, Phillippy, Adam M., Sharakhova, Maria V., Tannier, Eric, Unger, Maria F., Zhang, Simo V., Alekseyev, Max A., Besansky, Nora J., Chauve, Cedric, Emrich, Scott J., and Sharakhov, Igor V.

Published
2020
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18. Developing a FISH-based Method for Inversion Diagnostics in Culex pipiens Mosquitoes

Author

Hartigan, Daniel P., Sharakhova, Maria V., Hartigan, Daniel P., and Sharakhova, Maria V.

Abstract

This project developed an improved protocol for the dissections of imaginal discs from 4th instar Culicine larvae. The design of the protocol and use of visuals have now allowed dissections to be more accessible and streamline the learning process for undergraduate students or new lab members. The new protocol is important for instructional use in laboratories and classrooms with the aim of studying mitotic chromosomes isolated from mosquito larvae. For this project, probes were designed for diagnostics for the Chromosome 1 inversion 1p3” and the Chromosome 2 inversion 2q1 for the field-collected strains Cx. p. pipiens Northfield strain, Cx. p. molsestus Chicago strain, and the genomic standard JHB strain of Cx. quinquefasciatus. Primers were developed and used in PCR and produced products ranging between 3,000 and 4,500kb that are suitable for subsequent labeling by Nick Translation method and visualization of the status of inversions using Fluorescent in situ Hybridization (FISH). Lastly, a FISH-based approach for the detection of the chromosome 1 inversion, 1p3” was optimized for the mitotic chromosomes from the imaginal discs for the standard genomic strain JHB of Cx. quinquefasciatus. Two probes produced clear signals indicating a standard arrangement for this inversion in the chromosome 1 of this strain. This shows that probes developed for FISH-based inversion diagnostics using mitotic chromosomes have the potential for further method development.

Published
2023

19. Molecular signature of domestication in the arboviral vector Aedes aegypti

Author

Lozada-Chavez, Alejandro Nabor, primary, Lozada-Chavez, Irma, additional, Alfano, Niccolo, additional, Palatini, Umberto, additional, Sogliani, Davide, additional, Elfekih, Samia, additional, Degefa, Teshome, additional, Sharakhova, Maria V, additional, Badolo, Athanase, additional, Patchara, Sri, additional, Casas-Martinez, Mauricio, additional, Carlos, Bianca, additional, Carballar-Lejarazu, Rebeca, additional, Lambrechts, Louis, additional, Souza-Neto, Jayme, additional, and Bonizzoni, Mariangela, additional

Published
2023
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21. A male-determining factor in the mosquito Aedes aegypti

Author

Hall, Andrew Brantley, Basu, Sanjay, Jiang, Xiaofang, Qi, Yumin, Timoshevskiy, Vladimir A., Biedler, James K., Sharakhova, Maria V., Elahi, Rubayet, Anderson, Michelle A. E., Chen, Xiao-Guang, Sharakhov, Igor V., Adelman, Zach N., and Tu, Zhijian

Published
2015

22. Additional file 1 of Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group

Author

Yurchenko, Andrey A., Naumenko, Anastasia N., Artemov, Gleb N., Karagodin, Dmitry A., Hodge, James M., Velichevskaya, Alena I., Kokhanenko, Alina A., Bondarenko, Semen M., Abai, Mohammad R., Kamali, Maryam, Gordeev, Mikhail I., Moskaev, Anton V., Caputo, Beniamino, Aghayan, Sargis A., Baricheva, Elina M., Stegniy, Vladimir N., Sharakhova, Maria V., and Sharakhov, Igor V.

Abstract

Additional file 1: Table S1. Statistics of the transcriptome assemblies for species of the Maculipennis Group. Table S2. Genes of An. atroparvus used as markers for detection of interspecies chromosome rearrangements on the X chromosome in five species of the Maculipennis Subgroup. Table S3. Mosquito species and sampling sites. Figure S1. A phylogenetic analysis of ortholog groups split into 4 equally-sized datasets based on the length of the alignments after trimal filtration. Figure S2. A phylogenetic analysis using whole-genome datasets from six Anopheles species.

Published
2023
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28. Patterns of genetic differentiation imply distinct evolutionary histories of the sibling mosquito speciesAnopheles messeaeandAnopheles daciaein Eurasia

Author

Brusentsov, Ilya I., primary, Gordeev, Mikhail I., additional, Yurchenko, Andrey A., additional, Karagodin, Dimitriy A., additional, Moskaev, Anton V., additional, Hodge, James M., additional, Burlak, Vladimir A., additional, Artemov, Gleb N., additional, Sibataev, Anuarbek K., additional, Becker, Norbert, additional, Sharakhov, Igor V., additional, Baricheva, Elina M., additional, and Sharakhova, Maria V., additional

Published
2022
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30. Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria vectors of the Maculipennis group

Author

Yurchenko, Andrey A., primary, Naumenko, Anastasia N., additional, Artemov, Gleb N., additional, Karagodin, Dmitry A., additional, Hodge, James M., additional, Velichevskaya, Alena I., additional, Kokhanenko, Alina A., additional, Bondarenko, Semen M., additional, Abai, Mohammad R., additional, Kamali, Maryam, additional, Gordeev, Mikhail I., additional, Moskaev, Anton V., additional, Caputo, Beniamino, additional, Aghayan, Sargis A., additional, Baricheva, Elina M., additional, Stegniy, Vladimir N., additional, Sharakhova, Maria V., additional, and Sharakhov, Igor V., additional

Published
2022
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37. GENOME BIOLOGY

Author

Palatini, Umberto, Masri, Reem A., Cosme, Luciano V., Koren, Sergey, Thibaud-Nissen, Francoise, Biedler, James K., Krsticevic, Flavia, Johnston, J. Spencer, Halbach, Rebecca, Crawford, Jacob E., Antoshechkin, Igor, Failloux, Anna-Bella, Pischedda, Elisa, Marconcini, Michele, Ghurye, Jay, Rhie, Arang, Sharma, Atashi, Karagodin, Dmitry A., Jenrette, Jeremy, Gamez, Stephanie, Miesen, Pascal, Masterson, Patrick, Caccone, Adalgisa, Sharakhova, Maria V., Tu, Zhijian, Papathanos, Philippos A., Van Rij, Ronald P., Akbari, Omar S., Powell, Jeffrey, Phillippy, Adam M., and Bonizzoni, Mariangela

Subjects
Genetics & Heredity, Science & Technology, Biotechnology & Applied Microbiology, Bioinformatics, 05 Environmental Sciences, 08 Information and Computing Sciences, 06 Biological Sciences, Life Sciences & Biomedicine
Abstract

Following publication of the original article [1], the authors identified an error in the section "Distribution and structure of piRNA clusters" on page 7. The value of the SD is not correct. Instead of a SD 634.885 Kb, it should be SD 16.79. The correct statement should read: “We used small RNA libraries generated from somatic tissues (female carcass) as well as germline tissues (ovaries) to annotate 1441 piRNA clusters with an average size of 10.911 kb (SD 16.79 kb; max: 139.92 kb) … ”. Published version

Published
2021

39. Physical Mapping of the Anopheles (Nyssorhynchus) darlingi Genomic Scaffolds

Author

Rafael, Míriam Silva, Bridi, Leticia Cegatti, Sharakhov, Igor V., Marinotti, Osvaldo, Sharakhova, Maria V., Timoshevskiy, Vladimir, Guimarães-Marques, Giselle Moura, Santos, Valéria Silva, da Silva, Carlos Gustavo Nunes, Astolfi-Filho, Spartaco, Tadei, Wanderli Pedro, Entomology, and Fralin Life Sciences Institute

Subjects
stomatognathic system, parasitic diseases, synteny, polytene chromosome, in situ hybridization, genomics and cytogenetics
Abstract

The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping is a useful tool for anchoring genome assemblies to mosquito chromosomes. Published version

Published
2021

40. Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex

Author

Sharma, Atashi, Kinney, Nicholas A., Timoshevskiy, Vladimir A., Sharakhova, Maria V., Sharakhov, Igor V., and Entomology

Subjects
X chromosome, parasitic diseases, Anopheles, heterochromatin, satellite DNA, mosquito, sex chromosome, mitotic chromosome
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. Published version

Published
2020

41. A Gene-Based Method for Cytogenetic Mapping of Repeat-Rich Mosquito Genomes

Author

Masri, Reem A., Karagodin, Dmitriy A., Sharma, Atashi, Sharakhova, Maria V., Masri, Reem A., Karagodin, Dmitriy A., Sharma, Atashi, and Sharakhova, Maria V.

Abstract

Long-read sequencing technologies have opened up new avenues of research on the mosquito genome biology, enabling scientists to better understand the remarkable abilities of vectors for transmitting pathogens. Although new genome mapping technologies such as Hi-C scaffolding and optical mapping may significantly improve the quality of genomes, only cytogenetic mapping, with the help of fluorescence in situ hybridization (FISH), connects genomic scaffolds to a particular chromosome and chromosome band. This mapping approach is important for creating and validating chromosome-scale genome assemblies for mosquitoes with repeat-rich genomes, which can potentially be misassembled. In this study, we describe a new gene-based physical mapping approach that was optimized using the newly assembled Aedes albopictus genome, which is enriched with transposable elements. To avoid amplification of the repetitive DNA, 15 protein-coding gene transcripts were used for the probe design. Instead of using genomic DNA, complementary DNA was utilized as a template for development of the PCR-amplified probes for FISH. All probes were successfully amplified and mapped to specific chromosome bands. The genome-unique probes allowed to perform unambiguous mapping of genomic scaffolds to chromosome regions. The method described in detail here can be used for physical genome mapping in other insects.

Published
2021
Full Text
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43. New Cytogenetic Photomap and Molecular Diagnostics for the Cryptic Species of the Malaria Mosquitoes Anopheles messeae and Anopheles daciae from Eurasia

Author

Artemov, Gleb N., Fedorova, Valentina S., Karagodin, Dmitriy A., Brusentsov, Ilya I., Baricheva, Elina M., Sharakhov, Igor V., Gordeev, Mikhail I., Sharakhova, Maria V., Artemov, Gleb N., Fedorova, Valentina S., Karagodin, Dmitriy A., Brusentsov, Ilya I., Baricheva, Elina M., Sharakhov, Igor V., Gordeev, Mikhail I., and Sharakhova, Maria V.

Abstract

The Eurasian malaria vector Anopheles messeae is a widely spread and genetically diverse species. Five widespread polymorphic chromosomal inversions were found in natural populations of this mosquito. A cryptic species, Anopheles daciae, was differentiated from An. messeae by the presence of several nucleotide substitutions in the Internal Transcribed Spacer 2 (ITS2) region of ribosomal DNA. However, because of the absence of a high-quality reference cytogenetic map, the inversion polymorphisms in An. daciae and An. messeae remain poorly understood. Moreover, a recently determined heterogeneity in ITS2 in An. daciae questioned the accuracy of the previously used Restriction Fragment Length Polymorphism (RFLP) assay for species diagnostics. In this study, a standard-universal cytogenetic map was constructed based on orcein stained images of chromosomes from salivary glands for population studies of the chromosomal inversions that can be used for both An. messeae and An. daciae. In addition, a new ITS2-RFLP approach for species diagnostics was developed. Both methods were applied to characterize inversion polymorphism in populations of An. messeae and An. daciae from a single location in Western Siberia in Russia. The analysis demonstrates that cryptic species are remarkably different in their frequencies of chromosomal inversion variants. Our study supports previous observations that An. messeae has higher inversion polymorphism in all autosomes than the cryptic species An. daciae.

Published
2021
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44. Physical Mapping of the Anopheles (Nyssorhynchus) darlingi Genomic Scaffolds

Author

Entomology, Fralin Life Sciences Institute, Rafael, Míriam Silva, Bridi, Leticia Cegatti, Sharakhov, Igor V., Marinotti, Osvaldo, Sharakhova, Maria V., Timoshevskiy, Vladimir, Guimarães-Marques, Giselle Moura, Santos, Valéria Silva, da Silva, Carlos Gustavo Nunes, Astolfi-Filho, Spartaco, Tadei, Wanderli Pedro, Entomology, Fralin Life Sciences Institute, Rafael, Míriam Silva, Bridi, Leticia Cegatti, Sharakhov, Igor V., Marinotti, Osvaldo, Sharakhova, Maria V., Timoshevskiy, Vladimir, Guimarães-Marques, Giselle Moura, Santos, Valéria Silva, da Silva, Carlos Gustavo Nunes, Astolfi-Filho, Spartaco, and Tadei, Wanderli Pedro

Abstract

The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping is a useful tool for anchoring genome assemblies to mosquito chromosomes.

Published
2021

45. A Gene-Based Method for Cytogenetic Mapping of Repeat-Rich Mosquito Genomes

Author

Entomology, Fralin Life Sciences Institute, Biochemistry, Masri, Reem A., Karagodin, Dmitriy A., Sharma, Atashi, Sharakhova, Maria V., Entomology, Fralin Life Sciences Institute, Biochemistry, Masri, Reem A., Karagodin, Dmitriy A., Sharma, Atashi, and Sharakhova, Maria V.

Abstract

Long-read sequencing technologies have opened up new avenues of research on the mosquito genome biology, enabling scientists to better understand the remarkable abilities of vectors for transmitting pathogens. Although new genome mapping technologies such as Hi-C scaffolding and optical mapping may significantly improve the quality of genomes, only cytogenetic mapping, with the help of fluorescence in situ hybridization (FISH), connects genomic scaffolds to a particular chromosome and chromosome band. This mapping approach is important for creating and validating chromosome-scale genome assemblies for mosquitoes with repeat-rich genomes, which can potentially be misassembled. In this study, we describe a new gene-based physical mapping approach that was optimized using the newly assembled Aedes albopictus genome, which is enriched with transposable elements. To avoid amplification of the repetitive DNA, 15 protein-coding gene transcripts were used for the probe design. Instead of using genomic DNA, complementary DNA was utilized as a template for development of the PCR-amplified probes for FISH. All probes were successfully amplified and mapped to specific chromosome bands. The genome-unique probes allowed to perform unambiguous mapping of genomic scaffolds to chromosome regions. The method described in detail here can be used for physical genome mapping in other insects.

Published
2021

46. The new Internal Transcribed Spacer 2 diagnostic tool clarifies the taxonomic position and geographic distribution of the North American malaria vector Anopheles punctipennis

Author

Entomology, Fralin Life Sciences Institute, Hodge, James M., Yurchenko, Andrey A., Karagodin, Dmitriy A., Masri, Reem A., Smith, Ryan C., Gordeev, Mikhail I., Sharakhova, Maria V., Entomology, Fralin Life Sciences Institute, Hodge, James M., Yurchenko, Andrey A., Karagodin, Dmitriy A., Masri, Reem A., Smith, Ryan C., Gordeev, Mikhail I., and Sharakhova, Maria V.

Abstract

Background The malaria mosquito Anopheles punctipennis, a widely distributed species in North America, is capable of transmitting human malaria and is actively involved in the transmission of the ungulate malaria parasite Plasmodium odocoilei. However, molecular diagnostic tools based on Internal Transcribed Spacer 2 (ITS2) of ribosomal DNA are lacking for this species. Anopheles punctipennis is a former member of the Anopheles maculipennis complex but its systematic position remains unclear. Methods In this study, ITS2 sequences were obtained from 276 An. punctipennis specimens collected in the eastern and midwestern United States and a simple and robust Restriction Fragment Length Polymorphism approach for species identification was developed. The maximum-likelihood phylogenetic tree was constructed based on ITS2 sequences available through this study and from GenBank for 20 species of Anopheles. Results The analysis demonstrated a consistent ITS2 sequence length and showed no indications of intragenomic variation among the samples based on ITS2, suggesting that An. punctipennis represents a single species in the studied geographic locations. In this study, An. punctipennis was found in urban, rural, and forest settings, suggesting its potential broad role in pathogen transmission. Phylogeny based on ITS2 sequence comparison demonstrated the close relationship of this species with other members of the Maculipennis group. Conclusions This study developed molecular tools based on ITS2 sequences for the malaria vector An. punctipennis and clarified the phylogenetic position of the species within the Maculipennis group.

Published
2021

47. Chromosome-Centric View of Genome Organization and Evolution

Author

Entomology, Fralin Life Sciences Institute, Sharakhova, Maria V., Trifonov, Vladimir, Entomology, Fralin Life Sciences Institute, Sharakhova, Maria V., and Trifonov, Vladimir

Abstract

Genetic material in all cellular organisms is packed into chromosomes, which represent essential units of inheritance, recombination, and evolution [...]

Published
2021

48. New Cytogenetic Photomap and Molecular Diagnostics for the Cryptic Species of the Malaria Mosquitoes Anopheles messeae and Anopheles daciae from Eurasia

Author

Entomology, Artemov, Gleb N., Fedorova, Valentina S., Karagodin, Dmitriy A., Brusentsov, Ilya I., Baricheva, Elina M., Sharakhov, Igor V., Gordeev, Mikhail I., Sharakhova, Maria V., Entomology, Artemov, Gleb N., Fedorova, Valentina S., Karagodin, Dmitriy A., Brusentsov, Ilya I., Baricheva, Elina M., Sharakhov, Igor V., Gordeev, Mikhail I., and Sharakhova, Maria V.

Abstract

The Eurasian malaria vector Anopheles messeae is a widely spread and genetically diverse species. Five widespread polymorphic chromosomal inversions were found in natural populations of this mosquito. A cryptic species, Anopheles daciae, was differentiated from An. messeae by the presence of several nucleotide substitutions in the Internal Transcribed Spacer 2 (ITS2) region of ribosomal DNA. However, because of the absence of a high-quality reference cytogenetic map, the inversion polymorphisms in An. daciae and An. messeae remain poorly understood. Moreover, a recently determined heterogeneity in ITS2 in An. daciae questioned the accuracy of the previously used Restriction Fragment Length Polymorphism (RFLP) assay for species diagnostics. In this study, a standard-universal cytogenetic map was constructed based on orcein stained images of chromosomes from salivary glands for population studies of the chromosomal inversions that can be used for both An. messeae and An. daciae. In addition, a new ITS2-RFLP approach for species diagnostics was developed. Both methods were applied to characterize inversion polymorphism in populations of An. messeae and An. daciae from a single location in Western Siberia in Russia. The analysis demonstrates that cryptic species are remarkably different in their frequencies of chromosomal inversion variants. Our study supports previous observations that An. messeae has higher inversion polymorphism in all autosomes than the cryptic species An. daciae.

Published
2021

49. Physical Mapping of the Anopheles (Nyssorhynchus) darlingi Genomic Scaffolds

Author

Rafael, Míriam Silva, primary, Bridi, Leticia Cegatti, additional, Sharakhov, Igor V., additional, Marinotti, Osvaldo, additional, Sharakhova, Maria V., additional, Timoshevskiy, Vladimir, additional, Guimarães-Marques, Giselle Moura, additional, Santos, Valéria Silva, additional, da Silva, Carlos Gustavo Nunes, additional, Astolfi-Filho, Spartaco, additional, and Tadei, Wanderli Pedro, additional

Published
2021
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