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2. 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. The chromosome-level genome of Chinese praying mantis Tenodera sinensis (Mantodea: Mantidae) reveals its biology as a predator.

Author

Yuan, Ruizhong, Zheng, Boying, Li, Zekai, Ma, Xingzhou, Shu, Xiaohan, Qu, Qiuyu, Ye, Xiqian, Li, Sheng, Tang, Pu, and Chen, Xuexin

Subjects
INSECT genomes, MANTODEA, GENE families, GENOMES, GENOME size, GENETICS, PREDATION
Abstract

Background The Chinese praying mantis, Tenodera sinensis (Saussure), is a carnivorous insect that preys on a variety of arthropods and small vertebrates, including pest species. Several studies have been conducted to understand its behavior and physiology. However, there is limited knowledge about the genetic information underlying its genome evolution, digestive demands, and predatory behaviors. Findings Here we have assembled the chromosome-level genome of T. sinensis , representing the first sequenced genome of the family Mantidae, with a genome size of 2.54 Gb and scaffold N50 of 174.78 Mb. Our analyses revealed that 98.6% of BUSCO genes are present, resulting in a well-annotated assembly compared to other insect genomes, containing 25,022 genes. The reconstructed phylogenetic analysis showed the expected topology placing the praying mantis in an appropriate position. Analysis of transposon elements suggested the Gypsy/Dirs family, which belongs to long terminal repeat (LTR) transposons, may be a key factor resulting in the larger genome size. The genome shows expansions in several digestion and detoxification associated gene families, including trypsin and glycosyl hydrolase (GH) genes, ATP-binding cassette (ABC) transporter, and carboxylesterase (CarE), reflecting the possible genomic basis of digestive demands. Furthermore, we have found 1 ultraviolet-sensitive opsin and 2 long-wavelength-sensitive (LWS) opsins, emphasizing the core role of LWS opsins in regulating predatory behaviors. Conclusions The high-quality genome assembly of the praying mantis provides a valuable repository for studying the evolutionary patterns of the mantis genomes and the gene expression profiles of insect predators. [ABSTRACT FROM AUTHOR]

Published
2023
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7. 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

8. 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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9. 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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10. InsectBase: a resource for insect genomes and transcriptomes

Author

Yin, Chuanlin, primary, Shen, Gengyu, additional, Guo, Dianhao, additional, Wang, Shuping, additional, Ma, Xingzhou, additional, Xiao, Huamei, additional, Liu, Jinding, additional, Zhang, Zan, additional, Liu, Ying, additional, Zhang, Yiqun, additional, Yu, Kaixiang, additional, Huang, Shuiqing, additional, and Li, Fei, additional

Published
2015
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12. InsectBase: a resource for insect genomes and transcriptomes.

Author

Yin C, Shen G, Guo D, Wang S, Ma X, Xiao H, Liu J, Zhang Z, Liu Y, Zhang Y, Yu K, Huang S, and Li F

Subjects
Animals, Genes, Insect, Genomics, Insecta classification, Phylogeny, Software, Databases, Genetic, Gene Expression Profiling, Genome, Insect, Insecta genetics
Abstract

The genomes and transcriptomes of hundreds of insects have been sequenced. However, insect community lacks an integrated, up-to-date collection of insect gene data. Here, we introduce the first release of InsectBase, available online at http://www.insect-genome.com. The database encompasses 138 insect genomes, 116 insect transcriptomes, 61 insect gene sets, 36 gene families of 60 insects, 7544 miRNAs of 69 insects, 96,925 piRNAs of Drosophila melanogaster and Chilo suppressalis, 2439 lncRNA of Nilaparvata lugens, 22,536 pathways of 78 insects, 678,881 untranslated regions (UTR) of 84 insects and 160,905 coding sequences (CDS) of 70 insects. This release contains over 12 million sequences and provides search functionality, a BLAST server, GBrowse, insect pathway construction, a Facebook-like network for the insect community (iFacebook), and phylogenetic analysis of selected genes., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2016
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