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3. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta

Author

Kanost, Michael R, Arrese, Estela L, Cao, Xiaolong, Chen, Yun-Ru, Chellapilla, Sanjay, Goldsmith, Marian R, Grosse-Wilde, Ewald, Heckel, David G, Herndon, Nicolae, Jiang, Haobo, Papanicolaou, Alexie, Qu, Jiaxin, Soulages, Jose L, Vogel, Heiko, Walters, James, Waterhouse, Robert M, Ahn, Seung-Joon, Almeida, Francisca C, An, Chunju, Aqrawi, Peshtewani, Bretschneider, Anne, Bryant, William B, Bucks, Sascha, Chao, Hsu, Chevignon, Germain, Christen, Jayne M, Clarke, David F, Dittmer, Neal T, Ferguson, Laura CF, Garavelou, Spyridoula, Gordon, Karl HJ, Gunaratna, Ramesh T, Han, Yi, Hauser, Frank, He, Yan, Heidel-Fischer, Hanna, Hirsh, Ariana, Hu, Yingxia, Jiang, Hongbo, Kalra, Divya, Klinner, Christian, König, Christopher, Kovar, Christie, Kroll, Ashley R, Kuwar, Suyog S, Lee, Sandy L, Lehman, Rüdiger, Li, Kai, Li, Zhaofei, Liang, Hanquan, Lovelace, Shanna, Lu, Zhiqiang, Mansfield, Jennifer H, McCulloch, Kyle J, Mathew, Tittu, Morton, Brian, Muzny, Donna M, Neunemann, David, Ongeri, Fiona, Pauchet, Yannick, Pu, Ling-Ling, Pyrousis, Ioannis, Rao, Xiang-Jun, Redding, Amanda, Roesel, Charles, Sanchez-Gracia, Alejandro, Schaack, Sarah, Shukla, Aditi, Tetreau, Guillaume, Wang, Yang, Xiong, Guang-Hua, Traut, Walther, Walsh, Tom K, Worley, Kim C, Wu, Di, Wu, Wenbi, Wu, Yuan-Qing, Zhang, Xiufeng, Zou, Zhen, Zucker, Hannah, Briscoe, Adriana D, Burmester, Thorsten, Clem, Rollie J, Feyereisen, René, Grimmelikhuijzen, Cornelis JP, Hamodrakas, Stavros J, Hansson, Bill S, Huguet, Elisabeth, Jermiin, Lars S, Lan, Que, Lehman, Herman K, Lorenzen, Marce, Merzendorfer, Hans, Michalopoulos, Ioannis, Morton, David B, Muthukrishnan, Subbaratnam, Oakeshott, John G, Palmer, Will, Park, Yoonseong, and Passarelli, A Lorena

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Tobacco, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Gene Expression, Gene Expression Profiling, Genome, Insect, Larva, Manduca, Pupa, Sequence Analysis, DNA, Synteny, Lepidoptera, Insect, Tobacco hornworm, Moth, Insect biochemistry, Innate immunity, Medicinal and Biomolecular Chemistry, Biochemistry and Cell Biology, Zoology, Entomology, Biochemistry and cell biology
Abstract

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

Published
2016

4. Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Author

Chen, Zhen-Xia, Sturgill, David, Qu, Jiaxin, Jiang, Huaiyang, Park, Soo, Boley, Nathan, Suzuki, Ana Maria, Fletcher, Anthony R, Plachetzki, David C, FitzGerald, Peter C, Artieri, Carlo G, Atallah, Joel, Barmina, Olga, Brown, James B, Blankenburg, Kerstin P, Clough, Emily, Dasgupta, Abhijit, Gubbala, Sai, Han, Yi, Jayaseelan, Joy C, Kalra, Divya, Kim, Yoo-Ah, Kovar, Christie L, Lee, Sandra L, Li, Mingmei, Malley, James D, Malone, John H, Mathew, Tittu, Mattiuzzo, Nicolas R, Munidasa, Mala, Muzny, Donna M, Ongeri, Fiona, Perales, Lora, Przytycka, Teresa M, Pu, Ling-Ling, Robinson, Garrett, Thornton, Rebecca L, Saada, Nehad, Scherer, Steven E, Smith, Harold E, Vinson, Charles, Warner, Crystal B, Worley, Kim C, Wu, Yuan-Qing, Zou, Xiaoyan, Cherbas, Peter, Kellis, Manolis, Eisen, Michael B, Piano, Fabio, Kionte, Karin, Fitch, David H, Sternberg, Paul W, Cutter, Asher D, Duff, Michael O, Hoskins, Roger A, Graveley, Brenton R, Gibbs, Richard A, Bickel, Peter J, Kopp, Artyom, Carninci, Piero, Celniker, Susan E, Oliver, Brian, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Animals, Cluster Analysis, Computational Biology, Drosophila melanogaster, Evolution, Molecular, Exons, Female, Gene Expression Profiling, Genome, Insect, Humans, Male, Molecular Sequence Annotation, Nucleotide Motifs, Phylogeny, Position-Specific Scoring Matrices, Promoter Regions, Genetic, RNA Editing, RNA Splice Sites, RNA Splicing, Reproducibility of Results, Transcription Initiation Site, Transcriptome, Medical and Health Sciences, Bioinformatics
Abstract

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

Published
2014

5. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

Author

Dasmahapatra, Kanchon K, Walters, James R, Briscoe, Adriana D, Davey, John W, Whibley, Annabel, Nadeau, Nicola J, Zimin, Aleksey V, Hughes, Daniel ST, Ferguson, Laura C, Martin, Simon H, Salazar, Camilo, Lewis, James J, Adler, Sebastian, Ahn, Seung-Joon, Baker, Dean A, Baxter, Simon W, Chamberlain, Nicola L, Chauhan, Ritika, Counterman, Brian A, Dalmay, Tamas, Gilbert, Lawrence E, Gordon, Karl, Heckel, David G, Hines, Heather M, Hoff, Katharina J, Holland, Peter WH, Jacquin-Joly, Emmanuelle, Jiggins, Francis M, Jones, Robert T, Kapan, Durrell D, Kersey, Paul, Lamas, Gerardo, Lawson, Daniel, Mapleson, Daniel, Maroja, Luana S, Martin, Arnaud, Moxon, Simon, Palmer, William J, Papa, Riccardo, Papanicolaou, Alexie, Pauchet, Yannick, Ray, David A, Rosser, Neil, Salzberg, Steven L, Supple, Megan A, Surridge, Alison, Tenger-Trolander, Ayse, Vogel, Heiko, Wilkinson, Paul A, Wilson, Derek, Yorke, James A, Yuan, Furong, Balmuth, Alexi L, Eland, Cathlene, Gharbi, Karim, Thomson, Marian, Gibbs, Richard A, Han, Yi, Jayaseelan, Joy C, Kovar, Christie, Mathew, Tittu, Muzny, Donna M, Ongeri, Fiona, Pu, Ling-Ling, Qu, Jiaxin, Thornton, Rebecca L, Worley, Kim C, Wu, Yuan-Qing, Linares, Mauricio, Blaxter, Mark L, Ffrench-Constant, Richard H, Joron, Mathieu, Kronforst, Marcus R, Mullen, Sean P, Reed, Robert D, Scherer, Steven E, Richards, Stephen, Mallet, James, McMillan, W Owen, and Jiggins, Chris D

Subjects
Adaptation, Physiological, Animals, Bombyx, Butterflies, Chromosomes, Insect, Evolution, Molecular, Gene Flow, Genes, Homeobox, Genes, Insect, Genome, Insect, Genomics, Hybridization, Genetic, Molecular Mimicry, Molecular Sequence Data, Phylogeny, Pigmentation, Sequence Analysis, DNA, Species Specificity, Synteny, Wings, Animal, Heliconius Genome Consortium, General Science & Technology
Abstract

The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.

Published
2012

6. The Drosophila melanogaster Genetic Reference Panel.

Author

Mackay, Trudy FC, Richards, Stephen, Stone, Eric A, Barbadilla, Antonio, Ayroles, Julien F, Zhu, Dianhui, Casillas, Sònia, Han, Yi, Magwire, Michael M, Cridland, Julie M, Richardson, Mark F, Anholt, Robert RH, Barrón, Maite, Bess, Crystal, Blankenburg, Kerstin Petra, Carbone, Mary Anna, Castellano, David, Chaboub, Lesley, Duncan, Laura, Harris, Zeke, Javaid, Mehwish, Jayaseelan, Joy Christina, Jhangiani, Shalini N, Jordan, Katherine W, Lara, Fremiet, Lawrence, Faye, Lee, Sandra L, Librado, Pablo, Linheiro, Raquel S, Lyman, Richard F, Mackey, Aaron J, Munidasa, Mala, Muzny, Donna Marie, Nazareth, Lynne, Newsham, Irene, Perales, Lora, Pu, Ling-Ling, Qu, Carson, Ràmia, Miquel, Reid, Jeffrey G, Rollmann, Stephanie M, Rozas, Julio, Saada, Nehad, Turlapati, Lavanya, Worley, Kim C, Wu, Yuan-Qing, Yamamoto, Akihiko, Zhu, Yiming, Bergman, Casey M, Thornton, Kevin R, Mittelman, David, and Gibbs, Richard A

Subjects
X Chromosome, Centromere, Telomere, Animals, Drosophila melanogaster, Starvation, Genomics, Genotype, Phenotype, Polymorphism, Single Nucleotide, Alleles, Quantitative Trait Loci, Genome-Wide Association Study, Selection, Genetic, Chromosomes, Insect, Chromosomes, Insect, Polymorphism, Single Nucleotide, Selection, Genetic, General Science & Technology
Abstract

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.

Published
2012

9. Epistasis dominates the genetic architecture of Drosophila quantitative traits

Author

Huang, Wen, Richards, Stephen, Carbone, Mary Anna, Zhu, Dianhui, Anholt, Robert R. H., Ayroles, Julien F., Duncan, Laura, Jordan, Katherine W., Lawrence, Faye, Magwire, Michael M., Warner, Crystal B., Blankenburg, Kerstin, Han, Yi, Javaid, Mehwish, Jayaseelan, Joy, Jhangiani, Shalini N., Muzny, Donna, Ongeri, Fiona, Perales, Lora, Wu, Yuan-Qing, Zhang, Yiqing, Zou, Xiaoyan, Stone, Eric A., Gibbs, Richard A., and Mackay, Trudy F. C.

Published
2012

13. Comprehensive molecular characterization of human colon and rectal cancer

Author

Muzny, Donna M., Bainbridge, Matthew N., Chang, Kyle, Dinh, Huyen H., Drummond, Jennifer A., Fowler, Gerald, Kovar, Christie L., Lewis, Lora R., Morgan, Margaret B., Newsham, Irene F., Reid, Jeffrey G., Santibanez, Jireh, Shinbrot, Eve, Trevino, Lisa R., Wu, Yuan-Qing, Wang, Min, Gunaratne, Preethi, Donehower, Lawrence A., Creighton, Chad J., Wheeler, David A., Gibbs, Richard A., Lawrence, Michael S., Voet, Douglas, Jing, Rui, Cibulskis, Kristian, Sivachenko, Andrey, Stojanov, Petar, McKenna, Aaron, Lander, Eric S., Gabriel, Stacey, Getz, Gad, Ding, Li, Fulton, Robert S., Koboldt, Daniel C., Wylie, Todd, Walker, Jason, Dooling, David J., Fulton, Lucinda, Delehaunty, Kim D., Fronick, Catrina C., Demeter, Ryan, Mardis, Elaine R., Wilson, Richard K., Chu, Andy, Chun, Hye-Jung E., Mungall, Andrew J., Pleasance, Erin, Robertson, Gordon A., Stoll, Dominik, Balasundaram, Miruna, Birol, Inanc, Butterfield, Yaron S. N., Chuah, Eric, Coope, Robin J. N., Dhalla, Noreen, Guin, Ranabir, Hirst, Carrie, Hirst, Martin, Holt, Robert A., Lee, Darlene, Li, Haiyan I., Mayo, Michael, Moore, Richard A., Schein, Jacqueline E., Slobodan, Jared R., Tam, Angela, Thiessen, Nina, Varhol, Richard, Zeng, Thomas, Zhao, Yongjun, Jones, Steven J. M., Marra, Marco A., Bass, Adam J., Ramos, Alex H., Saksena, Gordon, Cherniack, Andrew D., Schumacher, Stephen E., Tabak, Barbara, Carter, Scott L., Pho, Nam H., Nguyen, Huy, Onofrio, Robert C., Crenshaw, Andrew, Ardlie, Kristin, Beroukhim, Rameen, Winckler, Wendy, Meyerson, Matthew, Protopopov, Alexei, Zhang, Juinhua, Hadjipanayis, Angela, Lee, Eunjung, Xi, Ruibin, Yang, Lixing, Ren, Xiaojia, Zhang, Hailei, Sathiamoorthy, Narayanan, Shukla, Sachet, Chen, Peng-Chieh, Haseley, Psalm, Xiao, Yonghong, Lee, Semin, Seidman, Jonathan, Chin, Lynda, Park, Peter J., Kucherlapati, Raju, Auman, Todd J., Hoadley, Katherine A., Du, Ying, Wilkerson, Matthew D., Shi, Yan, Liquori, Christina, Meng, Shaowu, Li, Ling, Turman, Yidi J., Topal, Michael D., Tan, Donghui, Waring, Scot, Buda, Elizabeth, Walsh, Jesse, Jones, Corbin D., Mieczkowski, Piotr A., Singh, Darshan, Wu, Junyuan, Gulabani, Anisha, Dolina, Peter, Bodenheimer, Tom, Hoyle, Alan P., Simons, Janae V., Soloway, Matthew, Mose, Lisle E., Jefferys, Stuart R., Balu, Saianand, O’Connor, Brian D., Prins, Jan F., Chiang, Derek Y., Hayes, Neil D., Perou, Charles M., Hinoue, Toshinori, Weisenberger, Daniel J., Maglinte, Dennis T., Pan, Fei, Berman, Benjamin P., Van Den Berg, David J., Shen, Hui, Triche, Timothy, Jr, Baylin, Stephen B., Laird, Peter W., Noble, Michael, Voet, Doug, Gehlenborg, Nils, DiCara, Daniel, Wu, Chang-Jiun, Yingchun Liu, Spring, Zhou, Lihua, Lin, Pei, Park, Richard W., Nazaire, Marc-Danie, Robinson, Jim, Thorvaldsdottir, Helga, Mesirov, Jill, Thorsson, Vesteinn, Reynolds, Sheila M., Bernard, Brady, Kreisberg, Richard, Lin, Jake, Iype, Lisa, Bressler, Ryan, Erkkilä, Timo, Gundapuneni, Madhumati, Liu, Yuexin, Norberg, Adam, Robinson, Tom, Yang, Da, Zhang, Wei, Shmulevich, Ilya, de Ronde, Jorma J., Schultz, Nikolaus, Cerami, Ethan, Ciriello, Giovanni, Goldberg, Arthur P., Gross, Benjamin, Jacobsen, Anders, Gao, Jianjiong, Kaczkowski, Bogumil, Sinha, Rileen, Aksoy, Arman B., Antipin, Yevgeniy, Reva, Boris, Shen, Ronglai, Taylor, Barry S., Chan, Timothy A., Ladanyi, Marc, Sander, Chris, Akbani, Rehan, Zhang, Nianxiang, Broom, Bradley M., Casasent, Tod, Unruh, Anna, Wakefield, Chris, Hamilton, Stanley R., Cason, Craig R., Baggerly, Keith A., Weinstein, John N., Haussler, David, Benz, Christopher C., Stuart, Joshua M., Benz, Stephen C., Sanborn, Zachary J., Vaske, Charles J., Zhu, Jingchun, Szeto, Christopher, Scott, Gary K., Yau, Christina, Ng, Sam, Goldstein, Ted, Ellrott, Kyle, Collisson, Eric, Cozen, Aaron E., Zerbino, Daniel, Wilks, Christopher, Craft, Brian, Spellman, Paul, Penny, Robert, Shelton, Troy, Hatfield, Martha, Morris, Scott, Yena, Peggy, Shelton, Candace, Sherman, Mark, Paulauskis, Joseph, Gastier-Foster, Julie M., Bowen, Jay, Ramirez, Nilsa C., Black, Aaron, Pyatt, Robert, Wise, Lisa, White, Peter, Bertagnolli, Monica, Brown, Jen, Chu, Gerald C., Czerwinski, Christine, Denstman, Fred, Dhir, Rajiv, Dörner, Arnulf, Fuchs, Charles S., Guillem, Jose G., Iacocca, Mary, Juhl, Hartmut, Kaufman, Andrew, Kohl, Bernard, III, Van Le, Xuan, Mariano, Maria C., Medina, Elizabeth N., Meyers, Michael, Nash, Garrett M., Paty, Phillip B., Petrelli, Nicholas, Rabeno, Brenda, Richards, William G., Solit, David, Swanson, Pat, Temple, Larissa, Tepper, Joel E., Thorp, Richard, Vakiani, Efsevia, Weiser, Martin R., Willis, Joseph E., Witkin, Gary, Zeng, Zhaoshi, Zinner, Michael J., Zornig, Carsten, Jensen, Mark A., Sfeir, Robert, Kahn, Ari B., Chu, Anna L., Kothiyal, Prachi, Wang, Zhining, Snyder, Eric E., Pontius, Joan, Pihl, Todd D., Ayala, Brenda, Backus, Mark, Walton, Jessica, Whitmore, Jon, Baboud, Julien, Berton, Dominique L., Nicholls, Matthew C., Srinivasan, Deepak, Raman, Rohini, Girshik, Stanley, Kigonya, Peter A., Alonso, Shelley, Sanbhadti, Rashmi N., Barletta, Sean P., Greene, John M., Pot, David A., Mills Shaw, Kenna R., Dillon, Laura A. L., Buetow, Ken, Davidsen, Tanja, Demchok, John A., Eley, Greg, Ferguson, Martin, Fielding, Peter, Schaefer, Carl, Sheth, Margi, Yang, Liming, Guyer, Mark S., Ozenberger, Bradley A., Palchik, Jacqueline D., Peterson, Jane, Sofia, Heidi J., and Thomson, Elizabeth

Published
2012
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14. A framework for human microbiome research

Author

Methé, Barbara A., Nelson, Karen E., Pop, Mihai, Creasy, Heather H., Giglio, Michelle G., Huttenhower, Curtis, Gevers, Dirk, Petrosino, Joseph F., Abubucker, Sahar, Badger, Jonathan H., Chinwalla, Asif T., Earl, Ashlee M., FitzGerald, Michael G., Fulton, Robert S., Hallsworth-Pepin, Kymberlie, Lobos, Elizabeth A., Madupu, Ramana, Magrini, Vincent, Martin, John C., Mitreva, Makedonka, Muzny, Donna M., Sodergren, Erica J., Versalovic, James, Wollam, Aye M., Worley, Kim C., Wortman, Jennifer R., Young, Sarah K., Zeng, Qiandong, Aagaard, Kjersti M., Abolude, Olukemi O., Allen-Vercoe, Emma, Alm, Eric J., Alvarado, Lucia, Andersen, Gary L., Anderson, Scott, Appelbaum, Elizabeth, Arachchi, Harindra M., Armitage, Gary, Arze, Cesar A., Ayvaz, Tulin, Baker, Carl C., Begg, Lisa, Belachew, Tsegahiwot, Bhonagiri, Veena, Bihan, Monika, Blaser, Martin J., Bloom, Toby, Bonazzi, Vivien R., Brooks, Paul, Buck, Gregory A., Buhay, Christian J., Busam, Dana A., Campbell, Joseph L., Canon, Shane R., Cantarel, Brandi L., Chain, Patrick S., Chen, I-Min A., Chen, Lei, Chhibba, Shaila, Chu, Ken, Ciulla, Dawn M., Clemente, Jose C., Clifton, Sandra W., Conlan, Sean, Crabtree, Jonathan, Cutting, Mary A., Davidovics, Noam J., Davis, Catherine C., DeSantis, Todd Z., Deal, Carolyn, Delehaunty, Kimberley D., Dewhirst, Floyd E., Deych, Elena, Ding, Yan, Dooling, David J., Dugan, Shannon P., Dunne, Michael W., Jr, Durkin, Scott A., Edgar, Robert C., Erlich, Rachel L., Farmer, Candace N., Farrell, Ruth M., Faust, Karoline, Feldgarden, Michael, Felix, Victor M., Fisher, Sheila, Fodor, Anthony A., Forney, Larry, Foster, Leslie, Di Francesco, Valentina, Friedman, Jonathan, Friedrich, Dennis C., Fronick, Catrina C., Fulton, Lucinda L., Gao, Hongyu, Garcia, Nathalia, Giannoukos, Georgia, Giblin, Christina, Giovanni, Maria Y., Goldberg, Jonathan M., Goll, Johannes, Gonzalez, Antonio, Griggs, Allison, Gujja, Sharvari, Haas, Brian J., Hamilton, Holli A., Harris, Emily L., Hepburn, Theresa A., Herter, Brandi, Hoffmann, Diane E., Holder, Michael E., Howarth, Clinton, Huang, Katherine H., Huse, Susan M., Izard, Jacques, Jansson, Janet K., Jiang, Huaiyang, Jordan, Catherine, Joshi, Vandita, Katancik, James A., Keitel, Wendy A., Kelley, Scott T., Kells, Cristyn, Kinder-Haake, Susan, King, Nicholas B., Knight, Rob, Knights, Dan, Kong, Heidi H., Koren, Omry, Koren, Sergey, Kota, Karthik C., Kovar, Christie L., Kyrpides, Nikos C., La Rosa, Patricio S., Lee, Sandra L., Lemon, Katherine P., Lennon, Niall, Lewis, Cecil M., Lewis, Lora, Ley, Ruth E., Li, Kelvin, Liolios, Konstantinos, Liu, Bo, Liu, Yue, Lo, Chien-Chi, Lozupone, Catherine A., Lunsford, Dwayne R., Madden, Tessa, Mahurkar, Anup A., Mannon, Peter J., Mardis, Elaine R., Markowitz, Victor M., Mavrommatis, Konstantinos, McCorrison, Jamison M., McDonald, Daniel, McEwen, Jean, McGuire, Amy L., McInnes, Pamela, Mehta, Teena, Mihindukulasuriya, Kathie A., Miller, Jason R., Minx, Patrick J., Newsham, Irene, Nusbaum, Chad, O’Laughlin, Michelle, Orvis, Joshua, Pagani, Ioanna, Palaniappan, Krishna, Patel, Shital M., Pearson, Matthew, Peterson, Jane, Podar, Mircea, Pohl, Craig, Pollard, Katherine S., Priest, Margaret E., Proctor, Lita M., Qin, Xiang, Raes, Jeroen, Ravel, Jacques, Reid, Jeffrey G., Rho, Mina, Rhodes, Rosamond, Riehle, Kevin P., Rivera, Maria C., Rodriguez-Mueller, Beltran, Rogers, Yu-Hui, Ross, Matthew C., Russ, Carsten, Sanka, Ravi K., Sankar, Pamela, Sathirapongsasuti, Fah J., Schloss, Jeffery A., Schloss, Patrick D., Schmidt, Thomas M., Scholz, Matthew, Schriml, Lynn, Schubert, Alyxandria M., Segata, Nicola, Segre, Julia A., Shannon, William D., Sharp, Richard R., Sharpton, Thomas J., Shenoy, Narmada, Sheth, Nihar U., Simone, Gina A., Singh, Indresh, Smillie, Chris S., Sobel, Jack D., Sommer, Daniel D., Spicer, Paul, Sutton, Granger G., Sykes, Sean M., Tabbaa, Diana G., Thiagarajan, Mathangi, Tomlinson, Chad M., Torralba, Manolito, Treangen, Todd J., Truty, Rebecca M., Vishnivetskaya, Tatiana A., Walker, Jason, Wang, Lu, Wang, Zhengyuan, Ward, Doyle V., Warren, Wesley, Watson, Mark A., Wellington, Christopher, Wetterstrand, Kris A., White, James R., Wilczek-Boney, Katarzyna, Wu, Yuan Qing, Wylie, Kristine M., Wylie, Todd, Yandava, Chandri, Ye, Liang, Ye, Yuzhen, Yooseph, Shibu, Youmans, Bonnie P., Zhang, Lan, Zhou, Yanjiao, Zhu, Yiming, Zoloth, Laurie, Zucker, Jeremy D., Birren, Bruce W., Gibbs, Richard A., Highlander, Sarah K., Weinstock, George M., Wilson, Richard K., and White, Owen

Published
2012
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21. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta

Author

Kanost, Michael, Arrese, Estela, Cao, Xiaolong, Chen, Yun-Ru, Chellapilla, Sanjay, Goldsmith, Marian, Grosse-Wilde, Ewald, Heckel, David, Herndon, Nicolae, Jiang, Haobo, Papanicolaou, Alexie, Qu, Jiaxin, Soulages, Jose, Vogel, Heiko, Walters, James, Waterhouse, Robert, Ahn, Seung-Joon, Almeida, Francisca, An, Chunju, Aqrawi, Peshtewani, An, Anne, Bryant, William, Bucks, Sascha, Chao, Hsu, Chevignon, Germain, Christen, Jayne, Clarke, David, Dittmer, Neal, Ferguson, Laura C.F., Garavelou, Spyridoula, Gordon, Karl H.J., Gunaratna, Ramesh, Han, Yi, Hauser, Frank, He, Yan, Hirsh, Ariana, Hu, Yi, Jiang, Hongbo, Kalra, Divya, Klinner, Christian, König, Christopher, Kovar, Christie, Kroll, Ashley, Kuwar, Suyog, Lee, Sandy, Lehman, Rüdiger, Li, Kai, Li, Zhaofei, Han, Hanquan, Lovelace, Shanna, Lu, Zhiqiang, Mansfield, Jennifer, Mcculloch, Kyle, Mathew, Tittu, Morton, Brian, Muzny, Donna, Neunemann, David, Ongeri, Fiona, Pauchet, Yan, Li, Ling-Ling, Pyrousis, Ioannis, Rao, Xiang-Jun, Redding, Amanda, Roesel, Charles, Sanchez-Gracia, Alejandro, Schaack, Sarah, Shukla, Aditi, Tetreau, Guillaume, Wang, Yan, Hu, Guang-Hua, Traut, Walther, Walsh, Tom, Worley, Kim, Wu, Di, Wu, Wenbi, Wu, Yuan-Qing, Zhang, Xiufeng, Zou, Zhen, Han, Hanna, Briscoe, Adriana, Burmester, Thorsten, Clem, Rollie, Feyereisen, René, Grimmelikhuijzen, Cornelis J.P., Hamodrakas, Stavros, Han, Bill, Hu, Elisabeth, Jermiin, Lars, Qu, Que, He, Herman, Lorenzen, Marce, Han, Hans, Michalopoulos, Ioannis, Morton, David, Muthukrishnan, Subbaratnam, Oakeshott, John, Palmer, Will, Park, Yoonseong, Passarelli, A. Lorena, Rozas, Julio, Schwartz, Lawrence, Smith, Wendy, Southgate, Agnes, An, Andreas, Vogt, Richard, Wang, Ping, Werren, John, Yu, Xiao-Qiang, Jiang, Jing-Jiang, Brown, Susan, Scherer, Steven, Richards, Richard, Blissard, Gary, National Tsing Hua University [Hsinchu] (NTHU), University of Rhode Island (URI), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, Dpt of Entomology and Plant Pathology, Oklahoma State University [Stillwater], Ecosystem Sciences, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), MRC Centre for Neuropsychiatric Genetics and Genomics, Medical Research Council-Cardiff University, Université de Lausanne (UNIL), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), University of Melbourne, Institut de biotechnologie des plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Huazhong University of Science and Technology [Wuhan] (HUST), Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS)-École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Matériaux et nanosciences d'Alsace (FMNGE), Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Human Genome Sequencing Center, Baylor College of Medicine, Baylor College of Medicine (BCM), Baylor University-Baylor University, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire Interdisciplinaire Carnot de Bourgogne [Dijon] (LICB), Université de Bourgogne (UB)-Université de Technologie de Belfort-Montbeliard (UTBM)-Centre National de la Recherche Scientifique (CNRS), Human Genome Sequencing Center [Houston] (HGSC), Laboratoire de Recherche en Informatique et ses Applications de Vannes et Lorient (VALORIA), Université de Bretagne Sud (UBS), Régulation des gènes et signalisation cellulaire, Institut National de la Santé et de la Recherche Médicale (INSERM), Biocenter Grindel, Zoological Museum-University of Hamburg, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Biophysics and Bioinformatics Laboratory, Northwestern University [Evanston], Department of Entomology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Departament de Genètica and Institut de Recerca de la Biodiversitat, Universitat de Barcelona (UB), Laboratoire d'informatique de l'École polytechnique [Palaiseau] (LIX), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), University of Turku, Nottingham University Business School, The Hospital for sick children [Toronto] (SickKids), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Matériaux et nanosciences d'Alsace, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université de Technologie de Belfort-Montbeliard (UTBM)-Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Department of Industrial Engineering and Management Sciences, Northwestern University, Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), TETREAU, Guillaume, Oklahoma State University [Stillwater] (OSU), Université de Lausanne = University of Lausanne (UNIL), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Department of Entomology and Plant Pathology [Oklahoma State University], Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), and Nottingham University Business School [Nottingham]

Subjects
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016

22. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta

Author

Kanost, Michael R., Arrese, Estela L., Cao, Xiaolong, Chen, Yun-ru, Chellapilla, Sanjay, Goldsmith, Marian R., Grosse-wilde, Ewald, Heckel, David G., Herndon, Nicolae, Jiang, Haobo, Papanicolaou, Alexie, Qu, Jiaxin, Soulages, Jose L., Vogel, Heiko, Walters, James, Waterhouse, Robert M., Ahn, Seung-joon, Almeida, Francisca C., An, Chunju, Aqrawi, Peshtewani, Bretschneider, Anne, Bryant, William B., Bucks, Sascha, Chao, Hsu, Chevignon, Germain, Christen, Jayne M., Clarke, David F., Dittmer, Neal T., Ferguson, Laura C. F., Garavelou, Spyridoula, Gordon, Karl H. J., Gunaratna, Ramesh T., Han, Yi, Hauser, Frank, He, Yan, Heidel-fischer, Hanna, Hirsh, Ariana, Hu, Yingxia, Jiang, Hongbo, Kalra, Divya, Klinner, Christian, Konig, Christopher, Kovar, Christie, Kroll, Ashley R., Kuwar, Suyog S., Lee, Sandy L., Lehman, Rudiger, Li, Kai, Li, Zhaofei, Liang, Hanquan, Lovelace, Shanna, Lu, Zhiqiang, Mansfield, Jennifer H., Mcculloch, Kyle J., Mathew, Tittu, Morton, Brian, Muzny, Donna M., Neunemann, David, Ongeri, Fiona, Pauchet, Yannick, Pu, Ling -ling, Pyrousis, Ioannis, Rao, Xiang -jun, Redding, Amanda, Roesel, Charles, Sanchez-gracia, Alejandro, Schaack, Sarah, Shukla, Aditi, Tetreau, Guillaume, Wang, Yang, Xiong, Guang-hua, Traut, Walther, Walsh, Tom K., Worley, Kim C., Wu, Di, Wu, Wenbi, Wu, Yuan-qing, Zhang, Xiufeng, Zou, Zhen, Zucker, Hannah, Briscoe, Adriana D., Burmester, Thorsten, Clem, Rollie J., Feyereisen, Rene, Grimmelikhuijzen, Cornelis J. P., Hamodrakas, Stavros J., Hansson, Bill S., Huguet, Elisabeth, Jermiin, Lars S., Lan, Que, Lehman, Herman K., Lorenzen, Marce, Merzendorfer, Hans, Michalopoulos, Ioannis, Morton, David B., Muthukrishnan, Subbaratnam, Oakeshott, John G., Palmer, Will, Park, Yoonseong, Passarelli, A. Lorena, Rozas, Julio, Schwartz, Lawrence M., Smith, Wendy, Southgate, Agnes, Vilcinskas, Andreas, Vogt, Richard, Wang, Ping, Werren, John, Yu, Xiao-qiang, Zhou, Jing-jiang, Brown, Susan J., Scherer, Steven E., Richards, Stephen, Blissard, Gary W., Kanost, Michael R., Arrese, Estela L., Cao, Xiaolong, Chen, Yun-ru, Chellapilla, Sanjay, Goldsmith, Marian R., Grosse-wilde, Ewald, Heckel, David G., Herndon, Nicolae, Jiang, Haobo, Papanicolaou, Alexie, Qu, Jiaxin, Soulages, Jose L., Vogel, Heiko, Walters, James, Waterhouse, Robert M., Ahn, Seung-joon, Almeida, Francisca C., An, Chunju, Aqrawi, Peshtewani, Bretschneider, Anne, Bryant, William B., Bucks, Sascha, Chao, Hsu, Chevignon, Germain, Christen, Jayne M., Clarke, David F., Dittmer, Neal T., Ferguson, Laura C. F., Garavelou, Spyridoula, Gordon, Karl H. J., Gunaratna, Ramesh T., Han, Yi, Hauser, Frank, He, Yan, Heidel-fischer, Hanna, Hirsh, Ariana, Hu, Yingxia, Jiang, Hongbo, Kalra, Divya, Klinner, Christian, Konig, Christopher, Kovar, Christie, Kroll, Ashley R., Kuwar, Suyog S., Lee, Sandy L., Lehman, Rudiger, Li, Kai, Li, Zhaofei, Liang, Hanquan, Lovelace, Shanna, Lu, Zhiqiang, Mansfield, Jennifer H., Mcculloch, Kyle J., Mathew, Tittu, Morton, Brian, Muzny, Donna M., Neunemann, David, Ongeri, Fiona, Pauchet, Yannick, Pu, Ling -ling, Pyrousis, Ioannis, Rao, Xiang -jun, Redding, Amanda, Roesel, Charles, Sanchez-gracia, Alejandro, Schaack, Sarah, Shukla, Aditi, Tetreau, Guillaume, Wang, Yang, Xiong, Guang-hua, Traut, Walther, Walsh, Tom K., Worley, Kim C., Wu, Di, Wu, Wenbi, Wu, Yuan-qing, Zhang, Xiufeng, Zou, Zhen, Zucker, Hannah, Briscoe, Adriana D., Burmester, Thorsten, Clem, Rollie J., Feyereisen, Rene, Grimmelikhuijzen, Cornelis J. P., Hamodrakas, Stavros J., Hansson, Bill S., Huguet, Elisabeth, Jermiin, Lars S., Lan, Que, Lehman, Herman K., Lorenzen, Marce, Merzendorfer, Hans, Michalopoulos, Ioannis, Morton, David B., Muthukrishnan, Subbaratnam, Oakeshott, John G., Palmer, Will, Park, Yoonseong, Passarelli, A. Lorena, Rozas, Julio, Schwartz, Lawrence M., Smith, Wendy, Southgate, Agnes, Vilcinskas, Andreas, Vogt, Richard, Wang, Ping, Werren, John, Yu, Xiao-qiang, Zhou, Jing-jiang, Brown, Susan J., Scherer, Steven E., Richards, Stephen, and Blissard, Gary W.

Abstract

Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

Published
2016
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24. The genomes of two key bumblebee species with primitive eusocial organization

Author

Sadd, Ben M., Barribeau, Seth M., Bloch, Guy, de Graaf, Dirk C., Dearden, Peter, Elsik, Christine G., Gadau, Jürgen, Grimmelikhuijzen, Cornelis J. P., Hasselmann, Martin, Lozier, Jeffrey D., Robertson, Hugh M., Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M., Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K., Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V., Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M. G., Blaxter, Mark L., Bourke, Andrew F. G., Brown, Mark J. F., Buechel, Severine D., Cameron, Rossanah, Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Ciborowski, Kate L., Clarke, David F., Colgan, Thomas J., Collins, David H., Cridge, Andrew G., Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C. P., Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C., Irvine, Frano, Jermiin, Lars S., Johnson, Claire E., Johnson, Reed M., Jones, Andrew K., Kadowaki, Tatsuhiko, Kidner, Jonathan H., Koch, Vasco, Köhler, Arian, Kraus, F. Bernhard, Lattorff, H. Michael G., Leask, Megan, Lockett, Gabrielle A., Mallon, Eamonn B., Antonio, David S. Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F. A., Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M. F., Oakeshott, John G., Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G., Rossié, Nina, Rueppell, Olav, Santos, Carolina G., Schmid-Hempel, Regula, Schmitt, Björn D., Schulte, Christina, Simões, Zilá L. P., Soares, Michelle P. M., Swevers, Luc, Winnebeck, Eva C., Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M., Aqrawi, Peshtewani K., Blankenburg, Kerstin P., Coyle, Marcus, Francisco, Liezl, Hernandez, Alvaro G., Holder, Michael, Hudson, Matthew E., Jackson, LaRonda, Jayaseelan, Joy, Joshi, Vandita, Kovar, Christie, Lee, Sandra L., Mata, Robert, Mathew, Tittu, Newsham, Irene F., Ngo, Robin, Okwuonu, Geoffrey, Pham, Christopher, Pu, Ling-Ling, Saada, Nehad, Santibanez, Jireh, Simmons, DeNard, Thornton, Rebecca, Venkat, Aarti, Walden, Kimberly Ko, Wu, Yuan-Qing, Debyser, Griet, Devreese, Bart, Asher, Claire, Blommaert, Julie, Chipman, Ariel D., Chittka, Lars, Fouks, Bertrand, Liu, Jisheng, O'Neill, Meaghan P., Sumner, Seirian, Puiu, Daniela, Qu, Jiaxin, Salzberg, Steven L., Scherer, Steven E., Muzny, Donna M., Richards, Stephen, Robinson, Gene E., Gibbs, Richard A., Schmid-Hempel, Paul, Worley, Kim C., Sadd, Ben M., Barribeau, Seth M., Bloch, Guy, de Graaf, Dirk C., Dearden, Peter, Elsik, Christine G., Gadau, Jürgen, Grimmelikhuijzen, Cornelis J. P., Hasselmann, Martin, Lozier, Jeffrey D., Robertson, Hugh M., Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M., Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K., Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V., Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M. G., Blaxter, Mark L., Bourke, Andrew F. G., Brown, Mark J. F., Buechel, Severine D., Cameron, Rossanah, Cappelle, Kaat, Carolan, James C., Christiaens, Olivier, Ciborowski, Kate L., Clarke, David F., Colgan, Thomas J., Collins, David H., Cridge, Andrew G., Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C. P., Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C., Irvine, Frano, Jermiin, Lars S., Johnson, Claire E., Johnson, Reed M., Jones, Andrew K., Kadowaki, Tatsuhiko, Kidner, Jonathan H., Koch, Vasco, Köhler, Arian, Kraus, F. Bernhard, Lattorff, H. Michael G., Leask, Megan, Lockett, Gabrielle A., Mallon, Eamonn B., Antonio, David S. Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F. A., Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M. F., Oakeshott, John G., Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G., Rossié, Nina, Rueppell, Olav, Santos, Carolina G., Schmid-Hempel, Regula, Schmitt, Björn D., Schulte, Christina, Simões, Zilá L. P., Soares, Michelle P. M., Swevers, Luc, Winnebeck, Eva C., Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M., Aqrawi, Peshtewani K., Blankenburg, Kerstin P., Coyle, Marcus, Francisco, Liezl, Hernandez, Alvaro G., Holder, Michael, Hudson, Matthew E., Jackson, LaRonda, Jayaseelan, Joy, Joshi, Vandita, Kovar, Christie, Lee, Sandra L., Mata, Robert, Mathew, Tittu, Newsham, Irene F., Ngo, Robin, Okwuonu, Geoffrey, Pham, Christopher, Pu, Ling-Ling, Saada, Nehad, Santibanez, Jireh, Simmons, DeNard, Thornton, Rebecca, Venkat, Aarti, Walden, Kimberly Ko, Wu, Yuan-Qing, Debyser, Griet, Devreese, Bart, Asher, Claire, Blommaert, Julie, Chipman, Ariel D., Chittka, Lars, Fouks, Bertrand, Liu, Jisheng, O'Neill, Meaghan P., Sumner, Seirian, Puiu, Daniela, Qu, Jiaxin, Salzberg, Steven L., Scherer, Steven E., Muzny, Donna M., Richards, Stephen, Robinson, Gene E., Gibbs, Richard A., Schmid-Hempel, Paul, and Worley, Kim C.

Abstract

BACKGROUND: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. RESULTS: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. CONCLUSIONS: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.

Published
2015
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25. The genomes of two key bumblebee species with primitive eusocial organization

Author

Sadd, Ben M, primary, Barribeau, Seth M, additional, Bloch, Guy, additional, de Graaf, Dirk C, additional, Dearden, Peter, additional, Elsik, Christine G, additional, Gadau, Jürgen, additional, Grimmelikhuijzen, Cornelis JP, additional, Hasselmann, Martin, additional, Lozier, Jeffrey D, additional, Robertson, Hugh M, additional, Smagghe, Guy, additional, Stolle, Eckart, additional, Van Vaerenbergh, Matthias, additional, Waterhouse, Robert M, additional, Bornberg-Bauer, Erich, additional, Klasberg, Steffen, additional, Bennett, Anna K, additional, Câmara, Francisco, additional, Guigó, Roderic, additional, Hoff, Katharina, additional, Mariotti, Marco, additional, Munoz-Torres, Monica, additional, Murphy, Terence, additional, Santesmasses, Didac, additional, Amdam, Gro V, additional, Beckers, Matthew, additional, Beye, Martin, additional, Biewer, Matthias, additional, Bitondi, Márcia MG, additional, Blaxter, Mark L, additional, Bourke, Andrew FG, additional, Brown, Mark JF, additional, Buechel, Severine D, additional, Cameron, Rossanah, additional, Cappelle, Kaat, additional, Carolan, James C, additional, Christiaens, Olivier, additional, Ciborowski, Kate L, additional, Clarke, David F, additional, Colgan, Thomas J, additional, Collins, David H, additional, Cridge, Andrew G, additional, Dalmay, Tamas, additional, Dreier, Stephanie, additional, du Plessis, Louis, additional, Duncan, Elizabeth, additional, Erler, Silvio, additional, Evans, Jay, additional, Falcon, Tiago, additional, Flores, Kevin, additional, Freitas, Flávia CP, additional, Fuchikawa, Taro, additional, Gempe, Tanja, additional, Hartfelder, Klaus, additional, Hauser, Frank, additional, Helbing, Sophie, additional, Humann, Fernanda C, additional, Irvine, Frano, additional, Jermiin, Lars S, additional, Johnson, Claire E, additional, Johnson, Reed M, additional, Jones, Andrew K, additional, Kadowaki, Tatsuhiko, additional, Kidner, Jonathan H, additional, Koch, Vasco, additional, Köhler, Arian, additional, Kraus, F Bernhard, additional, Lattorff, H Michael G, additional, Leask, Megan, additional, Lockett, Gabrielle A, additional, Mallon, Eamonn B, additional, Antonio, David S Marco, additional, Marxer, Monika, additional, Meeus, Ivan, additional, Moritz, Robin FA, additional, Nair, Ajay, additional, Näpflin, Kathrin, additional, Nissen, Inga, additional, Niu, Jinzhi, additional, Nunes, Francis MF, additional, Oakeshott, John G, additional, Osborne, Amy, additional, Otte, Marianne, additional, Pinheiro, Daniel G, additional, Rossié, Nina, additional, Rueppell, Olav, additional, Santos, Carolina G, additional, Schmid-Hempel, Regula, additional, Schmitt, Björn D, additional, Schulte, Christina, additional, Simões, Zilá LP, additional, Soares, Michelle PM, additional, Swevers, Luc, additional, Winnebeck, Eva C, additional, Wolschin, Florian, additional, Yu, Na, additional, Zdobnov, Evgeny M, additional, Aqrawi, Peshtewani K, additional, Blankenburg, Kerstin P, additional, Coyle, Marcus, additional, Francisco, Liezl, additional, Hernandez, Alvaro G, additional, Holder, Michael, additional, Hudson, Matthew E, additional, Jackson, LaRonda, additional, Jayaseelan, Joy, additional, Joshi, Vandita, additional, Kovar, Christie, additional, Lee, Sandra L, additional, Mata, Robert, additional, Mathew, Tittu, additional, Newsham, Irene F, additional, Ngo, Robin, additional, Okwuonu, Geoffrey, additional, Pham, Christopher, additional, Pu, Ling-Ling, additional, Saada, Nehad, additional, Santibanez, Jireh, additional, Simmons, DeNard, additional, Thornton, Rebecca, additional, Venkat, Aarti, additional, Walden, Kimberly KO, additional, Wu, Yuan-Qing, additional, Debyser, Griet, additional, Devreese, Bart, additional, Asher, Claire, additional, Blommaert, Julie, additional, Chipman, Ariel D, additional, Chittka, Lars, additional, Fouks, Bertrand, additional, Liu, Jisheng, additional, O’Neill, Meaghan P, additional, Sumner, Seirian, additional, Puiu, Daniela, additional, Qu, Jiaxin, additional, Salzberg, Steven L, additional, Scherer, Steven E, additional, Muzny, Donna M, additional, Richards, Stephen, additional, Robinson, Gene E, additional, Gibbs, Richard A, additional, Schmid-Hempel, Paul, additional, and Worley, Kim C, additional

Published
2015
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32. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Author

Huang, Wen, primary, Massouras, Andreas, additional, Inoue, Yutaka, additional, Peiffer, Jason, additional, Ràmia, Miquel, additional, Tarone, Aaron M., additional, Turlapati, Lavanya, additional, Zichner, Thomas, additional, Zhu, Dianhui, additional, Lyman, Richard F., additional, Magwire, Michael M., additional, Blankenburg, Kerstin, additional, Carbone, Mary Anna, additional, Chang, Kyle, additional, Ellis, Lisa L., additional, Fernandez, Sonia, additional, Han, Yi, additional, Highnam, Gareth, additional, Hjelmen, Carl E., additional, Jack, John R., additional, Javaid, Mehwish, additional, Jayaseelan, Joy, additional, Kalra, Divya, additional, Lee, Sandy, additional, Lewis, Lora, additional, Munidasa, Mala, additional, Ongeri, Fiona, additional, Patel, Shohba, additional, Perales, Lora, additional, Perez, Agapito, additional, Pu, LingLing, additional, Rollmann, Stephanie M., additional, Ruth, Robert, additional, Saada, Nehad, additional, Warner, Crystal, additional, Williams, Aneisa, additional, Wu, Yuan-Qing, additional, Yamamoto, Akihiko, additional, Zhang, Yiqing, additional, Zhu, Yiming, additional, Anholt, Robert R.H., additional, Korbel, Jan O., additional, Mittelman, David, additional, Muzny, Donna M., additional, Gibbs, Richard A., additional, Barbadilla, Antonio, additional, Johnston, J. Spencer, additional, Stone, Eric A., additional, Richards, Stephen, additional, Deplancke, Bart, additional, and Mackay, Trudy F.C., additional

Published
2014
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33. Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing

Author

Stark, Mitchell, Woods, Susan, Gartside, Michael, Bonazzi, Vanessa, Dutton-Regester, Ken, Aoude, Lauren, Chow, Donald, Sereduk, Chris, Niemi, Natalie, Tang, Nanyun, Ellis, Jonathan, Reid, Jeffrey, Zismann, Victoria, Tyagi, Sonika, Muzny, Donna, Newsham, Irene, Wu, Yuan-Qing, Palmer, Jane, Pollak, Thomas, Youngkin, David, Brooks, Bradford, Lanagan, Catherine, Schmidt, Christopher, Kobe, Bostjan, MacKeigan, Jeffrey, Yin, Hongwei, Brown, Kevin, Gibbs, Richard, Trent, Jeffrey, Hayward, Nicholas, Stark, Mitchell, Woods, Susan, Gartside, Michael, Bonazzi, Vanessa, Dutton-Regester, Ken, Aoude, Lauren, Chow, Donald, Sereduk, Chris, Niemi, Natalie, Tang, Nanyun, Ellis, Jonathan, Reid, Jeffrey, Zismann, Victoria, Tyagi, Sonika, Muzny, Donna, Newsham, Irene, Wu, Yuan-Qing, Palmer, Jane, Pollak, Thomas, Youngkin, David, Brooks, Bradford, Lanagan, Catherine, Schmidt, Christopher, Kobe, Bostjan, MacKeigan, Jeffrey, Yin, Hongwei, Brown, Kevin, Gibbs, Richard, Trent, Jeffrey, and Hayward, Nicholas

Abstract

We sequenced eight melanoma exomes to identify new somatic mutations in metastatic melanoma. Focusing on the mitogen-activated protein (MAP) kinase kinase kinase (MAP3K) family, we found that 24% of melanoma cell lines have mutations in the protein-coding regions of either MAP3K5 or MAP3K9. Structural modeling predicted that mutations in the kinase domain may affect the activity and regulation of these protein kinases. The position of the mutations and the loss of heterozygosity of MAP3K5 and MAP3K9 in 85% and 67% of melanoma samples, respectively, together suggest that the mutations are likely to be inactivating. In in vitro kinase assays, MAP3K5 I780F and MAP3K9 W333* variants had reduced kinase activity. Overexpression of MAP3K5 or MAP3K9 mutants in HEK293T cells reduced the phosphorylation of downstream MAP kinases. Attenuation of MAP3K9 function in melanoma cells using siRNA led to increased cell viability after temozolomide treatment, suggesting that decreased MAP3K pathway activity can lead to chemoresistance in melanoma. © 2012 Nature America, Inc. All rights reserved.

Published
2012

35. Impulsive controller for wireless networked control system: Switched system approach.

Author

Wu, Yuan-Qing, Su, Hongye, and Mathiyalagan, Kalidass

Subjects
WIRELESS communications, TIME delay systems, PACKET switching
Abstract

The problem of stabilization for wireless networked control system (NCS) with packet dropout and time delay is studied in this article. The impulsive control law for the NCS is defined with time delay and impulse. Using a switching model, the network-induced imperfections can be treated as three switching subsystems. Therein, in the case of packet dropout, the control law use the previous state via the first-order hold. The impulsive control law is designed using the switched system approach and the average dwell time method. The obtained sufficient conditions which can guarantee the exponential stability of switched system are in the form of linear matrix inequalities. Finally, a numerical example is used to demonstrate the merits and applicabilities of the proposed method. © 2015 Wiley Periodicals, Inc. Complexity 21: 291-299, 2016 [ABSTRACT FROM AUTHOR]

Published
2016
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40. Assignment of a 2nd locus for multiple exostoses to the pericentromeric region of chromosome-11

Author

Wu, Yuan-Qing, Heutink, Peter, de Vries, Bert B.A., Sandkuijl, Lodewijk A., van den Ouweland, Ans M.W., Niermeijer, Martinus F., Galjaard, Hans, Reyniers, Edwin, Willems, Patrick J., and Halley, Dickey J.J.

Subjects
musculoskeletal diseases, Chemistry, Human medicine, human activities, Biology
Abstract

Hereditary multiple exostoses (EXT) is an autosomal dominant disorder of enchondral bone formation characterized by multiple bony outgrowths (exostoses), with progression to osteosarcoma in a minority of cases. The exclusive involvement of skeletal abnormalities distinguishes EXT from the clinically more complex Langer-Giedion syndrome (LGS), which is associated with deletions at chromosome 8q24. Previously, linkage analysis has revealed a locus for EXT in the LGS region on chromosome 8q24. However, locus heterogeneity was apparent with 30% of the families being unlinked to 8q24. We report on two large pedigrees segregating EXT in which linkage to the LGS region was excluded. To localize the EXT gene(s) in these families we performed a genome search including 254 microsatellite markers dispersed over all autosomes and the X chromosome. In both families evidence was obtained for linkage to markers from the proximal short and long arms of chromosome 11. Two-point analysis gave the highest lod score for D11S554 (Z(max) = 7.148 at theta = 0.03). Multipoint analysis indicated a map position for the EXT gene between D11S905 and D11S916, with a peak multipoint lod score of 8.10 at 6 cM from D11S935. The assignment of a second locus for EXT to the pericentromeric region of chromosome 11 implicates an area that is particularly rich in genes responsible for developmental abnormalities and neoplasia.

Published
1994

41. Abstract 2218: Whole exome DNA sequencing in human cancers of the digestive system

Author

Wheeler, David A., primary, Gingras, Marie-Claude, additional, Cotton, Ronald, additional, Guiteau, Jacques, additional, Hodges, Sally, additional, Wang, Min, additional, Wu, Yuan-Qing, additional, Newsham, Irene, additional, Nazareth, Lynne V., additional, Fisher, William E., additional, Goss, John A., additional, Brunicardi, Francis C., additional, Muzny, Donna M., additional, and Gibbs, Richard A., additional

Published
2010
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42. Whole exome capture in solution with 3 Gbp of data

Author

Bainbridge, Matthew N, primary, Wang, Min, additional, Burgess, Daniel L, additional, Kovar, Christie, additional, Rodesch, Matthew J, additional, D'Ascenzo, Mark, additional, Kitzman, Jacob, additional, Wu, Yuan-Qing, additional, Newsham, Irene, additional, Richmond, Todd A, additional, Jeddeloh, Jeffrey A, additional, Muzny, Donna, additional, Albert, Thomas J, additional, and Gibbs, Richard A, additional

Published
2010
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43. H ∞ filtering for impulsive networked control systems with random packet dropouts and randomly occurring nonlinearities.

Author

Kalidass, Mathiyalagan, Su, Hongye, Wu, Yuan‐Qing, and Rathinasamy, Sakthivel

Subjects
BINOMIAL distribution, LINEAR matrix inequalities, MATHEMATICAL optimization, DETECTORS, ACTUATORS
Abstract

In this paper, the problem of H ∞ filtering for impulsive networked control systems with random packet dropouts and randomly occurring nonlinearities is investigated. By utilizing an impulsive model, the network-induced imperfections including packet dropout and delay are described by the Bernoulli distributed sequence. The delay in the model is assumed to be time varying. Moreover, nonlinearity in the model is assumed to satisfy sector-like nonlinearities. The H ∞ filter is designed by using the linear matrix inequality (LMI) approach and convex optimization technique. The filter gain matrices for the nonlinear networked control systems can be achieved by solving LMIs, which can be easily facilitated by using some standard numerical packages. Finally, a numerical example is presented to demonstrate the effectiveness and applicability of the proposed results. Copyright © 2014 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Published
2015
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45. Loss of the Potassium Channel β-Subunit Gene, KCNAB2, Is Associated with Epilepsy in Patients with 1p36 Deletion Syndrome

Author

Heilstedt, Heidi A., primary, Burgess, Daniel L., additional, Anderson, Anne E., additional, Chedrawi, Aziza, additional, Tharp, Barry, additional, Lee, Olivia, additional, Kashork, Catherine D., additional, Starkey, David E., additional, Wu, Yuan-Qing, additional, Noebels, Jeffrey L., additional, Shaffer, Lisa G., additional, and Shapira, Stuart K., additional

Published
2002
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