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1. Giant tortoise genomes provide insights into longevity and age-related disease

Author

Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G, Jiang, Zi-Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas FK, Quinzin, Maud, Álvarez, Miguel G, Carrero, Dido, Beheregaray, Luciano B, Gibbs, James P, Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R, Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R, Edwards, Danielle L, Garrick, Ryan C, Russello, Michael A, Poulakakis, Nikos, Gaughran, Stephen J, Rueda, Danny O, Bretones, Gabriel, Marquès-Bonet, Tomàs, White, Kevin P, Caccone, Adalgisa, and López-Otín, Carlos

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Aging, Biotechnology, Generic health relevance, Animals, DNA Repair, Evolution, Molecular, Genome, HEK293 Cells, Humans, Inflammation Mediators, Male, Neoplasms, Phylogeny, Population Density, Turtles, Ecology, Evolutionary biology, Environmental management
Abstract

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.

Published
2019

2. 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

3. A Framework for Scalable Ambient Air Pollution Concentration Estimation

Author

Berrisford, Liam J, Neal, Lucy S, Buttery, Helen J, Evans, Benjamin R, Menezes, Ronaldo, Berrisford, Liam J, Neal, Lucy S, Buttery, Helen J, Evans, Benjamin R, and Menezes, Ronaldo

Abstract

Ambient air pollution remains a critical issue in the United Kingdom, where data on air pollution concentrations form the foundation for interventions aimed at improving air quality. However, the current air pollution monitoring station network in the UK is characterized by spatial sparsity, heterogeneous placement, and frequent temporal data gaps, often due to issues such as power outages. We introduce a scalable data-driven supervised machine learning model framework designed to address temporal and spatial data gaps by filling missing measurements. This approach provides a comprehensive dataset for England throughout 2018 at a 1kmx1km hourly resolution. Leveraging machine learning techniques and real-world data from the sparsely distributed monitoring stations, we generate 355,827 synthetic monitoring stations across the study area, yielding data valued at approximately \pounds70 billion. Validation was conducted to assess the model's performance in forecasting, estimating missing locations, and capturing peak concentrations. The resulting dataset is of particular interest to a diverse range of stakeholders engaged in downstream assessments supported by outdoor air pollution concentration data for NO2, O3, PM10, PM2.5, and SO2. This resource empowers stakeholders to conduct studies at a higher resolution than was previously possible., Comment: Main: 27 pages, 11 figures, 6 tables. Supplementary: 32 pages, 21 figures, 11 tables

Published
2024

4. Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

Author

Eytan, Ron I, Evans, Benjamin R, Dornburg, Alex, Lemmon, Alan R, Lemmon, Emily Moriarty, Wainwright, Peter C, and Near, Thomas J

Subjects
Genetics, Animals, Bayes Theorem, Fishes, High-Throughput Nucleotide Sequencing, Multilocus Sequence Typing, Phylogeny, Ovalentaria, Anchored hybrid enrichment, Phylogenomics, Cichlidae, Blenniiformes, Acanthomorpha, Percomorpha, Pholidichthys
Abstract

BackgroundThe past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be.ResultsAfter using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree.ConclusionsAlthough it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.

Published
2015

10. Giant tortoise genomes provide insights into longevity and age-related disease

Author

Banco Santander, Principado de Asturias, Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi-Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F. K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danille L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, Marqués-Bonet, Tomàs, White, Kevin P., Caccone, Adalgisa, López-Otín, Carlos, Banco Santander, Principado de Asturias, Ministerio de Economía y Competitividad (España), European Commission, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi-Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F. K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danille L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, Marqués-Bonet, Tomàs, White, Kevin P., Caccone, Adalgisa, and López-Otín, Carlos

Abstract

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelonoidis abingdonii—and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.

Published
2019

11. Aedes aegypti in its ancestral range, Africa

Author

Kotsakiozi, Panayiota, Evans, Benjamin R., Gloria-Soria, Andrea, Kamgang, Basile, Mayanja, Martin, Lutwama, Julius, Le Goff, Gilbert, Ayala, Diego, Paupy, Christophe, Badolo, Athanase, Pinto, Joao, Sousa, Carla A., Troco, Arlete D., Powell, Jeffrey R., Vector borne diseases and pathogens (VBD), Instituto de Higiene e Medicina Tropical (IHMT), and Global Health and Tropical Medicine (GHTM)

Subjects
Aedes aegypti, Infectious Diseases, SDG 3 - Good Health and Well-being, Insect Science, Africa, Genetics, SNP-chip, Population structure, Migration, Ecology, Evolution, Behavior and Systematics, SDG 15 - Life on Land
Abstract

Aedes aegypti, the major vector of dengue, yellow fever, chikungunya, and Zika viruses, remains of great medical and public health concern. There is little doubt thatthe ancestral home of the species is Africa. This mosquito invaded the New World400-500 years ago and later, Asia. However, little is known about the genetic structure and history of Ae. aegypti across Africa, as well as the possible origin(s) of theNew World invasion. Here, we use ∼17,000 genome-wide single nucleotide polymorphisms (SNPs) to characterize a heretofore undocumented complex picture of thismosquito across its ancestral range in Africa. We find signatures of human-assistedmigrations, connectivity across long distances in sylvan populations, and of local admixture between domestic and sylvan populations. Finally, through a phylogeneticanalysis combined with the genetic structure analyses, we suggest West Africa andespecially Angola as the source of the New World's invasion, a scenario that fits wellwith the historic record of 16th-century slave trade between Africa and Americas. publishersversion published

Published
2018

12. Giant tortoise genomes provide insights into longevity and age-related disease

Author

Quesada, Víctor, primary, Freitas-Rodríguez, Sandra, additional, Miller, Joshua, additional, Pérez-Silva, José G., additional, Jiang, Zi-Feng, additional, Tapia, Washington, additional, Santiago-Fernández, Olaya, additional, Campos-Iglesias, Diana, additional, Kuderna, Lukas F. K., additional, Quinzin, Maud, additional, Álvarez, Miguel G., additional, Carrero, Dido, additional, Beheregaray, Luciano B., additional, Gibbs, James P., additional, Chiari, Ylenia, additional, Glaberman, Scott, additional, Ciofi, Claudio, additional, Araujo-Voces, Miguel, additional, Mayoral, Pablo, additional, Arango, Javier R., additional, Tamargo-Gómez, Isaac, additional, Roiz-Valle, David, additional, Pascual-Torner, María, additional, Evans, Benjamin R., additional, Edwards, Danielle L., additional, Garrick, Ryan C., additional, Russello, Michael A., additional, Poulakakis, Nikos, additional, Gaughran, Stephen J., additional, Rueda, Danny O., additional, Bretones, Gabriel, additional, Marquès-Bonet, Tomàs, additional, White, Kevin P., additional, Caccone, Adalgisa, additional, and López-Otín, Carlos, additional

Published
2018
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13. Population structure of a vector of human diseases:Aedes aegyptiin its ancestral range, Africa

Author

Kotsakiozi, Panayiota, primary, Evans, Benjamin R., additional, Gloria‐Soria, Andrea, additional, Kamgang, Basile, additional, Mayanja, Martin, additional, Lutwama, Julius, additional, Le Goff, Gilbert, additional, Ayala, Diego, additional, Paupy, Christophe, additional, Badolo, Athanase, additional, Pinto, Joao, additional, Sousa, Carla A., additional, Troco, Arlete D., additional, and Powell, Jeffrey R., additional

Published
2018
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14. 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, Filipovic, Igor, Fontaine, Albin, Gloria-Soria, Andrea, Hall, Richard, Joardar, Vinita S., Jones, Andrew K., Kay, Raissa G. G., 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, Rasic, 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 Jake, Robertson, Hugh M., McBride, Carolyn S., Hastic, Alex R., Korlach, Jonas, Neafsey, Daniel E., Phillippy, Adam M., Vosshall, Leslie B., 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, Filipovic, Igor, Fontaine, Albin, Gloria-Soria, Andrea, Hall, Richard, Joardar, Vinita S., Jones, Andrew K., Kay, Raissa G. G., 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, Rasic, 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 Jake, Robertson, Hugh M., McBride, Carolyn S., Hastic, Alex R., Korlach, Jonas, Neafsey, Daniel E., Phillippy, Adam M., and Vosshall, Leslie B.

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

Author

Biochemistry, Entomology, Fralin Life Sciences Institute, 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, Filipovic, Igor, Fontaine, Albin, Gloria-Soria, Andrea, Hall, Richard, Joardar, Vinita S., Jones, Andrew K., Kay, Raissa G. G., 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, Rasic, 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 Jake, Robertson, Hugh M., McBride, Carolyn S., Hastic, Alex R., Korlach, Jonas, Neafsey, Daniel E., Phillippy, Adam M., Vosshall, Leslie B., Biochemistry, Entomology, Fralin Life Sciences Institute, 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, Filipovic, Igor, Fontaine, Albin, Gloria-Soria, Andrea, Hall, Richard, Joardar, Vinita S., Jones, Andrew K., Kay, Raissa G. G., 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, Rasic, 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 Jake, Robertson, Hugh M., McBride, Carolyn S., Hastic, Alex R., Korlach, Jonas, Neafsey, Daniel E., Phillippy, Adam M., and Vosshall, Leslie B.

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

16. Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

Author

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

Published
2017
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22. Human impacts have shaped historical and recent evolution in Aedes aegypti, the dengue and yellow fever mosquito

Author

Brown, Julia E., Evans, Benjamin R., Zheng, Wei, Obas, Vanessa, Barrera-Martinez, Laura, Egizi, Andrea, Zhao, Hongyu, Caccone, Adalgisa, and Powell, Jeffrey R.

Subjects
Evolution, Molecular, Phylogeography, Aedes, Human Migration, Animals, Humans, Genes, Insect, Selection, Genetic, Polymorphism, Single Nucleotide, Article
Abstract

Although anthropogenic impacts are often considered harmful to species, human modifications to the landscape can actually create novel niches to which other species can adapt. These "domestication" processes are especially important in the context of arthropod disease vectors, where ecological overlap of vector and human populations may lead to epidemics. Here, we present results of a global genetic study of one such species, the dengue and yellow fever mosquito, Aedes aegypti, whose evolutionary history and current distribution have been profoundly shaped by humans. We used DNA sequences of four nuclear genes and 1504 single nucleotide polymorphism (SNP) markers developed with restriction-site associated DNA (RAD) sequencing to test the hypothesis that Ae. aegypti originated in Africa, where a domestic form arose and spread throughout the tropical and subtropical world with human trade and movement. Results confirmed African ancestry of the species, and supported a single subspeciation event leading to the pantropical domestic form. In addition, genetic data strongly supported the hypothesis that human trade routes first moved domestic Ae. aegypti out of Africa into the New World, followed by a later invasion from the New World into Southeast Asia and the Pacific. These patterns of domestication and invasion are relevant to many species worldwide, as anthropogenic forces increasingly impact evolutionary processes.

Published
2013

23. Population structure of a vector of human diseases: Aedes aegypti in its ancestral range, Africa.

Author

Kotsakiozi, Panayiota, Evans, Benjamin R., Gloria‐Soria, Andrea, Kamgang, Basile, Mayanja, Martin, Lutwama, Julius, Le Goff, Gilbert, Ayala, Diego, Paupy, Christophe, Badolo, Athanase, Pinto, Joao, Sousa, Carla A., Troco, Arlete D., and Powell, Jeffrey R.

Subjects
*DISEASE vectors, *AEDES aegypti, *POPULATION biology, *SINGLE nucleotide polymorphisms
Abstract

Abstract: Aedes aegypti, the major vector of dengue, yellow fever, chikungunya, and Zika viruses, remains of great medical and public health concern. There is little doubt that the ancestral home of the species is Africa. This mosquito invaded the New World 400‐500 years ago and later, Asia. However, little is known about the genetic structure and history of Ae. aegypti across Africa, as well as the possible origin(s) of the New World invasion. Here, we use ~17,000 genome‐wide single nucleotide polymorphisms (SNPs) to characterize a heretofore undocumented complex picture of this mosquito across its ancestral range in Africa. We find signatures of human‐assisted migrations, connectivity across long distances in sylvan populations, and of local admixture between domestic and sylvan populations. Finally, through a phylogenetic analysis combined with the genetic structure analyses, we suggest West Africa and especially Angola as the source of the New World's invasion, a scenario that fits well with the historic record of 16th‐century slave trade between Africa and Americas. [ABSTRACT FROM AUTHOR]

Published
2018
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26. Improved reference genome of Aedes aegyptiinforms 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 G. G., 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.

Abstract

Female Aedes aegyptimosquitoes 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
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28. Giant tortoise genomes provide insights into longevity and age-related disease

Author

Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F.K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danielle L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, Marquès-Bonet, Tomàs, Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F.K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danielle L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, and Marquès-Bonet, Tomàs

29. Giant tortoise genomes provide insights into longevity and age-related disease

Author

Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F.K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danielle L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, Marquès-Bonet, Tomàs, Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F.K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danielle L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, and Marquès-Bonet, Tomàs

30. Giant tortoise genomes provide insights into longevity and age-related disease

Author

Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F.K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danielle L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, Marquès-Bonet, Tomàs, Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F.K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danielle L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, and Marquès-Bonet, Tomàs

31. Giant tortoise genomes provide insights into longevity and age-related disease

Author

Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F.K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danielle L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, Marquès-Bonet, Tomàs, Quesada, Víctor, Freitas-Rodríguez, Sandra, Miller, Joshua, Pérez-Silva, José G., Jiang, Zi Feng, Tapia, Washington, Santiago-Fernández, Olaya, Campos-Iglesias, Diana, Kuderna, Lukas F.K., Quinzin, Maud, Álvarez, Miguel G., Carrero, Dido, Beheregaray, Luciano B., Gibbs, James P., Chiari, Ylenia, Glaberman, Scott, Ciofi, Claudio, Araujo-Voces, Miguel, Mayoral, Pablo, Arango, Javier R., Tamargo-Gómez, Isaac, Roiz-Valle, David, Pascual-Torner, María, Evans, Benjamin R., Edwards, Danielle L., Garrick, Ryan C., Russello, Michael A., Poulakakis, Nikos, Gaughran, Stephen J., Rueda, Danny O., Bretones, Gabriel, and Marquès-Bonet, Tomàs

33. A Multipurpose, High-Throughput Single-Nucleotide Polymorphism Chip for the Dengue and Yellow Fever Mosquito, Aedes aegypti.

Author

Evans BR, Gloria-Soria A, Hou L, McBride C, Bonizzoni M, Zhao H, and Powell JR

Subjects
Animals, Dengue transmission, Genetic Variation, Genetics, Population, Genomics, Genotype, High-Throughput Nucleotide Sequencing, Humans, Inheritance Patterns, Linkage Disequilibrium, Yellow Fever transmission, Aedes genetics, Genome, Insect, Insect Vectors genetics, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide
Abstract

The dengue and yellow fever mosquito, Aedes aegypti, contributes significantly to global disease burden. Genetic study of Aedes aegypti is essential to understanding its evolutionary history, competence as a disease vector, and the effects and efficacy of vector control methods. The prevalence of repeats and transposable elements in the Aedes aegypti genome complicates marker development and makes genome-wide genetic study challenging. To overcome these challenges, we developed a high-throughput genotyping chip, Axiom_aegypti1. This chip screens for 50,000 single-nucleotide polymorphisms present in Aedes aegypti populations from around the world. The array currently used genotypes 96 samples simultaneously. To ensure that these markers satisfy assumptions commonly made in many genetic analyses, we tested for Mendelian inheritance and linkage disequilibrium in laboratory crosses and a wild population, respectively. We have validated more than 25,000 of these markers to date, and expect this number to increase with more sampling. We also present evidence of the chip's efficacy in distinguishing populations throughout the world. The markers on this chip are ideal for applications ranging from population genetics to genome-wide association studies. This tool makes rapid, cost-effective, and comparable genotype data attainable to diverse sets of Aedes aegypti researchers, from those interested in potential range shifts due to climate change to those characterizing the genetic underpinnings of its competence to transmit disease., (Copyright © 2015 Evans et al.)

Published
2015
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