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1. Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability.

Author

Finch, Geoffrey, Nandyal, Sonya, Perretta, Carlie, Davies, Benjamin, Rosendale, Andrew J, Holmes, Christopher J, Gantz, JD, Spacht, Drew E, Bailey, Samuel T, Chen, Xiaoting, Oyen, Kennan, Didion, Elise M, Chakraborty, Souvik, Lee, Richard E, Denlinger, David L, Matter, Stephen F, Attardo, Geoffrey M, Weirauch, Matthew T, and Benoit, Joshua B

Abstract

The Antarctic midge, Belgica antarctica, is a wingless, non-biting midge endemic to Antarctica. Larval development requires at least 2 years, but adults live only 2 weeks. The nonfeeding adults mate in swarms and females die shortly after oviposition. Eggs are suspended in a gel of unknown composition that is expressed from the female accessory gland. This project characterizes molecular mechanisms underlying reproduction in this midge by examining differential gene expression in whole males, females, and larvae, as well as in male and female accessory glands. Functional studies were used to assess the role of the gel encasing the eggs, as well as the impact of stress on reproductive biology. RNA-seq analyses revealed sex- and development-specific gene sets along with those associated with the accessory glands. Proteomic analyses were used to define the composition of the egg-containing gel, which is generated during multiple developmental stages and derived from both the accessory gland and other female organs. Functional studies indicate the gel provides a larval food source as well as a buffer for thermal and dehydration stress. All of these function are critical to juvenile survival. Larval dehydration stress directly reduces production of storage proteins and key accessory gland components, a feature that impacts adult reproductive success. Modeling reveals that bouts of dehydration may have a significant impact on population growth. This work lays a foundation for further examination of reproduction in midges and provides new information related to general reproduction in dipterans. A key aspect of this work is that reproduction and stress dynamics, currently understudied in polar organisms, are likely to prove critical in determining how climate change will alter their survivability.

Published
2020

2. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author

Panfilio, Kristen A, Vargas Jentzsch, Iris M, Benoit, Joshua B, Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M, Poelchau, Monica F, Waterhouse, Robert M, Ioannidis, Panagiotis, Weirauch, Matthew T, Hughes, Daniel ST, Murali, Shwetha C, Werren, John H, Jacobs, Chris GC, Duncan, Elizabeth J, Armisén, David, Vreede, Barbara MI, Baa-Puyoulet, Patrice, Berger, Chloé S, Chang, Chun-che, Chao, Hsu, Chen, Mei-Ju M, Chen, Yen-Ta, Childers, Christopher P, Chipman, Ariel D, Cridge, Andrew G, Crumière, Antonin JJ, Dearden, Peter K, Didion, Elise M, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G, Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J, Horn, Thorsten, Hsiao, Yi-min, Jennings, Emily C, Johnston, J Spencer, Jones, Tamsin E, Jones, Jeffery W, Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L, Lee, Chien-Yueh, Lovegrove, Mackenzie R, Lu, Hsiao-ling, Lu, Yong, Moore, Patricia J, Munoz-Torres, Monica C, Muzny, Donna M, Palli, Subba R, Parisot, Nicolas, Pick, Leslie, Porter, Megan L, Qu, Jiaxin, Refki, Peter N, Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J, Roth, Siegfried, Sachs, Lena, Santos, M Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N, Stancliffe, Richard J, Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Amino Acid Sequence, Animals, CYS2-HIS2 Zinc Fingers, Evolution, Molecular, Feeding Behavior, Gene Dosage, Gene Expression Profiling, Gene Transfer, Horizontal, Genes, Homeobox, Genome, Insect, Hemiptera, Pigmentation, Smell, Transcription Factors, Evolution of development, Gene family evolution, Gene structure, Lateral gene transfer, Phytophagy, RNAi, Transcription factors, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundThe Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae.ResultsThe 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding.ConclusionsWith the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus's strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes.

Published
2019

3. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).

Author

Schoville, Sean D, Chen, Yolanda H, Andersson, Martin N, Benoit, Joshua B, Bhandari, Anita, Bowsher, Julia H, Brevik, Kristian, Cappelle, Kaat, Chen, Mei-Ju M, Childers, Anna K, Childers, Christopher, Christiaens, Olivier, Clements, Justin, Didion, Elise M, Elpidina, Elena N, Engsontia, Patamarerk, Friedrich, Markus, García-Robles, Inmaculada, Gibbs, Richard A, Goswami, Chandan, Grapputo, Alessandro, Gruden, Kristina, Grynberg, Marcin, Henrissat, Bernard, Jennings, Emily C, Jones, Jeffery W, Kalsi, Megha, Khan, Sher A, Kumar, Abhishek, Li, Fei, Lombard, Vincent, Ma, Xingzhou, Martynov, Alexander, Miller, Nicholas J, Mitchell, Robert F, Munoz-Torres, Monica, Muszewska, Anna, Oppert, Brenda, Palli, Subba Reddy, Panfilio, Kristen A, Pauchet, Yannick, Perkin, Lindsey C, Petek, Marko, Poelchau, Monica F, Record, Éric, Rinehart, Joseph P, Robertson, Hugh M, Rosendale, Andrew J, Ruiz-Arroyo, Victor M, Smagghe, Guy, Szendrei, Zsofia, Thomas, Gregg WC, Torson, Alex S, Vargas Jentzsch, Iris M, Weirauch, Matthew T, Yates, Ashley D, Yocum, George D, Yoon, June-Sun, and Richards, Stephen

Subjects
Animals, Insect Proteins, Transcription Factors, DNA Transposable Elements, Genetics, Population, Genomics, Pest Control, Biological, Evolution, Molecular, Phylogeny, Gene Expression Regulation, RNA Interference, Insecticide Resistance, Multigene Family, Agriculture, Female, Male, Solanum tuberosum, Genome, Insect, Host-Parasite Interactions, Genetic Variation, Molecular Sequence Annotation, Coleoptera, Genetics, Population, Pest Control, Biological, Evolution, Molecular, Genome, Insect, Biochemistry and Cell Biology, Other Physical Sciences
Abstract

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

Published
2018

4. Rapid autophagic regression of the milk gland during involution is critical for maximizing tsetse viviparous reproductive output.

Author

Benoit, Joshua B, Michalkova, Veronika, Didion, Elise M, Xiao, Yanyu, Baumann, Aaron A, Attardo, Geoffrey M, and Aksoy, Serap

Subjects
Animal Structures, Animals, Tsetse Flies, Gene Expression Profiling, Fertility, Autophagy, Sexual Behavior, Animal, Tropical Medicine, Biological Sciences, Medical and Health Sciences
Abstract

Tsetse flies are important vectors of human and animal trypanosomiasis. Ability to reduce tsetse populations is an effective means of disease control. Lactation is an essential component of tsetse's viviparous reproductive physiology and requires a dramatic increase in the expression and synthesis of milk proteins by the milk gland organ in order to nurture larval growth. In between each gonotrophic cycle, tsetse ceases milk production and milk gland tubules undergo a nearly two-fold reduction in width (involution). In this study, we examined the role autophagy plays during tsetse fly milk gland involution and reproductive output. Autophagy genes show elevated expression in tissues associated with lactation, immediately before or within two hours post-parturition, and decline at 24-48h post-parturition. This expression pattern is inversely correlated with that of the milk gland proteins (lactation-specific protein coding genes) and the autophagy inhibitor fk506-bp1. Increased expression of Drosophila inhibitor of apoptosis 1, diap1, was also observed in the milk gland during involution, when it likely prevents apoptosis of milk gland cells. RNAi-mediated knockdown of autophagy related gene 8a (atg8a) prevented rapid milk gland autophagy during involution, prolonging gestation, and reducing fecundity in the subsequent gonotrophic cycle. The resultant inhibition of autophagy reduced the recovery of stored lipids during the dry (non-lactating) periods by 15-20%. Ecdysone application, similar to levels that occur immediately before birth, induced autophagy, and increased milk gland involution even before abortion. This suggests that the ecdysteroid peak immediately preceding parturition likely triggers milk gland autophagy. Population modeling reveals that a delay in involution would yield a negative population growth rate. This study indicates that milk gland autophagy during involution is critical to restore nutrient reserves and allow efficient transition between pregnancy cycles. Targeting post-birth phases of reproduction could be utilized as a novel mechanism to suppress tsetse populations and reduce trypanosomiasis.

Published
2018

5. Neutralization and binding antibody response to second bivalent COVID‐19 vaccination in nursing home residents

Author

Oyebanji, Oladayo A., primary, Abul, Yasin, additional, Wilson, Brigid M., additional, Bosch, Jurgen, additional, Didion, Elise M., additional, Paxitzis, Alexandra N., additional, Sundheimer, Nicholas, additional, Ragavapuram, Vaishnavi, additional, Wilk, Dennis, additional, Keresztesy, Debbie, additional, Aung, Htin, additional, Cao, Yi, additional, King, Christopher L., additional, Balazs, Alejandro B., additional, White, Elizabeth M., additional, Gravenstein, Stefan, additional, and Canaday, David H., additional

Published
2023
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6. SARS-CoV-2 Antibody Responses to the Ancestral SARS-CoV-2 Strain and Omicron BA.1 and BA.4/BA.5 Variants in Nursing Home Residents After Receipt of Bivalent COVID-19 Vaccine--Ohio and Rhode Island, September-November 2022

Author

Canaday, David H., Oyebanji, Oladayo A., White, Elizabeth M., Bosch, Jurgen, Nugent, Clare, Vishnepolskiy, Igor, Abul, Yasin, Didion, Elise M., Paxitzis, Alexandra, Sundheimer, Nicholas, Ragavapuram, Vaishnavi, Wilk, Dennis, Keresztesy, Debbie, Cao, Yi, St. Denis, Kerri, McConeghy, Kevin W., McDonald, L. Clifford, Jernigan, John A., Mylonakis, Eleftherios, Wilson, Brigid M., King, Christopher L., Balazs, Alejandro B., and Gravenstein, Stefan

Subjects
Infection -- Health aspects, RNA -- Health aspects, Vaccines -- Health aspects, Nursing homes -- Health aspects, Health
Abstract

Introduction of monovalent COVID-19 mRNA vaccines in late 2020 helped to mitigate disproportionate COVID-19--related morbidity and mortality in U.S. nursing homes (1); however, reduced effectiveness of monovalent vaccines during the [...]

Published
2023

7. Second monovalent SARS-CoV-2 mRNA booster restores Omicron-specific neutralizing activity in both nursing home residents and health care workers

Author

Nugent, Clare, primary, Abul, Yasin, additional, White, Elizabeth M., additional, Shehadeh, Fadi, additional, Kaczynski, Matthew, additional, Oscar Felix, Lewis, additional, Ganesan, Narchonai, additional, Oyebanji, Oladayo A., additional, Vishnepolskiy, Igor, additional, Didion, Elise M., additional, Paxitzis, Alexandra, additional, Sheehan, Maegan L., additional, Chan, Philip A., additional, Pfeifer, Walther M., additional, Dickerson, Evan, additional, Kamojjala, Shreya, additional, Wilson, Brigid M., additional, Mylonakis, Eleftherios, additional, King, Christopher L., additional, Balazs, Alejandro B., additional, Canaday, David H., additional, and Gravenstein, Stefan, additional

Published
2023
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8. The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Author

Armisén, David, Rajakumar, Rajendhran, Friedrich, Markus, Benoit, Joshua B., Robertson, Hugh M., Panfilio, Kristen A., Ahn, Seung-Joon, Poelchau, Monica F., Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Gibbs, Richard A., Hughes, Daniel S. T., Han, Yi, Lee, Sandra L., Murali, Shwetha C., Muzny, Donna M., Qu, Jiaxin, Worley, Kim C., Munoz-Torres, Monica, Abouheif, Ehab, Bonneton, François, Chen, Travis, Chiang, Li-Mei, Childers, Christopher P., Cridge, Andrew G., Crumière, Antonin J. J., Decaras, Amelie, Didion, Elise M., Duncan, Elizabeth J., Elpidina, Elena N., Favé, Marie-Julie, Finet, Cédric, Jacobs, Chris G. C., Cheatle Jarvela, Alys M., Jennings, Emily C., Jones, Jeffery W., Lesoway, Maryna P., Lovegrove, Mackenzie R., Martynov, Alexander, Oppert, Brenda, Lillico-Ouachour, Angelica, Rajakumar, Arjuna, Refki, Peter Nagui, Rosendale, Andrew J., Santos, Maria Emilia, Toubiana, William, van der Zee, Maurijn, Vargas Jentzsch, Iris M., Lowman, Aidamalia Vargas, Viala, Severine, Richards, Stephen, and Khila, Abderrahman

Published
2018
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11. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author

Panfilio, Kristen A., Vargas Jentzsch, Iris M., Benoit, Joshua B., Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M., Poelchau, Monica F., Waterhouse, Robert M., Ioannidis, Panagiotis, Weirauch, Matthew T., Hughes, Daniel S. T., Murali, Shwetha C., Werren, John H., Jacobs, Chris G. C., Duncan, Elizabeth J., Armisén, David, Vreede, Barbara M. I., Baa-Puyoulet, Patrice, Berger, Chloé S., Chang, Chun-che, Chao, Hsu, Chen, Mei-Ju M., Chen, Yen-Ta, Childers, Christopher P., Chipman, Ariel D., Cridge, Andrew G., Crumière, Antonin J. J., Dearden, Peter K., Didion, Elise M., Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G., Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J., Horn, Thorsten, Hsiao, Yi-min, Jennings, Emily C., Johnston, J. Spencer, Jones, Tamsin E., Jones, Jeffery W., Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L., Lee, Chien-Yueh, Lovegrove, Mackenzie R., Lu, Hsiao-ling, Lu, Yong, Moore, Patricia J., Munoz-Torres, Monica C., Muzny, Donna M., Palli, Subba R., Parisot, Nicolas, Pick, Leslie, Porter, Megan L., Qu, Jiaxin, Refki, Peter N., Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J., Roth, Siegfried, Sachs, Lena, Santos, M. Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N., Stancliffe, Richard J., Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., Richards, Stephen, Panfilio, Kristen A., Vargas Jentzsch, Iris M., Benoit, Joshua B., Erezyilmaz, Deniz, Suzuki, Yuichiro, Colella, Stefano, Robertson, Hugh M., Poelchau, Monica F., Waterhouse, Robert M., Ioannidis, Panagiotis, Weirauch, Matthew T., Hughes, Daniel S. T., Murali, Shwetha C., Werren, John H., Jacobs, Chris G. C., Duncan, Elizabeth J., Armisén, David, Vreede, Barbara M. I., Baa-Puyoulet, Patrice, Berger, Chloé S., Chang, Chun-che, Chao, Hsu, Chen, Mei-Ju M., Chen, Yen-Ta, Childers, Christopher P., Chipman, Ariel D., Cridge, Andrew G., Crumière, Antonin J. J., Dearden, Peter K., Didion, Elise M., Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Dugan, Shannon, Extavour, Cassandra G., Febvay, Gérard, Friedrich, Markus, Ginzburg, Neta, Han, Yi, Heger, Peter, Holmes, Christopher J., Horn, Thorsten, Hsiao, Yi-min, Jennings, Emily C., Johnston, J. Spencer, Jones, Tamsin E., Jones, Jeffery W., Khila, Abderrahman, Koelzer, Stefan, Kovacova, Viera, Leask, Megan, Lee, Sandra L., Lee, Chien-Yueh, Lovegrove, Mackenzie R., Lu, Hsiao-ling, Lu, Yong, Moore, Patricia J., Munoz-Torres, Monica C., Muzny, Donna M., Palli, Subba R., Parisot, Nicolas, Pick, Leslie, Porter, Megan L., Qu, Jiaxin, Refki, Peter N., Richter, Rose, Rivera-Pomar, Rolando, Rosendale, Andrew J., Roth, Siegfried, Sachs, Lena, Santos, M. Emília, Seibert, Jan, Sghaier, Essia, Shukla, Jayendra N., Stancliffe, Richard J., Tidswell, Olivia, Traverso, Lucila, van der Zee, Maurijn, Viala, Séverine, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen

Published
2019

12. Bacterial Communities of Lab and Field Northern House Mosquitoes (Diptera: Culicidae) Throughout Diapause

Author

Didion, Elise M, Doyle, Megan, and Benoit, Joshua B

Abstract

Diapause is a hormonally driven response which is triggered by environmental cues that signal impending adverse conditions and prompts metabolic, developmental, and behavioral changes to allow survival until the return of favorable conditions. Microbial symbionts have been shown to influence the metabolism, development, and behavior of their host organisms, all of which are common diapause-associated characteristics. Surveys of bacterial components in relation to diapause have been examined in few systems, of which the species are usually inactive during dormancy, such as eggs or pupae. This is specifically intriguing as adult female diapause in Culex pipiens(Diptera: Culicidae) can last between 4 and 7 mo and females remain mobile within their hibernacula. Furthermore, it is unknown how microbiota changes associated with prolonged dormancy are different between the lab and field for insect systems. This study aims to characterize how the microbiota of C. pipienschanges throughout diapause under both field and lab settings when provided identical food and water resources. Based on these studies, C. pipiensmicrobiota shifts as diapause progresses and there are considerable differences between field and lab individuals even when provided the same carbohydrate and water sources. Specific bacterial communities have more association with different periods of diapause, field and lab rearing conditions, and nutritional reserve levels. These studies highlight that diapausing mosquito microbiota studies ideally should occur in field mesocosms and at multiple locations, to increase applicability to wild C. pipiensas prolonged exposure to artificial rearing conditions could impact metrics related to diapause-microbiome interactions. Additionally, these findings suggest that it would be worthwhile to establish if the microbiota shift during diapause impacts host physiology and whether this shift is critical to diapause success.

Published
2022
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13. Multi-level analysis of reproduction in the Antarctic midge,Belgica antarctica, identifies female and male accessory gland products that are altered by larval stress and impact progeny viability

Author

Finch, Geoffrey, primary, Nandyal, Sonya, additional, Perrieta, Carlie, additional, Davies, Benjamin, additional, Rosendale, Andrew J., additional, Holmes, Christopher J., additional, Gantz, Josiah D., additional, Spacht, Drew, additional, Bailey, Samuel T., additional, Chen, Xiaoting, additional, Oyen, Kennan, additional, Didion, Elise M., additional, Chakraborty, Souvik, additional, Lee, Richard E., additional, Denlinger, David L., additional, Matter, Stephen F., additional, Attardo, Geoffrey M., additional, Weirauch, Matthew T., additional, and Benoit, Joshua B., additional

Published
2019
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14. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

Author

Schoville, Sean D., Chen, Yolanda H., Andersson, Martin N., Benoit, Joshua B., Bhandari, Anita, Bowsher, Julia H., Brevik, Kristian, Cappelle, Kaat, Chen, Mei-Ju M., Childers, Anna K., Childers, Christopher, Christiaens, Olivier, Clements, Justin, Didion, Elise M., Elpidina, Elena N., Engsontia, Patamarerk, Friedrich, Markus, Garcia-Robles, Inmaculada, Gibbs, Richard A., Goswami, Chandan, Grapputo, Alessandro, Gruden, Kristina, Grynberg, Marcin, Henrissat, Bernard, Jennings, Emily C., Jones, Jeffery W., Kalsi, Megha, Khan, Sher A., Kumar, Abhishek, Li, Fei, Lombard, Vincent, Ma, Xingzhou, Martynov, Alexander, Miller, Nicholas J., Mitchell, Robert F., Munoz-Torres, Monica, Muszewska, Anna, Oppert, Brenda, Palli, Subba Reddy, Panfilio, Kristen A., Pauchet, Yannick, Perkin, Lindsey C., Petek, Marko, Poelchau, Monica F., Record, Eric, Rinehart, Joseph P., Robertson, Hugh M., Rosendale, Andrew J., Ruiz-Arroyo, Victor M., Smagghe, Guy, Szendrei, Zsofia, Thomas, Gregg W. C., Torson, Alex S., Jentzsch, Iris M. Vargas, Weirauch, Matthew T., Yates, Ashley D. T., Yocum, George D., Yoon, June-Sun, Richards, Stephen, Schoville, Sean D., Chen, Yolanda H., Andersson, Martin N., Benoit, Joshua B., Bhandari, Anita, Bowsher, Julia H., Brevik, Kristian, Cappelle, Kaat, Chen, Mei-Ju M., Childers, Anna K., Childers, Christopher, Christiaens, Olivier, Clements, Justin, Didion, Elise M., Elpidina, Elena N., Engsontia, Patamarerk, Friedrich, Markus, Garcia-Robles, Inmaculada, Gibbs, Richard A., Goswami, Chandan, Grapputo, Alessandro, Gruden, Kristina, Grynberg, Marcin, Henrissat, Bernard, Jennings, Emily C., Jones, Jeffery W., Kalsi, Megha, Khan, Sher A., Kumar, Abhishek, Li, Fei, Lombard, Vincent, Ma, Xingzhou, Martynov, Alexander, Miller, Nicholas J., Mitchell, Robert F., Munoz-Torres, Monica, Muszewska, Anna, Oppert, Brenda, Palli, Subba Reddy, Panfilio, Kristen A., Pauchet, Yannick, Perkin, Lindsey C., Petek, Marko, Poelchau, Monica F., Record, Eric, Rinehart, Joseph P., Robertson, Hugh M., Rosendale, Andrew J., Ruiz-Arroyo, Victor M., Smagghe, Guy, Szendrei, Zsofia, Thomas, Gregg W. C., Torson, Alex S., Jentzsch, Iris M. Vargas, Weirauch, Matthew T., Yates, Ashley D. T., Yocum, George D., Yoon, June-Sun, and Richards, Stephen

Abstract

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

Published
2018

15. Dehydration prompts increased activity and blood feeding by mosquitoes

Author

Hagan, Richard W., primary, Didion, Elise M., additional, Rosselot, Andrew E., additional, Holmes, Christopher J., additional, Siler, Samantha C., additional, Rosendale, Andrew J., additional, Hendershot, Jacob M., additional, Elliot, Kiaira S. B., additional, Jennings, Emily C., additional, Nine, Gabriela A., additional, Perez, Paula L., additional, Rizlallah, Alexandre E., additional, Watanabe, Miki, additional, Romick-Rosendale, Lindsey E., additional, Xiao, Yanyu, additional, Rasgon, Jason L., additional, and Benoit, Joshua B., additional

Published
2018
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16. The genome of the water striderGerris buenoireveals expansions of gene repertoires associated with adaptations to life on the water

Author

Armisén, David, primary, Rajakumar, Rajendhran, additional, Friedrich, Markus, additional, Benoit, Joshua B, additional, Robertson, Hugh M., additional, Panfilio, Kristen A., additional, Ahn, Seung-Joon, additional, Poelchau, Monica F., additional, Chao, Hsu, additional, Dinh, Huyen, additional, Doddapaneni, HarshaVardhan, additional, Dugan, Shannon, additional, Gibbs, Richard A., additional, Hughes, Daniel S.T., additional, Han, Yi, additional, Lee, Sandra L., additional, Murali, Shwetha C., additional, Muzny, Donna M., additional, Qu, Jiaxin, additional, Worley, Kim C., additional, Munoz-Torres, Monica, additional, Abouheif, Ehab, additional, Bonneton, François, additional, Chen, Travis, additional, Chiang, Li-Mei, additional, Childers, Christopher P., additional, Cridge, Andrew Graham, additional, Crumière, Antonin Jean Johan, additional, Decaras, Amelie, additional, Didion, Elise M., additional, Duncan, Elizabeth, additional, Elpidina, Elena N., additional, Favé, Marie-Julie, additional, Finet, Cédric, additional, Jacobs, Chris G.C., additional, Jarvela, Alys, additional, Jennings, Emily J., additional, Jones, Jeffery W., additional, Lesoway, Maryna P., additional, Lovegrove, Mackenzie, additional, Martynov, Alexander, additional, Oppert, Brenda, additional, Lillico-Ouachour, Angelica, additional, Rajakumar, Arjuna, additional, Refki, Peter Nagui, additional, Rosendale, Andrew J., additional, Santos, Maria Emilia, additional, Toubiana, William, additional, van der Zee, Maurijn, additional, Vargas Jentzsch, Iris M., additional, Lowman, Aidamalia Vargas, additional, Viala, Severine, additional, Richards, Stephen, additional, and Khila, Abderrahman, additional

Published
2018
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17. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author

Panfilio, Kristen A., primary, Jentzsch, Iris M. Vargas, additional, Benoit, Joshua B., additional, Erezyilmaz, Deniz, additional, Suzuki, Yuichiro, additional, Colella, Stefano, additional, Robertson, Hugh M., additional, Poelchau, Monica F., additional, Waterhouse, Robert M., additional, Ioannidis, Panagiotis, additional, Weirauch, Matthew T., additional, Hughes, Daniel S.T., additional, Murali, Shwetha C., additional, Werren, John H., additional, Jacobs, Chris G.C., additional, Duncan, Elizabeth J., additional, Armisén, David, additional, Vreede, Barbara M.I., additional, Baa-Puyoulet, Patrice, additional, Berger, Chloé S., additional, Chang, Chun-che, additional, Chao, Hsu, additional, Chen, Mei-Ju M., additional, Chen, Yen-Ta, additional, Childers, Christopher P., additional, Chipman, Ariel D., additional, Cridge, Andrew G., additional, Crumière, Antonin J.J., additional, Dearden, Peter K., additional, Didion, Elise M., additional, Dinh, Huyen, additional, Doddapaneni, HarshaVardhan, additional, Dolan, Amanda, additional, Dugan, Shannon, additional, Extavour, Cassandra G., additional, Febvay, Gérard, additional, Friedrich, Markus, additional, Ginzburg, Neta, additional, Han, Yi, additional, Heger, Peter, additional, Holmes, Christopher J., additional, Horn, Thorsten, additional, Hsiao, Yi-min, additional, Jennings, Emily C., additional, Johnston, J. Spencer, additional, Jones, Tamsin E., additional, Jones, Jeffery W., additional, Khila, Abderrahman, additional, Koelzer, Stefan, additional, Kovacova, Viera, additional, Leask, Megan, additional, Lee, Sandra L., additional, Lee, Chien-Yueh, additional, Lovegrove, Mackenzie R., additional, Lu, Hsiao-ling, additional, Lu, Yong, additional, Moore, Patricia J., additional, Munoz-Torres, Monica C., additional, Muzny, Donna M., additional, Palli, Subba R., additional, Parisot, Nicolas, additional, Pick, Leslie, additional, Porter, Megan, additional, Qu, Jiaxin, additional, Refki, Peter N., additional, Richter, Rose, additional, Pomar, Rolando Rivera, additional, Rosendale, Andrew J., additional, Roth, Siegfried, additional, Sachs, Lena, additional, Santos, M. Emília, additional, Seibert, Jan, additional, Sghaier, Essia, additional, Shukla, Jayendra N., additional, Stancliffe, Richard J., additional, Tidswell, Olivia, additional, Traverso, Lucila, additional, Zee, Maurijn van der, additional, Viala, Séverine, additional, Worley, Kim C., additional, Zdobnov, Evgeny M., additional, Gibbs, Richard A., additional, and Richards, Stephen, additional

Published
2017
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18. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

Author

Schoville, Sean D., primary, Chen, Yolanda H., additional, Andersson, Martin N., additional, Benoit, Joshua B., additional, Bhandari, Anita, additional, Bowsher, Julia H., additional, Brevik, Kristian, additional, Cappelle, Kaat, additional, Chen, Mei-Ju M., additional, Childers, Anna K., additional, Childers, Christopher, additional, Christiaens, Olivier, additional, Clements, Justin, additional, Didion, Elise M., additional, Elpidina, Elena N., additional, Engsontia, Patamarerk, additional, Friedrich, Markus, additional, García-Robles, Inmaculada, additional, Gibbs, Richard A., additional, Goswami, Chandan, additional, Grapputo, Alessandro, additional, Gruden, Kristina, additional, Grynberg, Marcin, additional, Henrissat, Bernard, additional, Jennings, Emily C., additional, Jones, Jeffery W., additional, Kalsi, Megha, additional, Khan, Sher A., additional, Kumar, Abhishek, additional, Li, Fei, additional, Lombard, Vincent, additional, Ma, Xingzhou, additional, Martynov, Alexander, additional, Miller, Nicholas J., additional, Mitchell, Robert F., additional, Munoz-Torres, Monica, additional, Muszewska, Anna, additional, Oppert, Brenda, additional, Palli, Subba Reddy, additional, Panfilio, Kristen A., additional, Pauchet, Yannick, additional, Perkin, Lindsey C., additional, Petek, Marko, additional, Poelchau, Monica F., additional, Record, Éric, additional, Rinehart, Joseph P., additional, Robertson, Hugh M., additional, Rosendale, Andrew J., additional, Ruiz-Arroyo, Victor M., additional, Smagghe, Guy, additional, Szendrei, Zsofia, additional, Thomas, Gregg W. C., additional, Torson, Alex S., additional, Vargas Jentzsch, Iris M., additional, Weirauch, Matthew T., additional, Yates, Ashley D., additional, Yocum, George D., additional, Yoon, June-Sun, additional, and Richards, Stephen, additional

Published
2017
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19. The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

Author

Armisén, David, Rajakumar, Rajendhran, Friedrich, Markus, Benoit, Joshua B, Robertson, Hugh M, Panfilio, Kristen A, Ahn, Seung-Joon, Poelchau, Monica F, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Gibbs, Richard A, Hughes, Daniel ST, Han, Yi, Lee, Sandra L, Murali, Shwetha C, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Munoz-Torres, Monica, Abouheif, Ehab, Bonneton, François, Chen, Travis, Chiang, Li-Mei, Childers, Christopher P, Cridge, Andrew G, Crumière, Antonin JJ, Decaras, Amelie, Didion, Elise M, Duncan, Elizabeth J, Elpidina, Elena N, Favé, Marie-Julie, Finet, Cédric, Jacobs, Chris GC, Cheatle Jarvela, Alys M, Jennings, Emily C, Jones, Jeffery W, Lesoway, Maryna P, Lovegrove, Mackenzie R, Martynov, Alexander, Oppert, Brenda, Lillico-Ouachour, Angelica, Rajakumar, Arjuna, Refki, Peter Nagui, Rosendale, Andrew J, Santos, Maria Emilia, Toubiana, William, Van Der Zee, Maurijn, Vargas Jentzsch, Iris M, Lowman, Aidamalia Vargas, Viala, Severine, Richards, Stephen, and Khila, Abderrahman

Subjects
Genome, Evolution, Water striders, Genomics, Adaptation, Physiological, Evolution, Molecular, Heteroptera, Phenotype, Genome sequence, Animals, Insect Proteins, 14. Life underwater, Adaptation, Water surface locomotion, Phylogeny
Abstract

BACKGROUND: Having conquered water surfaces worldwide, the semi-aquatic bugs occupy ponds, streams, lakes, mangroves, and even open oceans. The diversity of this group has inspired a range of scientific studies from ecology and evolution to developmental genetics and hydrodynamics of fluid locomotion. However, the lack of a representative water strider genome hinders our ability to more thoroughly investigate the molecular mechanisms underlying the processes of adaptation and diversification within this group. RESULTS: Here we report the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle. These expansions may affect key processes associated with growth, vision, desiccation resistance, detoxification, olfaction and epigenetic regulation. Strikingly, the G. buenoi genome contains three insulin receptors, suggesting key changes in the rewiring and function of the insulin pathway. Other genomic changes affecting with opsin genes may be associated with wavelength sensitivity shifts in opsins, which is likely to be key in facilitating specific adaptations in vision for diverse water habitats. CONCLUSIONS: Our findings suggest that local gene duplications might have played an important role during the evolution of water striders. Along with these findings, the sequencing of the G. buenoi genome now provides us the opportunity to pursue exciting research opportunities to further understand the genomic underpinnings of traits associated with the extreme body plan and life history of water striders.

20. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome

Author

Shwetha C. Murali, Hsiao-ling Lu, Siegfried Roth, Huyen Dinh, Peter K. Dearden, Barbara M. I. Vreede, M. Emília Santos, Evgeny M. Zdobnov, Viera Kovacova, Christopher J. Holmes, Stefano Colella, Yuichiro Suzuki, Tamsin E. M. Jones, Chun-che Chang, Stefan Koelzer, Jeffery W. Jones, Essia Sghaier, Thorsten Horn, Richard A. Gibbs, Mackenzie Lovegrove, Panagiotis Ioannidis, Lucila Traverso, Subba Reddy Palli, Megan L. Porter, Olivia Tidswell, Peter Nagui Refki, Neta Ginzburg, Rolando Rivera-Pomar, Sandra L. Lee, Chris Jacobs, Cassandra G. Extavour, Jan Seibert, Amanda Dolan, David Armisén, Jayendra Nath Shukla, Kristen A. Panfilio, Christopher P. Childers, Matthew T. Weirauch, Daniel S.T. Hughes, Jiaxin Qu, Kim C. Worley, Hugh M. Robertson, Monica Munoz-Torres, Markus Friedrich, Emily C. Jennings, Elizabeth J. Duncan, Andrew G. Cridge, Hsu Chao, J. Spencer Johnston, Maurijn van der Zee, Mei-Ju May Chen, John H. Werren, Abderrahman Khila, Shannon Dugan, Stephen Richards, Lena Sachs, Joshua B. Benoit, Antonin J.J. Crumière, Nicolas Parisot, Megan Leask, Yen-Ta Chen, Harshavardhan Doddapaneni, Gérard Febvay, Donna M. Muzny, Ariel D. Chipman, Rose Richter, Robert M. Waterhouse, Leslie Pick, Monica F. Poelchau, Patricia J. Moore, Chloé Suzanne Berger, Richard J. Stancliffe, Yi Min Hsiao, Séverine Viala, Chien-Yueh Lee, Yi Han, Iris M. Vargas Jentzsch, Elise M. Didion, Deniz F. Erezyilmaz, Yong Lu, Andrew J. Rosendale, Peter Heger, Patrice Baa-Puyoulet, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), University of Illinois [Chicago] (UIC), University of Illinois System, Department of Biology, Georgetown University, Université de Lausanne (UNIL), Cincinnati Children's Hospital Medical Center, Biochemistry Department, University of Otago [Dunedin, Nouvelle-Zélande], Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, University of Edinburgh, Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Entomology [Lexington], University of Kentucky, Cologne Biocenter, Institute of Developmental Biology, Institute of Developmental Biology, University of Basel (Unibas), Institut de Génomique Fonctionnelle de Lyon (IGFL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Human Genome Sequencing Center [Houston] (HGSC), Department of Genetic Medicine and Development [Geneva], Université de Genève (UNIGE), United States Department of Health & Human Services National Institutes of Health (NIH) - USA [U54 HG003273], German Research Foundation (DFG) [PA 2044/1 1 SFB 680], Swiss National Science Foundation (SNSF) [31003A_143936, PP00P3_170664], European Research Council grant ERC-CoG [616346], German Research Foundation (DFG) [SFB 680], National Science Foundation (NSF) [US NSF DEB1257053], United States Department of Health & Human Services National Institutes of Health (NIH) - USA [5R01GM080203, 5R01HG004483, R01GM113230], United States Department of Energy (DOE) [DE-AC02-05CH11231], École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Georgetown University [Washington] (GU), Université de Lausanne = University of Lausanne (UNIL), University of Kentucky (UK), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Genève = University of Geneva (UNIGE), Panfilio, Kristen A [0000-0002-6417-251X], Vargas Jentzsch, Iris M [0000-0003-4527-1560], Benoit, Joshua B [0000-0002-4018-3513], Erezyilmaz, Deniz [0000-0001-8416-8561], Suzuki, Yuichiro [0000-0002-0957-3564], Colella, Stefano [0000-0003-3139-6055], Poelchau, Monica F [0000-0002-4584-6056], Waterhouse, Robert M [0000-0003-4199-9052], Ioannidis, Panagiotis [0000-0003-0939-6745], Weirauch, Matthew T [0000-0001-7977-9122], Werren, John H [0000-0001-9353-2070], Jacobs, Chris GC [0000-0002-3128-2288], Duncan, Elizabeth J [0000-0002-1841-504X], Vreede, Barbara MI [0000-0002-5023-4601], Chang, Chun-Che [0000-0002-3586-1607], Chen, Mei-Ju M [0000-0001-7768-8905], Chen, Yen-Ta [0000-0002-4570-6061], Childers, Christopher P [0000-0002-1253-5550], Chipman, Ariel D [0000-0001-6696-840X], Cridge, Andrew G [0000-0002-1399-5188], Crumière, Antonin JJ [0000-0003-2214-2993], Dearden, Peter K [0000-0001-7790-9675], Didion, Elise M [0000-0002-4987-8901], Dinh, Huyen [0000-0003-0336-0362], Doddapaneni, Harsha Vardhan [0000-0002-2433-633X], Dugan, Shannon [0000-0003-1482-816X], Extavour, Cassandra G [0000-0003-2922-5855], Febvay, Gérard [0000-0002-0654-2340], Friedrich, Markus [0000-0002-5622-7920], Han, Yi [0000-0001-7605-8979], Holmes, Christopher J [0000-0001-9612-366X], Horn, Thorsten [0000-0001-8181-939X], Hsiao, Yi-Min [0000-0002-1817-0302], Jennings, Emily C [0000-0002-7687-5319], Johnston, J Spencer [0000-0003-4792-2945], Jones, Tamsin E [0000-0002-0027-0858], Khila, Abderrahman [0000-0003-0908-483X], Kovacova, Viera [0000-0003-4581-4254], Lee, Chien-Yueh [0000-0002-4304-974X], Lu, Hsiao-Ling [0000-0002-4029-6470], Moore, Patricia J [0000-0001-9802-7217], Munoz-Torres, Monica C [0000-0001-8430-6039], Muzny, Donna M [0000-0002-3055-0359], Palli, Subba R [0000-0002-0873-3247], Parisot, Nicolas [0000-0001-5217-8415], Pick, Leslie [0000-0002-4505-5107], Porter, Megan L [0000-0001-7985-2887], Qu, Jiaxin [0000-0002-1122-9391], Rivera-Pomar, Rolando [0000-0002-7720-7064], Rosendale, Andrew J [0000-0002-2463-8856], Roth, Siegfried [0000-0001-5772-3558], Shukla, Jayendra N [0000-0003-1589-1929], Stancliffe, Richard J [0000-0002-6972-9655], van der Zee, Maurijn [0000-0002-8728-8646], Worley, Kim C [0000-0002-0282-1000], Richards, Stephen [0000-0001-8959-5466], and Apollo - University of Cambridge Repository

Subjects
gene family evolution, Lineage (evolution), [SDV]Life Sciences [q-bio], Genome, Insect, Gene Transfer, Gene Dosage, Insect, Genome, purl.org/becyt/ford/1 [https], 0302 clinical medicine, CYS2-HIS2 Zinc Fingers, phytophagy, ddc:576.5, lcsh:QH301-705.5, media_common, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, biology, Large milkweed bug, Ecology, Pigmentation, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genes, Homeobox, Biological Sciences, Lygaeidae, Hemiptera, séquence du génome, Smell, evolution of development, TRANSCRIPTION FACTORS, puceron, Biotechnology, lcsh:QH426-470, Gene Transfer, Horizontal, ddc:025.063/570, Evolution, Bioinformatics, media_common.quotation_subject, 1.1 Normal biological development and functioning, Transcription Factors/genetics, Zoology, Amino Acid Sequence, Animals, Evolution, Molecular, Feeding Behavior, Gene Expression Profiling, Hemiptera/genetics, Hemiptera/growth & development, Hemiptera/metabolism, Pigmentation/genetics, Evolution of development, Gene family evolution, Gene structure, Lateral gene transfer, Phytophagy, RNAi, Transcription factors, GENE FAMILY EVOLUTION, Genomics, Biotechnologies, LATERAL GENE TRANSFER, Horizontal, 03 medical and health sciences, Molecular evolution, Underpinning research, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Information and Computing Sciences, transcription factors, RNAI, Genetics, Homeobox, GENE STRUCTURE, purl.org/becyt/ford/1.6 [https], SB, Genome size, Ciencias Exactas, 030304 developmental biology, Whole genome sequencing, QL, QH, Research, gene structure, lateral gene transfer, Human Genome, fungi, Molecular, biology.organism_classification, Hemiptera/genetics/growth & development/metabolism, diversité des populations, lcsh:Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, PHYTOPHAGY, lcsh:Biology (General), Genes, Animal ecology, Evolutionary biology, EVOLUTION OF DEVELOPMENT, Evolutionary developmental biology, 030217 neurology & neurosurgery, Environmental Sciences
Abstract

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes., La lista completa de autores puede verse en el archivo asociado., Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos

Published
2019

21. SARS-CoV-2 Antibody Responses to the Ancestral SARS-CoV-2 Strain and Omicron BA.1 and BA.4/BA.5 Variants in Nursing Home Residents After Receipt of Bivalent COVID-19 Vaccine - Ohio and Rhode Island, September-November 2022.

Author

Canaday DH, Oyebanji OA, White EM, Bosch J, Nugent C, Vishnepolskiy I, Abul Y, Didion EM, Paxitzis A, Sundheimer N, Ragavapuram V, Wilk D, Keresztesy D, Cao Y, St Denis K, McConeghy KW, McDonald LC, Jernigan JA, Mylonakis E, Wilson BM, King CL, Balazs AB, and Gravenstein S

Subjects
Adult, Humans, SARS-CoV-2, COVID-19 Vaccines, Vaccines, Combined, Rhode Island, Antibody Formation, Ohio, Antibodies, Viral, Nursing Homes, Antibodies, Neutralizing, COVID-19 epidemiology, COVID-19 prevention & control
Abstract

Introduction of monovalent COVID-19 mRNA vaccines in late 2020 helped to mitigate disproportionate COVID-19-related morbidity and mortality in U.S. nursing homes (1); however, reduced effectiveness of monovalent vaccines during the period of Omicron variant predominance led to recommendations for booster doses with bivalent COVID-19 mRNA vaccines that include an Omicron BA.4/BA.5 spike protein component to broaden immune response and improve vaccine effectiveness against circulating Omicron variants (2). Recent studies suggest that bivalent booster doses provide substantial additional protection against SARS-CoV-2 infection and severe COVID-19-associated disease among immunocompetent adults who previously received only monovalent vaccines (3).* The immunologic response after receipt of bivalent boosters among nursing home residents, who often mount poor immunologic responses to vaccines, remains unknown. Serial testing of anti-spike protein antibody binding and neutralizing antibody titers in serum collected from 233 long-stay nursing home residents from the time of their primary vaccination series and including any subsequent booster doses, including the bivalent vaccine, was performed. The bivalent COVID-19 mRNA vaccine substantially increased anti-spike and neutralizing antibody titers against Omicron sublineages, including BA.1 and BA.4/BA.5, irrespective of previous SARS-CoV-2 infection or previous receipt of 1 or 2 booster doses. These data, in combination with evidence of low uptake of bivalent booster vaccination among residents and staff members in nursing homes (4), support the recommendation that nursing home residents and staff members receive a bivalent COVID-19 booster dose to reduce associated morbidity and mortality (2)., Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. Stefan Gravenstein and David H. Canaday are recipients of support from the U.S. Department of Veterans Affairs and investigator-initiated grants to their universities from the National Institute of Allergy and Infectious Diseases (NIAID) to study influenza vaccine and COVID-19 in the nursing home, Pfizer to study pneumococcal vaccines, and from Sanofi Pasteur and Seqirus to study influenza vaccines. Stefan Gravenstein also performs consulting work for Janssen, Merck, Moderna, Novavax, Pfizer, Sanofi, Seqirus, and Vaxart; has served on the speaker’s bureaus for Seqirus and Sanofi; and was paid to chair data safety monitoring boards from Longeveron and SciClone. David H. Canaday has performed consulting work for Seqirus. Elizabeth M. White reports support from the National Institute on Aging, and membership on the Society for Post-acute and Long-term Care Medicine Workforce Development Committee and on the John Hartford Foundation Moving Forward Coalition Workforce Committee. Jürgen Bosch is the cofounder and Chief Executive Officer of InterRayBio, LLC. Yi Cao, Kerri St. Denis, and Alejandro B. Balazs report support from the Ragon Institute of Massachusetts General Hospital, the Massachusetts Institute of Technology, and Harvard University for equipment used in the current study. Kevin W. McConeghy reports grant support from Sanofi-Pasteur, Sequirus Pharmaceuticals, Genentech, and Janssen, unrelated to the current work. Eleftherios Mylonakis reports institutional support from the Biomedical Advanced Research and Development Authority, NIAID, the National Institute of General Medical Sciences, National Institutes of Health, Leidos Biomedical Research, Inc., Regeneron, Pfizer, Chemic lags/KODA therapeutics, Cidara, the National Cancer Institute, and SciClone Pharmaceuticals, and receipt of consulting fees from Basilea Pharmaceutica International, Ltd. Christopher L. King reports National Cancer Institute support for Early Drivers of Humoral Immunity to SARS-CoV-2 Infections. No other potential conflicts of interest were disclosed.

Published
2023
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22. Second monovalent SARS-CoV-2 mRNA booster restores Omicron-specific neutralizing activity in both nursing home residents and health care workers.

Author

Nugent C, Abul Y, White E, Shehadeh F, Kaczynski M, Felix LO, Ganesan N, Oyebanji OA, Vishnepolskiy I, Didion EM, Paxitzis A, Sheehan ML, Mylonakis E, Wilson BM, Balazs AB, Chan PA, King CL, Pfeifer WM, Dickerson E, Canaday DH, and Gravenstein S

Abstract

We examined whether the second monovalent SARS-CoV-2 mRNA booster increased antibody levels and their neutralizing activity to Omicron variants in nursing home residents (NH) residents and healthcare workers (HCW). We sampled 367 NH residents and 60 HCW after primary mRNA vaccination, first and second boosters, for antibody response and pseudovirus neutralization assay against SARS-CoV-2 wild-type (WT) (Wuhan-Hu-1) strain and Omicron BA1 variant. Antibody levels and neutralizing activity progressively increased with each booster but subsequently waned over weeks. NH residents, both those without and with prior infection, had a robust geometric mean fold rise (GMFR) of 10.2 (95% CI 5.1, 20.3) and 6.5 (95% CI 4.5, 9.3) respectively in Omicron-BA.1 subvariant specific neutralizing antibody levels following the second booster vaccination (p<0.001). These results support the ongoing efforts to ensure that both NH residents and HCW are up to date on recommended SARS-CoV-2 vaccine booster doses.

Published
2023
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