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4. 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

17. Genomic signatures of evolutionary transitions from solitary to group living

Author

Kapheim, Karen M., Pan, Hailin, Li, Cai, Salzberg, Steven L., Puiu, Daniela, Magoc, Tanja, Robertson, Hugh M., Hudson, Matthew E., Venkat, Aarti, Fischman, Brielle J., Hernandez, Alvaro, Yandell, Mark, Ence, Daniel, Holt, Carson, Yocum, George D., Kemp, William P., Bosch, Jordi, Waterhouse, Robert M., Zdobnov, Evgeny M., Stolle, Eckart, Kraus, F. Bernhard, Helbing, Sophie, Moritz, Robin F. A., Glastad, Karl M., Hunt, Brendan G., Goodisman, Michael A. D., Hauser, Frank, Grimmelikhuijzen, Cornelis J. P., Pinheiro, Daniel Guariz, Nunes, Francis Morais Franco, Soares, Michelle Prioli Miranda, Tanaka, Érica Donato, Simões, Zilá Luz Paulino, Hartfelder, Klaus, Evans, Jay D., Barribeau, Seth M., Johnson, Reed M., Massey, Jonathan H., Southey, Bruce R., Hasselmann, Martin, Hamacher, Daniel, Biewer, Matthias, Kent, Clement F., Zayed, Amro, Blatti, Charles, Sinha, Saurabh, Johnston, J. Spencer, Hanrahan, Shawn J., Kocher, Sarah D., Wang, Jun, Robinson, Gene E., and Zhang, Guojie

Published
2015

32. Supplemental Methods, Figures and Tables from Diet quantity influences caste determination in honeybees (Apis mellifera)

Author

Slater, Garett P., Yocum, George D., and Bowsher, Julia H.

Abstract

In species that care for their young, provisioning has profound effects on offspring fitness. Provisioning is important in honeybees because nutritional cues determine whether a female becomes a reproductive queen or sterile worker. A qualitative difference between the larval diets of queens and workers is thought to drive this divergence; however, no single compound seems to be responsible. Diet quantity may have a role during honeybee caste determination yet has never been formally studied. Our goal was to determine the relative contributions of diet quantity and quality to queen development. Larvae were reared in vitro on nine diets varying in the amount of royal jelly and sugars, which were fed to larvae in eight different quantities. For the middle diet, an ad libitum quantity treatment was included. Once adults eclosed, the queenliness was determined using principal component analysis on seven morphological measurements. We found that larvae fed an ad libitum quantity of diet were indistinguishable from commercially reared queens, and that queenliness was independent of the proportion of protein and carbohydrate in the diet. Neither protein nor carbohydrate content had a significant influence on the first principle component 1 (PC1), which explained 64.4% of the difference between queens and workers. Instead, the total quantity of diet explained a significant amount of the variation in PC1. Large amounts of diet in the final instar were capable of inducing queen traits, contrary to the received wisdom that queen determination can only occur in the third instar. These results indicate that total diet quantity fed to larvae may regulate the difference between queen and worker castes in honeybees.

Published
2020
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34. Contributors

Author

Adams, Michael, primary, Antonova, Yevgeniya, additional, Arik, Anam J., additional, Blomquist, Gary J., additional, Bonneton, François, additional, Brown, Mark R., additional, Coast, Geoffrey M., additional, Cusson, Michel, additional, Dauphin-Villemant, C., additional, Denlinger, David L., additional, Emlen, Douglas J., additional, Goodman, Walter, additional, Hartfelder, Klaus, additional, Henrich, Vincent C., additional, Horodyski, Frank M., additional, Jurenka, Russell, additional, Lafont, Rene, additional, Laudet, Vincent, additional, Moore, Wendy, additional, Rees, H., additional, Riehle, Michael A., additional, Rinehart, Joseph P., additional, Rybczynski, Robert, additional, Schal, Coby, additional, Schooley, David A., additional, Smith, Wendy, additional, Song, Qisheng, additional, Tittiger, Claus, additional, Warren, J.T., additional, Yocum, George D., additional, and Zitnan, Dusan, additional

Published
2012
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37. Stress proteins

Author

Denlinger, David L., primary, Rinehart, Joseph P., additional, and Yocum, George D., additional

Published
2001
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44. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living

Author

Kapheim Karen M, Pan Hailin, Li Cai, Salzberg Steven L, Puiu Daniela, Magoc Tanja, Robertson Hugh M, Hudson Matthew E, Venkat Aarti, Fischman Brielle J, Hernandez Alvaro, Yandell Mark, Ence Daniel, Holt Carson, Yocum George D, Kemp William P, Bosch Jordi, Waterhouse Robert M, Zdobnov Evgeny M, Stolle Eckart, Kraus F Bernhard, Helbing Sophie, Moritz Robin F A, Glastad Karl M, and Hunt Brendan G

Abstract

The evolution of eusociality is one of the major transitions in evolution but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity representing multiple independent transitions in social evolution and report three major findings. First many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third though clearly independent in detail these transitions do have similar general features including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time but would likely always involve an increase in the complexity of gene networks.

Published
2015
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45. 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

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

Author

Ma, Sean, Chen, Yolanda, Ma, Martin, Benoit, Joshua, Bhandari, Anita, Bowsher, Julia, Brevik, Kristian, Cappelle, Kaat, Li, Mei-Ju, Childers, Anna, Li, Christopher, Christiaens, Olivier, Ma, Justin, Didion, Elise, Elpidina, Elena, Engsontia, Patamarerk, Ma, Markus, García-Robles, Inmaculada, Gibbs, Richard, Goswami, Chandan, Grapputo, Alessandro, Gruden, Kristina, Ma, Marcin, Ma, Bernard, Jennings, Emily, Jones, Jeffery, Kalsi, Megha, Khan, Sher, Kumar, Abhishek, Li, Fei, Ma, Vincent, Ma, Xingzhou, Martynov, Alex, Miller, Nicholas, Mitchell, Robert, Muñoz-Torres, Monica, Muszewska, Anna, Oppert, Brenda, Palli, Subba Reddy, Panfilio, Kristen, Pauchet, Yannick, Perkin, Lindsey, Petek, Marko, Poelchau, Monica, Record, Eric, Rinehart, Joseph, Robertson, Hugh, Rosendale, Andrew, Ruiz-Arroyo, Victor, Smagghe, Guy, Szendrei, Zsofia, Thomas, Gregg, Torson, Alex, Vargas Jentzsch, Iris, Weirauch, Matthew, Yates, Ashley, Yocum, George, Yoon, June-Sun, Richards, Stephen, Schoville, Sean, Andersson, Martin, Chen, Mei-Ju, Childers, Christopher, Clements, Justin, Friedrich, Markus, Grynberg, Marcin, Henrissat, Bernard, Lombard, Vincent, Ma, Alexander, Li, Lindsey, Ma, Marko, Robertson, Robert, Thomas, Gregg W.C., Ma, Matthew, Richards, Richard, Human Genome Sequencing Center [Houston] (HGSC), Baylor College of Medicine (BCM), Baylor University-Baylor University, Centre of Excellence in Biological interactions (CoE), University of Helsinki-Universität Zürich [Zürich] = University of Zurich (UZH)-University of Jyväskylä (JYU), National Institute of Biology, Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, Institut Pascal (IP), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-SIGMA Clermont (SIGMA Clermont)-Centre National de la Recherche Scientifique (CNRS), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Entomology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Department of Biology, Georgetown University, Biodiversité et Biotechnologie Fongiques (BBF), Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-École Centrale de Marseille (ECM), Faculty of Bioscience Engineering [Ghent], Universiteit Gent = Ghent University [Belgium] (UGENT), Indiana University [Bloomington], Indiana University System, Human Genome Sequencing Center, Institute of Modern Physics, Fudan University [Shanghai], Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), NIH NHGRI U54 HG003273 K12 GM000708, UVM Agricultural Experiment Station Hatch grant VT-H02010, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy DE-AC02-05CH11231, National Science Centre2012/07/D/NZ2/04286, NIH (NIGMS) 5R01GM080203, NIH (NHGRI)5R01HG004483, University of Helsinki-University of Zürich [Zürich] (UZH)-University of Jyväskylä, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS), École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Ghent University [Belgium] (UGENT), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Universität Zürich [Zürich] = University of Zurich (UZH)-University of Jyväskylä (JYU), Georgetown University [Washington] (GU), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM), and Universiteit Gent = Ghent University (UGENT)

Subjects
Male, 0106 biological sciences, 0301 basic medicine, Genome, Insect, lcsh:Medicine, 01 natural sciences, Genome, Nucleotide diversity, Insecticide Resistance, pomme de terre, TRIBOLIUM-CASTANEUM, lcsh:Science, Leptinotarsa, CYSTEINE PROTEINASES, Phylogeny, 2. Zero hunger, education.field_of_study, Multidisciplinary, biology, insecte ravageur, Ecology, Genètica vegetal, Agriculture, leptinotarsa decemlineata, Genomics, S-TRANSFERASE GENES, lutte contre les ravageurs, Coleoptera, Other Physical Sciences, phénotype, espèce modèle, Multigene Family, Insect Proteins, RNA Interference, Female, Biotechnology, Autre (Sciences du Vivant), Genome evolution, doryphore, coleoptera, Evolution, Population, RNA-INTERFERENCE, GEOGRAPHIC POPULATIONS, Article, DNA sequencing, Host-Parasite Interactions, Evolution, Molecular, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Animals, analyse génomique, Pest Control, Biological, education, QH426, Gene, Solanum tuberosum, Comparative genomics, business.industry, chrysomelidae, lcsh:R, Human Genome, fungi, Colorado potato beetle, Pest control, Biology and Life Sciences, Molecular, Genetic Variation, Molecular Sequence Annotation, Biological, biology.organism_classification, 010602 entomology, Genòmica, Genetics, Population, 030104 developmental biology, Gene Expression Regulation, DROSOPHILA-MELANOGASTER, PROTEINASE-INHIBITORS, Evolutionary biology, TRANSPOSABLE ELEMENTS, DNA Transposable Elements, lcsh:Q, Pest Control, Biochemistry and Cell Biology, PEST analysis, CAENORHABDITIS-ELEGANS, business, Insect, Transcription Factors
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
2017
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