20 results on '"Maslen, Gareth L."'
Search Results
2. Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors
- Author
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Campbell, Lahcen I., Nwezeobi, Joachim, van Brunschot, Sharon L., Kaweesi, Tadeo, Seal, Susan E., Swamy, Rekha A. R., Namuddu, Annet, Maslen, Gareth L., Mugerwa, Habibu, Armean, Irina M., Haggerty, Leanne, Martin, Fergal J., Malka, Osnat, Santos-Garcia, Diego, Juravel, Ksenia, Morin, Shai, Stephens, Michael E., Muhindira, Paul Visendi, Kersey, Paul J., Maruthi, M. N., Omongo, Christopher A., Navas-Castillo, Jesús, Fiallo-Olivé, Elvira, Mohammed, Ibrahim Umar, Wang, Hua-Ling, Onyeka, Joseph, Alicai, Titus, and Colvin, John
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- 2023
- Full Text
- View/download PDF
3. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.
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Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B
- Subjects
Chemoreceptor genes ,Gene regulation ,Insect adaptation ,Insect immunity ,Insect orthology ,Metabolic detoxification genes ,Muscid genomics ,Opsin gene duplication ,Stable fly genome ,Biological Sciences ,Developmental Biology - Abstract
BackgroundThe stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.ResultsThis study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.ConclusionsThe combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.
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- 2021
4. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes
- Author
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Attardo, Geoffrey M, Abd-Alla, Adly MM, Acosta-Serrano, Alvaro, Allen, James E, Bateta, Rosemary, Benoit, Joshua B, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel B, Farrow, David W, Friedrich, Markus, Hua-Van, Aurélie, Jennings, Emily C, Larkin, Denis M, Lawson, Daniel, Lehane, Michael J, Lenis, Vasileios P, Lowy-Gallego, Ernesto, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Masiga, Daniel, Maslen, Gareth L, Matetovici, Irina, Meisel, Richard P, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang J, Minx, Patrick, Mireji, Paul O, Ometto, Lino, Parker, Andrew G, Rio, Rita, Rose, Clair, Rosendale, Andrew J, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin T, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Van Den Abbeele, Jan, Vigneron, Aurelien, Wang, Jingwen, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Weiss, Brian L, Wilson, Richard K, Zhao, Xin, and Aksoy, Serap
- Subjects
Biological Sciences ,Genetics ,Vector-Borne Diseases ,Biotechnology ,Infectious Diseases ,Infection ,Good Health and Well Being ,Animals ,DNA Transposable Elements ,Drosophila melanogaster ,Female ,Gene Expression Regulation ,Genes ,Insect ,Genes ,X-Linked ,Genome ,Insect ,Genomics ,Geography ,Insect Proteins ,Insect Vectors ,Male ,Mutagenesis ,Insertional ,Phylogeny ,Repetitive Sequences ,Nucleic Acid ,Sequence Homology ,Amino Acid ,Synteny ,Trypanosoma ,Tsetse Flies ,Wolbachia ,Tsetse ,Trypanosomiasis ,Hematophagy ,Lactation ,Disease ,Neglected ,Symbiosis ,Environmental Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
BackgroundTsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity.ResultsGenomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges.ConclusionsExpanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
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- 2019
5. The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes
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Attardo, Geoffrey M, Abd-Alla, Adly MM, Acosta-Serrano, Alvaro, Allen, James E, Bateta, Rosemary, Benoit, Joshua B, Bourtzis, Kostas, Caers, Jelle, Caljon, Guy, Christensen, Mikkel B, Farrow, David W, Friedrich, Markus, Hua-Van, Aurélie, Jennings, Emily C, Larkin, Denis M, Lawson, Daniel, Lehane, Michael J, Lenis, Vasileios P, Lowy-Gallego, Ernesto, Macharia, Rosaline W, Malacrida, Anna R, Marco, Heather G, Masiga, Daniel, Maslen, Gareth L, Matetovici, Irina, Meisel, Richard P, Meki, Irene, Michalkova, Veronika, Miller, Wolfgang J, Minx, Patrick, Mireji, Paul O, Ometto, Lino, Parker, Andrew G, Rio, Rita, Rose, Clair, Rosendale, Andrew J, Rota-Stabelli, Omar, Savini, Grazia, Schoofs, Liliane, Scolari, Francesca, Swain, Martin T, Takáč, Peter, Tomlinson, Chad, Tsiamis, George, Van Den Abbeele, Jan, Vigneron, Aurelien, Wang, Jingwen, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Weiss, Brian L, Wilson, Richard K, Zhao, Xin, and Aksoy, Serap
- Subjects
Biological Sciences ,Genetics ,Infectious Diseases ,Vector-Borne Diseases ,Biotechnology ,Infection ,Good Health and Well Being - Abstract
Background: Tsetse flies (Glossina sp.) are the sole vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood specific diet by both sexes and obligate bacterial symbiosis. This work describes comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans (G.m. morsitans), G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes) and Fusca (G. brevipalpis) which represent different habitats, host preferences and vectorial capacity. Results: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex linked scaffolds show increased rates of female specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse specific genes are enriched in protease, odorant binding and helicase activities. Lactation associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other characterized insects. Vision associated Rhodopsin genes show conservation of motion detection/tracking functions and significant variance in the Rhodopsin detecting colors in the blue wavelength ranges. Conclusions: Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
- Published
- 2019
6. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates
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Yates, Andrew D, primary, Allen, James, additional, Amode, Ridwan M, additional, Azov, Andrey G, additional, Barba, Matthieu, additional, Becerra, Andrés, additional, Bhai, Jyothish, additional, Campbell, Lahcen I, additional, Carbajo Martinez, Manuel, additional, Chakiachvili, Marc, additional, Chougule, Kapeel, additional, Christensen, Mikkel, additional, Contreras-Moreira, Bruno, additional, Cuzick, Alayne, additional, Da Rin Fioretto, Luca, additional, Davis, Paul, additional, De Silva, Nishadi H, additional, Diamantakis, Stavros, additional, Dyer, Sarah, additional, Elser, Justin, additional, Filippi, Carla V, additional, Gall, Astrid, additional, Grigoriadis, Dionysios, additional, Guijarro-Clarke, Cristina, additional, Gupta, Parul, additional, Hammond-Kosack, Kim E, additional, Howe, Kevin L, additional, Jaiswal, Pankaj, additional, Kaikala, Vinay, additional, Kumar, Vivek, additional, Kumari, Sunita, additional, Langridge, Nick, additional, Le, Tuan, additional, Luypaert, Manuel, additional, Maslen, Gareth L, additional, Maurel, Thomas, additional, Moore, Benjamin, additional, Muffato, Matthieu, additional, Mushtaq, Aleena, additional, Naamati, Guy, additional, Naithani, Sushma, additional, Olson, Andrew, additional, Parker, Anne, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Preece, Justin, additional, Quinton-Tulloch, Mark, additional, Rodgers, Faye, additional, Rosello, Marc, additional, Ruffier, Magali, additional, Seager, James, additional, Sitnik, Vasily, additional, Szpak, Michal, additional, Tate, John, additional, Tello-Ruiz, Marcela K, additional, Trevanion, Stephen J, additional, Urban, Martin, additional, Ware, Doreen, additional, Wei, Sharon, additional, Williams, Gary, additional, Winterbottom, Andrea, additional, Zarowiecki, Magdalena, additional, Finn, Robert D, additional, and Flicek, Paul, additional
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- 2021
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- View/download PDF
7. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control
- Author
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Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., Benoit, Joshua B., Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.
- Abstract
Background: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. Conclusions: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.
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- 2021
8. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control (BMC Biology, (2021), 19, 1, (41), 10.1186/s12915-021-00975-9)
- Author
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Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., Benoit, Joshua B., Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.
- Abstract
Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.
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- 2021
9. Functional genomics of the stable fly,Stomoxys calcitrans, reveals mechanisms underlying reproduction, host interactions, and novel targets for pest control
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Olafson, Pia U., primary, Aksoy, Serap, additional, Attardo, Geoffrey M., additional, Buckmeier, Greta, additional, Chen, Xiaoting, additional, Coates, Craig J., additional, Davis, Megan, additional, Dykema, Justin, additional, Emrich, Scott J., additional, Friedrich, Markus, additional, Holmes, Christopher J., additional, Ioannidis, Panagiotis, additional, Jansen, Evan N., additional, Jennings, Emily C., additional, Lawson, Daniel, additional, Martinson, Ellen O., additional, Maslen, Gareth L., additional, Meisel, Richard P., additional, Murphy, Terence D., additional, Nayduch, Dana, additional, Nelson, David R., additional, Oyen, Kennan J., additional, Raszick, Tyler J., additional, Ribeiro, José M. C., additional, Robertson, Hugh M., additional, Rosendale, Andrew J., additional, Sackton, Timothy B., additional, Swiger, Sonja L., additional, Sze, Sing-Hoi, additional, Tarone, Aaron M., additional, Taylor, David B., additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Weirauch, Matthew T., additional, Werren, John H., additional, Wilson, Richard K., additional, Zdobnov, Evgeny M., additional, and Benoit, Joshua B., additional
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- 2019
- Full Text
- View/download PDF
10. The Glossina Genome Cluster: Comparative Genomic Analysis of the Vectors of African Trypanosomes
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Attardo, Geoffrey Michael, primary, Abd-Alla, Adly M.M., additional, Acosta-Serrano, Alvaro, additional, Allen, James E, additional, Bateta, Rosemary, additional, Benoit, Joshua, additional, Bourtzis, Kostas, additional, Caers, Jelle, additional, Caljon, Guy, additional, Christensen, Mikkel B., additional, Farrow, David W., additional, Friedrich, Markus, additional, Hua-Van, Aurélie, additional, Jennings, Emily C., additional, Larkin, Denis M, additional, Lawson, Daniel, additional, Lehane, Michael J., additional, Lenis, Vasileios P., additional, Lowy-Gallego, Ernesto, additional, Macharia, Rosaline W., additional, Malacrida, Anna R., additional, Marco, Heather G., additional, Masiga, Daniel, additional, Maslen, Gareth L., additional, Matetovici, Irina, additional, Meisel, Richard P., additional, Meki, Irene, additional, Michalkova, Veronika, additional, Miller, Wolfgang J., additional, Minx, Patrick, additional, Mireji, Paul O., additional, Ometto, Lino, additional, Parker, Andrew G., additional, Rio, Rita, additional, Rose, Clair, additional, Rosendale, Andrew J., additional, Rota Stabelli, Omar, additional, Savini, Grazia, additional, Schoofs, Liliane, additional, Scolari, Francesca, additional, Swain, Martin T., additional, Takáč, Peter, additional, Tomlinson, Chad, additional, Tsiamis, George, additional, Van Den Abbeele, Jan, additional, Vigneron, Aurélien, additional, Wang, Jingwen, additional, Warren, Wesley C., additional, Waterhouse, Robert M., additional, Weirauch, Matthew T., additional, Weiss, Brian L., additional, Wilson, Richard K., additional, Zhao, Xin, additional, and Aksoy, Serap, additional
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- 2019
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11. Advancing vector biology research : a community survey for future directions, research applications and infrastructure requirements
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Kohl, Alain, Pondeville, Emilie, Schnettler, Esther, Crisanti, Andrea, Supparo, Clelia, Christophides, George K., Kersey, Paul J., Maslen, Gareth L., Takken, Willem, Koenraadt, Constantianus J.M., Oliva, Clelia F., Busquets, Núria, Abad, F.X., Failloux, Anna Bella, Levashina, Elena A., Wilson, Anthony J., Veronesi, Eva, Pichard, Maëlle, Arnaud Marsh, Sarah, Simard, Frédéric, Vernick, Kenneth D., Kohl, Alain, Pondeville, Emilie, Schnettler, Esther, Crisanti, Andrea, Supparo, Clelia, Christophides, George K., Kersey, Paul J., Maslen, Gareth L., Takken, Willem, Koenraadt, Constantianus J.M., Oliva, Clelia F., Busquets, Núria, Abad, F.X., Failloux, Anna Bella, Levashina, Elena A., Wilson, Anthony J., Veronesi, Eva, Pichard, Maëlle, Arnaud Marsh, Sarah, Simard, Frédéric, and Vernick, Kenneth D.
- Abstract
Vector-borne pathogens impact public health, animal production, and animal welfare. Research on arthropod vectors such as mosquitoes, ticks, sandflies, and midges which transmit pathogens to humans and economically important animals is crucial for development of new control measures that target transmission by the vector. While insecticides are an important part of this arsenal, appearance of resistance mechanisms is increasingly common. Novel tools for genetic manipulation of vectors, use of Wolbachia endosymbiotic bacteria, and other biological control mechanisms to prevent pathogen transmission have led to promising new intervention strategies, adding to strong interest in vector biology and genetics as well as vector–pathogen interactions. Vector research is therefore at a crucial juncture, and strategic decisions on future research directions and research infrastructure investment should be informed by the research community. A survey initiated by the European Horizon 2020 INFRAVEC-2 consortium set out to canvass priorities in the vector biology research community and to determine key activities that are needed for researchers to efficiently study vectors, vector-pathogen interactions, as well as access the structures and services that allow such activities to be carried out. We summarize the most important findings of the survey which in particular reflect the priorities of researchers in European countries, and which will be of use to stakeholders that include researchers, government, and research organizations.
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- 2016
12. Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements
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Kohl, Alain, primary, Pondeville, Emilie, additional, Schnettler, Esther, additional, Crisanti, Andrea, additional, Supparo, Clelia, additional, Christophides, George K., additional, Kersey, Paul J., additional, Maslen, Gareth L., additional, Takken, Willem, additional, Koenraadt, Constantianus J. M., additional, Oliva, Clelia F., additional, Busquets, Núria, additional, Abad, F. Xavier, additional, Failloux, Anna-Bella, additional, Levashina, Elena A., additional, Wilson, Anthony J., additional, Veronesi, Eva, additional, Pichard, Maëlle, additional, Arnaud Marsh, Sarah, additional, Simard, Frédéric, additional, and Vernick, Kenneth D., additional
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- 2016
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13. Advancing insect vector biology research: a community survey for future directions, research applications and infrastructure requirements
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Kohl, Alain, primary, Pondeville, Emilie, additional, Schnettler, Esther, additional, Crisanti, Andrea, additional, Supparo, Clelia, additional, Christophides, George K, additional, Kersey, Paul J, additional, Maslen, Gareth L, additional, Takken, Willem, additional, Koenraadt, Constantianus J. M., additional, Oliva, Clelia F, additional, Busquets, Núria, additional, Abad, F Xavier, additional, Failloux, Anna-Bella, additional, Levashina, Elena A, additional, Wilson, Anthony J, additional, Veronesi, Eva, additional, Pichard, Maëlle, additional, Marsh, Sarah Arnaud, additional, Simard, Frédéric, additional, and Vernick, Kenneth D, additional
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- 2016
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14. Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients
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Robinson, Timothy, Campino, Susana G., Auburn, Sarah, Assefa, Samuel A., Polley, Spencer D., Manske, Magnus, MacInnis, Bronwyn, Rockett, Kirk A., Maslen, Gareth L., Sanders, Mandy, Quail, Michael A., Chiodini, Peter L., Kwiatkowski, Dominic P., Clark, Taane G., Sutherland, Colin J., Robinson, Timothy, Campino, Susana G., Auburn, Sarah, Assefa, Samuel A., Polley, Spencer D., Manske, Magnus, MacInnis, Bronwyn, Rockett, Kirk A., Maslen, Gareth L., Sanders, Mandy, Quail, Michael A., Chiodini, Peter L., Kwiatkowski, Dominic P., Clark, Taane G., and Sutherland, Colin J.
- Abstract
Naturally acquired blood-stage infections of the malaria parasite Plasmodium falciparum typically harbour multiple haploid clones. The apparent number of clones observed in any single infection depends on the diversity of the polymorphic markers used for the analysis, and the relative abundance of rare clones, which frequently fail to be detected among PCR products derived from numerically dominant clones. However, minority clones are of clinical interest as they may harbour genes conferring drug resistance, leading to enhanced survival after treatment and the possibility of subsequenttherapeutic failure. We deployed new generation sequencing to derive genome data for five non-propagated parasite isolates taken directly from 4 different patients treated for clinical malaria in a UK hospital. Analysis of depth of coverage and length of sequence intervals between paired reads identified both previously described and novel gene deletions and amplifications. Full-length sequence data was extracted for 6 loci considered to be under selection by antimalarial drugs, and both known and previously unknown amino acid substitutions were identified. Full mitochondrial genomes were extracted from the sequencing data for each isolate, and these are compared against a panel of polymorphic sites derived from published or unpublished but publicly available data. Finally, genome-wide analysis of clone multiplicity was performed, and the number of infecting parasite clones estimated for each isolate. Each patient harboured at least 3 clones of P. falciparum by this analysis, consistent with results obtained with conventional PCR analysis of polymorphic merozoite antigen loci. We conclude that genome sequencing of peripheral blood P. falciparum taken directly from malaria patients provides high quality data useful for drug resistance studies, genomic structural analyses and population genetics, and also robustly represents clonal multiplicity.
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- 2011
15. Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients
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Robinson, Timothy, primary, Campino, Susana G., additional, Auburn, Sarah, additional, Assefa, Samuel A., additional, Polley, Spencer D., additional, Manske, Magnus, additional, MacInnis, Bronwyn, additional, Rockett, Kirk A., additional, Maslen, Gareth L., additional, Sanders, Mandy, additional, Quail, Michael A., additional, Chiodini, Peter L., additional, Kwiatkowski, Dominic P., additional, Clark, Taane G., additional, and Sutherland, Colin J., additional
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- 2011
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16. Application of phage display to high throughput antibody generation and characterization
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Schofield, Darren J, primary, Pope, Anthony R, additional, Clementel, Veronica, additional, Buckell, Jenny, additional, Chapple, Susan DJ, additional, Clarke, Kay F, additional, Conquer, Jennie S, additional, Crofts, Anna M, additional, Crowther, Sandra RE, additional, Dyson, Michael R, additional, Flack, Gillian, additional, Griffin, Gareth J, additional, Hooks, Yvette, additional, Howat, William J, additional, Kolb-Kokocinski, Anja, additional, Kunze, Susan, additional, Martin, Cecile D, additional, Maslen, Gareth L, additional, Mitchell, Joanne N, additional, O'Sullivan, Maureen, additional, Perera, Rajika L, additional, Roake, Wendy, additional, Shadbolt, S Paul, additional, Vincent, Karen J, additional, Warford, Anthony, additional, Wilson, Wendy E, additional, Xie, Jane, additional, Young, Joyce L, additional, and McCafferty, John, additional
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- 2007
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17. High-Resolution Landmark Framework for the Sequence-Ready Mapping of Xq23–q26.1
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Steingruber, Helen E., primary, Dunham, Andrew, additional, Coffey, Alison J., additional, Clegg, Sheila M., additional, Howell, Gareth R., additional, Maslen, Gareth L., additional, Scott, Carol E., additional, Gwilliam, Rhian, additional, Hunt, Paul J., additional, Sotheran, Elizabeth C., additional, Huckle, Elizabeth J., additional, Hunt, Sarah E., additional, Dhami, Pawandeep, additional, Soderlund, Cari, additional, Leversha, Margaret A., additional, Bentley, David R., additional, and Ross, Mark T., additional
- Published
- 1999
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18. Additional file 1 of The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control
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Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Xiaoting Chen, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M. C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Perot Saelao, Swiger, Sonja L., Sing-Hoi Sze, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.
- Subjects
2. Zero hunger - Abstract
Additional file 1: Main supplementary text file, including supplementary Tables S1-S12 and supplementary Figures S1-S21; Table S1. RNA-Sequencing and Whole Genome Sequencing Accession Numbers and Statistics. Table S2. Summary of Dfam repeat elements with > 1000 copies including number of unique elements for each family of elements and total number of genomic copies for each family. Table S3. Detailed list of repeat elements with total genomic copy number > 1000. Table S4. Autophagy genes identified from the Stomoxys genome. Table S5. Validation of Stomoxys transcript expression by RT-qPCR. Table S6. Bacterial contaminating scaffolds located in the Stomoxys genome assembly. Table S7. Predicted lateral gene transfer events identified from the Stomoxys genome. Table S8. Components of the immune deficiency, Toll, and JAK/STAT pathways identified from the Stomoxys genome. Table S9. Manually annotated Stomoxys immune system gene family members. Table S10. RNA-Seq normalized expression values for transcripts annotated as antimicrobial peptides. Table S11. Stomoxys opsin gene compilation. Table S12. Aquaporin gene names and corresponding symbols, model numbers, scaffolds, and arthropod homologues. Figure S1. Phylogenetic placement and genomic comparisons for Stomoxys calcitrans and other fly species. Figure S2. Pearson's correlation of RNA-Seq and RT-qPCR results. Figure S3. Average read depth across predicted lateral gene transfer candidates. Figure S4. Stomoxys calcitrans genomic scaffold housing 11 defensin gene models. Figure S5. Maximum likelihood phylogenetic tree of PGRP protein sequences from S. calcitrans (red), M. domestica (black), and D. melanogaster (blue). Figure S6. Alignment of Stomoxys PGRP-S sequences with characterized D. melanogaster PGRP-SC1 (C0HK98) and –SC2 (Q9VX2) and N-acetylmuramoyl-L-alanine amidase (P00806). Figure S7. Alignment of Stomoxys PGRP-L sequences with characterized D. melanogaster PGRP-L proteins and N-acetylmuramoyl-L-alanine amidase. Figure S8. Stomoxys calcitrans Odorant Binding Protein Gene Family. Figure S9. Duplicated OS-E-like and an OS-X ortholog in Stomoxys and Musca. Figure S10. Stomoxys calcitrans Odorant Receptor Gene Family. Figure S11. Stomoxys calcitrans Gustatory Receptor Gene Family. Figure S12. Stomoxys calcitrans Ionotropic Receptor Gene Family. Figure S13. Maximum likelihood tree of dipteran opsin gene relationships. Figure S14. Phylogenetic analysis of the Stomoxys Rh1 gene cluster and Genomic organization and evolution of the S. calcitrans Rh1 opsin subfamily. Figure S15. Analysis of tuning site 17 variation in Stomoxys and Musca Rh1 paralogs. Figure S16, S18, S19. Phylogenetic relationship of catalytic carboxyesterases (S16), glutathione-S-transferases (S18), and Cys-Loop Ligand Gated Ion Channels (S19) from Stomoxys relative to Musca and Drosophila. Figure S17. Phylogenetic analysis of carboxylesterases with a role in neuronal development. Figure S20. Cytochrome P450 (CYP450) genes clustered on Stomoxys scaffolds and evidence for expansions in muscids relative to Drosophila. Figure S21. Phylogenetic analysis of cytochrome P450 genes from Stomoxys calcitrans.
19. Additional file 1 of The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control
- Author
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Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Xiaoting Chen, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M. C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Perot Saelao, Swiger, Sonja L., Sing-Hoi Sze, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.
- Subjects
2. Zero hunger - Abstract
Additional file 1: Main supplementary text file, including supplementary Tables S1-S12 and supplementary Figures S1-S21; Table S1. RNA-Sequencing and Whole Genome Sequencing Accession Numbers and Statistics. Table S2. Summary of Dfam repeat elements with > 1000 copies including number of unique elements for each family of elements and total number of genomic copies for each family. Table S3. Detailed list of repeat elements with total genomic copy number > 1000. Table S4. Autophagy genes identified from the Stomoxys genome. Table S5. Validation of Stomoxys transcript expression by RT-qPCR. Table S6. Bacterial contaminating scaffolds located in the Stomoxys genome assembly. Table S7. Predicted lateral gene transfer events identified from the Stomoxys genome. Table S8. Components of the immune deficiency, Toll, and JAK/STAT pathways identified from the Stomoxys genome. Table S9. Manually annotated Stomoxys immune system gene family members. Table S10. RNA-Seq normalized expression values for transcripts annotated as antimicrobial peptides. Table S11. Stomoxys opsin gene compilation. Table S12. Aquaporin gene names and corresponding symbols, model numbers, scaffolds, and arthropod homologues. Figure S1. Phylogenetic placement and genomic comparisons for Stomoxys calcitrans and other fly species. Figure S2. Pearson's correlation of RNA-Seq and RT-qPCR results. Figure S3. Average read depth across predicted lateral gene transfer candidates. Figure S4. Stomoxys calcitrans genomic scaffold housing 11 defensin gene models. Figure S5. Maximum likelihood phylogenetic tree of PGRP protein sequences from S. calcitrans (red), M. domestica (black), and D. melanogaster (blue). Figure S6. Alignment of Stomoxys PGRP-S sequences with characterized D. melanogaster PGRP-SC1 (C0HK98) and –SC2 (Q9VX2) and N-acetylmuramoyl-L-alanine amidase (P00806). Figure S7. Alignment of Stomoxys PGRP-L sequences with characterized D. melanogaster PGRP-L proteins and N-acetylmuramoyl-L-alanine amidase. Figure S8. Stomoxys calcitrans Odorant Binding Protein Gene Family. Figure S9. Duplicated OS-E-like and an OS-X ortholog in Stomoxys and Musca. Figure S10. Stomoxys calcitrans Odorant Receptor Gene Family. Figure S11. Stomoxys calcitrans Gustatory Receptor Gene Family. Figure S12. Stomoxys calcitrans Ionotropic Receptor Gene Family. Figure S13. Maximum likelihood tree of dipteran opsin gene relationships. Figure S14. Phylogenetic analysis of the Stomoxys Rh1 gene cluster and Genomic organization and evolution of the S. calcitrans Rh1 opsin subfamily. Figure S15. Analysis of tuning site 17 variation in Stomoxys and Musca Rh1 paralogs. Figure S16, S18, S19. Phylogenetic relationship of catalytic carboxyesterases (S16), glutathione-S-transferases (S18), and Cys-Loop Ligand Gated Ion Channels (S19) from Stomoxys relative to Musca and Drosophila. Figure S17. Phylogenetic analysis of carboxylesterases with a role in neuronal development. Figure S20. Cytochrome P450 (CYP450) genes clustered on Stomoxys scaffolds and evidence for expansions in muscids relative to Drosophila. Figure S21. Phylogenetic analysis of cytochrome P450 genes from Stomoxys calcitrans.
20. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.
- Author
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Yates AD, Allen J, Amode RM, Azov AG, Barba M, Becerra A, Bhai J, Campbell LI, Carbajo Martinez M, Chakiachvili M, Chougule K, Christensen M, Contreras-Moreira B, Cuzick A, Da Rin Fioretto L, Davis P, De Silva NH, Diamantakis S, Dyer S, Elser J, Filippi CV, Gall A, Grigoriadis D, Guijarro-Clarke C, Gupta P, Hammond-Kosack KE, Howe KL, Jaiswal P, Kaikala V, Kumar V, Kumari S, Langridge N, Le T, Luypaert M, Maslen GL, Maurel T, Moore B, Muffato M, Mushtaq A, Naamati G, Naithani S, Olson A, Parker A, Paulini M, Pedro H, Perry E, Preece J, Quinton-Tulloch M, Rodgers F, Rosello M, Ruffier M, Seager J, Sitnik V, Szpak M, Tate J, Tello-Ruiz MK, Trevanion SJ, Urban M, Ware D, Wei S, Williams G, Winterbottom A, Zarowiecki M, Finn RD, and Flicek P
- Subjects
- Animals, Computational Biology, Genome, Bacterial genetics, Genome, Fungal genetics, Genome, Plant genetics, Plants classification, Plants genetics, Vertebrates classification, Vertebrates genetics, Databases, Genetic, Genomics, Internet, Software
- Abstract
Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2022
- Full Text
- View/download PDF
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