Author: "Pu, Ling-Ling" - Searchworks@Jio Institute Digital Library Search Results

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26 results on '"Pu, Ling-Ling"'

1. Isoquercitrin attenuates the osteoclast-mediated bone loss in rheumatoid arthritis via the Nrf2/ROS/NF-κB pathway

Author: Liu, Yan, Li, Tian-qi, Bai, Jin, Liu, Wei-li, Wang, Zi-rou, Feng, Chong, Pu, Ling-ling, Wang, Xin-xing, and Liu, Hui
Published: 2024
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2. 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

3. Isoquercitrin attenuates the osteoclast-mediated bone loss in rheumatoid arthritis via the Nrf2/ROS/NF-κB pathway

Author: Liu, Yan, primary, Li, Tian-qi, additional, Bai, Jin, additional, Liu, Wei-li, additional, Wang, Zi-rou, additional, Feng, Chong, additional, Pu, Ling-ling, additional, Wang, Xin-xing, additional, and Liu, Hui, additional
Published: 2023
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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. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

Author: Chipman, Ariel D, Ferrier, David EK, Brena, Carlo, Qu, Jiaxin, Hughes, Daniel ST, Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer CJ, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis JP, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome HL, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, and Zou, Xiaoyan
Subjects: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Prevention, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Arthropods, Circadian Rhythm Signaling Peptides and Proteins, DNA Methylation, Evolution, Molecular, Female, Genome, Genome, Mitochondrial, Hormones, Male, Multigene Family, Phylogeny, Polymorphism, Genetic, Protein Kinases, RNA, Untranslated, Receptors, Odorant, Selenoproteins, Sex Chromosomes, Synteny, Transcription Factors, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Published: 2014

6. 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

7. 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

8. Insights into social insects from the genome of the honeybee Apis mellifera

Author: Weinstock, George M., Robinson, Gene E., Gibbs, Richard A., Worley, Kim C., Evans, Jay D., Maleszka, Ryszard, Robertson, Hugh M., Weaver, Daniel B., Beye, Martin, Bork, Peer, Elsik, Christine G., Hartfelder, Klaus, Hunt, Greg J., Zdobnov, Evgeny M., Amdam, Gro V., Bitondi, Mrcia M. G., Collins, Anita M., Cristino, Alexandre S., Michael, H., Lattorff, G., Lobo, Carlos H., Moritz, Robin F. A., Nunes, Francis M. F., Page, Jr, Robert E., Simoes, Zil L. P., Wheeler, Diana, Carninci, Piero, Fukuda, Shiro, Hayashizaki, Yoshihide, Kai, Chikatoshi, Kawai, Jun, Sakazume, Naoko, Sasaki, Daisuke, Tagami, Michihira, Albert, Stefan, Baggerman, Geert, Beggs, Kyle T., Bloch, Guy, Cazzamali, Giuseppe, Cohen, Mira, Drapeau, Mark David, Eisenhardt, Dorothea, Emore, Christine, Ewing, Michael A., Fahrbach, Susan E., Foret, Sylvain, Grimmelikhuijzen, Cornelis J. P., Hauser, Frank, Hummon, Amanda B., Huybrechts, Jurgen, Jones, Andrew K., Kadowaki, Tatsuhiko, Kaplan, Noam, Kucharski, Robert, Leboulle, Gerard, Linial, Michal, Littleton, J. Troy, Mercer, Alison R., Richmond, Timothy A., RodriguezZas, Sandra L., Rubin, Elad B., Sattelle, David B., Schlipalius, David, Schoofs, Liliane, Shemesh, Yair, Sweedler, Jonathan V., Velarde, Rodrigo, Verleyen, Peter, Vierstraete, Evy, Williamson, Michael R., Ament, Seth A., Brown, Susan J., Corona, Miguel, Dearden, Peter K., Dunn, W. Augustine, Elekonich, Michelle M., Fujiyuki, Tomoko, Gattermeier, Irene, Gempe, Tanja, Hasselmann, Martin, Kage, Eriko, Kamikouchi, Azusa, Kubo, Takeo, Kunieda, Takekazu, Lorenzen, Marce, Milshina, Natalia V., Morioka, Mizue, Ohashi, Kazuaki, Overbeek, Ross, Ross, Christian A., Schioett, Morten, Shippy, Teresa, Takeuchi, Hideaki, Toth, Amy L., Willis, Judith H., Wilson, Megan J., Gordon, Karl H. J., Letunic, Ivica, Hackett, Kevin, Peterson, Jane, Felsenfeld, Adam, Guyer, Mark, Solignac, Michel, Agarwala, Richa, Cornuet, Jean Marie, Monnerot, Monique, Mougel, Florence, Reese, Justin T., Vautrin, Dominique, Gillespie, Joseph J., Cannone, Jamie J., Gutell, Robin R., Johnston, J. Spencer, Eisen, Michael B., Iyer, Venky N., Iyer, Vivek, Kosarev, Peter, Mackey, Aaron J., Solovyev, Victor, Souvorov, Alexandre, Aronstein, Katherine A., Bilikova, Katarina, Chen, Yan Ping, Clark, Andrew G., Decanini, Laura I., Gelbart, William M., Hetru, Charles, Hultmark, Dan, Imler, Jean-Luc, Jiang, Haobo, Kanost, Michael, Kimura, Kiyoshi, Lazzaro, Brian P., Lopez, Dawn L., Simuth, Jozef, Thompson, Graham J., Zou, Zhen, De Jong, Pieter, Sodergren, Erica, Cs[u dbl acute]ros, Miklos, Milosavljevic, Aleksandar, Osoegawa, Kazutoyo, Richards, Stephen, Shu, Chung-Li, Duret, Laurent, Elhaik, Eran, Graur, Dan, Anzola, Juan M., Campbell, Kathryn S., Childs, Kevin L., Collinge, Derek, Crosby, Madeline A., Dickens, C. Michael, Gramates, L. Sian, Grozinger, Christina M., Jones, Peter L., Jorda, Mireia, Ling, Xu, Matthews, Beverly B., Miller, Jonathan, Mizzen, Craig, Peinado, Miguel A., Reid, Jeffrey G., Russo, Susan M., Schroeder, Andrew J., St Pierre, Susan E., Wang, Ying, Zhou, Pinglei, Jiang, Huaiyang, Kitts, Paul, Ruef, Barbara, Venkatraman, Anand, Zhang, Lan, Aquino-Perez, Gildardo, Whitfield, Charles W., Behura, Susanta K., Berlocher, Stewart H., Sheppard, Walter S., Smith, Deborah R., Suarez, Andrew V., Tsutsui, Neil D., Wei, Xuehong, Wheeler, David, Havlak, Paul, Li, Bingshan, Liu, Yue, Jolivet, Angela, Lee, Sandra, Nazareth, Lynne V., Pu, Ling-Ling, Thorn, Rachel, Stolc, Viktor, Newman, Thomas, Samanta, Manoj, Tongprasit, Waraporn A., Claudianos, Charles, Berenbaum, May R., Biswas, Sunita, de Graaf, Dirk C., Feyereisen, Rene, Johnson, Reed M., Oakeshott, John G., Ranson, Hilary, Schuler, Mary A., Muzny, Donna, Chacko, Joseph, Davis, Clay, Dinh, Huyen, Gill, Rachel, Hernandez, Judith, Hines, Sandra, Hume, Jennifer, Jackson, LaRonda, Kovar, Christie, Lewis, Lora, Miner, George, Morgan, Margaret, Nguyen, Ngoc, Okwuonu, Geoffrey, Paul, Heidi, Santibanez, Jireh, Savery, Glenford, Svatek, Amanda, Villasana, Donna, and Wright, Rita
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): The Honeybee Genome Sequencing Consortium; Overall project leadership: ; George M. Weinstock [1, 2]; Gene E. Robinson [7, 9, 13, 14]; Principal investigators: ; Richard A. Gibbs [1, 2]; [...]
Published: 2006
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9. The finished DNA sequence of human chromosome 12

Author: Scherer, Steven E., Muzny, Donna M., Buhay, Christian J., Chen, Rui, Cree, Andrew, Ding, Yan, Dugan-Rocha, Shannon, Gill, Rachel, Gunaratne, Preethi, Harris, R. Alan, Hawes, Alicia C., Hernandez, Judith, Hodgson, Anne V., Hume, Jennifer, Jackson, Andrew, Khan, Ziad Mohid, Kovar-Smith, Christie, Lewis, Lora R., Lozado, Ryan J., Metzker, Michael L., Milosavljevic, Aleksandar, Miner, George R., Montgomery, Kate T., Morgan, Margaret B., Nazareth, Lynne V., Scott, Graham, Sodergren, Erica, Song, Xing-Zhi, Steffen, David, Lovering, Ruth C., Wheeler, David A., Worley, Kim C., Yuan, Yi, Zhang, Zhengdong, Adams, Charles Q., Ansari-Lari, M. Ali, Ayele, Mulu, Brown, Mary J., Chen, Guan, Chen, Zhijian, Clerc-Blankenburg, Kerstin P., Davis, Clay, Delgado, Oliver, Dinh, Huyen H., Draper, Heather, Gonzalez-Garay, Manuel L., Havlak, Paul, Jackson, Laronda R., Jacob, Leni S., Kelly, Susan H., Li, Li, Li, Zhangwan, Liu, Jing, Liu, Wen, Lu, Jing, Maheshwari, Manjula, Nguyen, Bao-Viet, Okwuonu, Geoffrey O., Pasternak, Shiran, Perez, Lesette M., Plopper, Farah J. H., Santibanez, Jireh, Shen, Hua, Tabor, Paul E., Verduzco, Daniel, Waldron, Lenee, Wang, Qiaoyan, Williams, Gabrielle A., Zhang, JingKun, Zhou, Jianling, Allen, Carlana C., Amin, Anita G., Anyalebechi, Vivian, Bailey, Michael, Barbaria, Joseph A., Bimage, Kesha E., Bryant, Nathaniel P., Burch, Paula E., Burkett, Carrie E., Burrell, Kevin L., Calderon, Eliana, Cardenas, Veronica, Carter, Kelvin, Casias, Kristal, Cavazos, Iracema, Cavazos, Sandra R., Ceasar, Heather, Chacko, Joseph, Chan, Sheryl N., Chavez, Dean, Christopoulos, Constantine, Chu, Joseph, Cockrell, Raynard, Cox, Caroline D., Dang, Michelle, Dathorne, Stephanie R., David, Robert, Davis, Candi Mon'Et, Davy-Carroll, Latarsha, Deshazo, Denise R., Donlin, Jeremy E., D'Souza, Lisa, Eaves, Kristy A., Egan, Amy, Emery-Cohen, Alexandra J., Escotto, Michael, Flagg, Nicole, Forbes, Lisa D., Gabisi, Abdul M., Garza, Melissa, Hamilton, Cerissa, Henderson, Nicholas, Hernandez, Omar, Hines, Sandra, Hogues, Marilyn E., Huang, Mei, Idlebird, DeVincent G., Johnson, Rudy, Jolivet, Angela, Jones, Sally, Kagan, Ryan, King, Laquisha M., Leal, Belita, Lebow, Heather, Lee, Sandra, LeVan, Jaclyn M., Lewis, Lakeshia C., London, Pamela, Lorensuhewa, Lorna M., Loulseged, Hermela, Lovett, Demetria A., Lucier, Alice, Lucier, Raymond L., Ma, Jie, Madu, Renita C., Mapua, Patricia, Martindale, Ashley D., Martinez, Evangelina, Massey, Elizabeth, Mawhiney, Samantha, Meador, Michael G., Mendez, Sylvia, Mercado, Christian, Mercado, Iracema C., Merritt, Christina E., Miner, Zachary L., Minja, Emmanuel, Mitchell, Teresa, Mohabbat, Farida, Mohabbat, Khatera, Montgomery, Baize, Moore, Niki, Morris, Sidney, Munidasa, Mala, Ngo, Robin N., Nguyen, Ngoc B., Nickerson, Elizabeth, Nwaokelemeh, Ogechi O., Nwokenkwo, Stanley, Obregon, Melissa, Oguh, Maryann, Oragunye, Njideka, Oviedo, Rodolfo J., Parish, Bridgette J., Parker, David N., Parrish, Julia, Parks, Kenya L., Paul, Heidie A., Payton, Brett A., Perez, Agapito, Perrin, William, Pickens, Adam, Primus, Eltrick L., Pu, Ling-Ling, Puazo, Maria, Quiles, Miyo M., Quiroz, Juana B., Rabata, Dina, Reeves, Kacy, Ruiz, San Juana, Shao, Hongmei, Sisson, Ida, Sonaike, Titilola, Sorelle, Richard P., Sutton, Angelica E., Svatek, Amanda F., Svetz, Leah Anne, Tamerisa, Kavitha S., Taylor, Tineace R., Teague, Brian, Thomas, Nicole, Thorn, Rachel D., Trejos, Zulma Y., Trevino, Brenda K., Ukegbu, Ogechi N., Urban, Jeremy B., Vasquez, Lydia I., Vera, Virginia A., Villasana, Donna M., Wang, Ling, Ward-Moore, Stephanie, Warren, James T., Wei, Xuehong, White, Flower, Williamson, Angela L., Wleczyk, Regina, Wooden, Hailey S., Wooden, Steven H., Yen, Jennifer, Yoon, Lillienne, Yoon, Vivienne, Zorrilla, Sara E., Nelson, David, Kucherlapati, Raju, Weinstock, George, and Gibbs, Richard A.
Subjects: Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Steven E. Scherer (corresponding author) [1]; Donna M. Muzny [1]; Christian J. Buhay [1]; Rui Chen [1]; Andrew Cree [1]; Yan Ding [1]; Shannon Dugan-Rocha [1]; Rachel Gill [1]; [...]
Published: 2006
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10. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Author: Elsik, Christine G., Tellam, Ross L., Worley, Kim C., Gibbs, Richard A., Elsik, Christine G., Tellam, Ross L, Gibbs, Richard A., Muzny, Donna M., Weinstock, George M., Adelson, David L, Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Guigó, Roderic, Hamernik, Debora L., Kappes, Steve M., Lewin, Harris A, Lynn, David J., Nicholas, Frank W., Reymond, Alexandre, Rijnkels, Monique, Skow, Loren C., Tellam, Ross L, Worley, Kim C., Zdobnov, Evgeny M., Gibbs, Richard A., Kappes, Steve M., Schook, Lawrence, Skow, Loren C., Weinstock, George M., Womack, James, Alioto, Tyler, Antonarakis, Stylianos E., Astashyn, Alex, Chapple, Charles E., Chen, Hsiu-Chuan, Chrast, Jacqueline, Câmara, Francisco, Elsik, Christine G., Ermolaeva, Olga, Guigó, Roderic, Henrichsen, Charlotte N., Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Kokocinski, Felix, Landrum, Melissa, Maglott, Donna, Pruitt, Kim, Reymond, Alexandre, Sapojnikov, Victor, Searle, Stephen M., Solovyev, Victor, Souvorov, Alexandre, Ucla, Catherine, Weinstock, George M., Wyss, Carine, Alioto, Tyler, Antonarakis, Stylianos E., Chapple, Charles E., Chrast, Jacqueline, Câmara, Francisco, Guigó, Roderic, Henrichsen, Charlotte N., Reymond, Alexandre, Ucla, Catherine, Wyss, Carine, Anzola, Juan M., Gerlach, Daniel, Zdobnov, Evgeny M., Elhaik, Eran, Elsik, Christine G., Graur, Dan, Reese, Justin T., Adelson, David L., Edgar, Robert C., McEwan, John C., Payne, Gemma M., Raison, Joy M., Junier, Thomas, Kriventseva, Evgenia V., Zdobnov, Evgeny M., Chrast, Jacqueline, Eyras, Eduardo, Henrichsen, Charlotte N., Plass, Mireya, Reymond, Alexandre, Donthu, Ravikiran, Larkin, Denis M., Lewin, Harris A., Nicholas, Frank W., Elnitski, Laura, Larkin, Denis M., Lewin, Harris A., Reecy, James, Yang, Mary Q., Adelson, David L, Chen, Lin, Cheng, Ze, Chitko-McKown, Carol G., Eichler, Evan E., Elnitski, Laura, Elsik, Christine G., Liu, George E., Matukumalli, Lakshmi K., Song, Jiuzhou, Zhu, Bin, Elsik, Christine G., Lynn, David J., Reese, Justin T., Bradley, Daniel G., Brinkman, Fiona S.L, Lau, Lilian P.L., Lynn, David J., Whiteside, Matthew D., Tellam, Ross L, Walker, Angela, Wheeler, Thomas T., Casey, Theresa, German, Bruce J., Lemay, Danielle G., Lynn, David J., Maqbool, Nauman J., Molenaar, Adrian J., Rijnkels, Monique, Lewin, Harris A., Seo, Seongwon, Stothard, Paul, Baldwin, Cynthia L., Baxter, Rebecca, Brinkmeyer-Langford, Candice L., Brown, Wendy C., Childers, Christopher P., Connelley, Timothy, Ellis, Shirley A., Fritz, Krista, Glass, Elizabeth J., Herzig, Carolyn T.A., livanainen, Antti, Lahmers, Kevin K., Skow, Loren C., Bennett, Anna K., Childers, Christopher P., Dickens, Michael C., Elsik, Christine G., Gilbert, James G.R., Hagen, Darren E., Reese, Justin T., Salih, Hanni, Aerts, Jan, Caetano, Alexandre R., Dalrymple, Brian, Elsik, Christine G., Fernando Garcia, Jose, Gibbs, Richard A., Gill, Clare A., Hamernik, Debora L, Hiendleder, Stefan G., Memili, Erdogan, Nicholas, Frank W., Reecy, James, Rijnkels, Monique, Skow, Loren C., Spurlock, Diane, Stothard, Paul, Tellam, Ross L, Weinstock, George M., Williams, John L, Worley, Kim C., Alexander, Lee, Brownstein, Michael J., Guan, Leluo, Holt, Robert A., Jones, Steven J.M., Marra, Marco A., Moore, Richard, Moore, Stephen S., Roberts, Andy, Taniguchi, Masaaki, Waterman, Richard C., Chacko, Joseph, Chandrabose, Mimi M., Cree, Andy, Diep Dao, Marvin, Dinh, Huyen H., Ayiesha Gabisi, Ramatu, Hines, Sandra, Hume, Jennifer, Jhangiani, Shalini N., Joshi, Vandita, Kovar, Christie L., Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Muzny, Donna M., Bich Nguyen, Ngoc, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Buhay, Christian, Ding, Yan, Dugan-Rocha, Shannon, Herdandez, Judith, Holder, Michael, Sabo, Aniko, Egan, Amy, Goodell, Jason, Wilczek-Boney, Katarzyna, Fowler, Gerald R., Edward Hitchens, Matthew, Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Chiu, Readman, Jones, Steven J.M., Marra, Marco A., Schein, Jacqueline E., James Durbin, K., Havlak, Paul, Jiang, Huaiyang, Liu, Yue, Qin, Xiang, Ren, Yanru, Shen, Yufeng, Song, Henry, Weinstock, George M., Worley, Kim C., Nicole Bell, Stephanie, Davis, Clay, Jolivet Johnson, Angela, Lee, Sandra, Nazareth, Lynne V., Patel, Bella Mayurkumar, Pu, Ling-Ling, Vattathil, Selina, Williams, Rex Lee, Jr., Curry, Stacey, Hamilton, Cerissa, Sodergren, Erica, Nazareth, Lynne V., Wheeler, David A., Adelson, David L, Aerts, Jan, Barris, Wes, Bennett, Gary L, Dalrymple, Brian, Eggen, André, Gill, Clare A., Green, Ronnie D., Harhay, Gregory P., Hobbs, Matthew, Jann, Oliver, Kappes, Steve M., Keele, John W., Kent, Matthew P., Larkin, Denis M., Lewin, Harris A., Lien, Sigbjørn, McEwan, John C., McKay, Stephanie D., McWilliam, Sean, Moore, Stephen S., Nicholas, Frank W., Payne, Gemma M., Ratnakumar, Abhirami, Salih, Hanni, Schnabel, Robert D., Smith, Timothy, Snelling, Warren M., Sonstegard, Tad S., Stone, Roger T., Sugimoto, Yoshikazu, Takasuga, Akiko, Taylor, Jeremy F., Tellam, Ross L., Van Tassell, Curtis P., Williams, John L, MacNeil, Michael D., Abatepaulo, Antonio R.R., Abbey, Colette A., Aerts, Jan, Ahola, Virpi, Almeida, Iassudara G., Amadio, Ariel F., Anatriello, Elen, Bahadue, Suria M., Baldwin, Cynthia L., Baxter, Rebecca, Bennett, Anna K., Biase, Fernando H., Boldt, Clayton R., Brinkmeyer-Langford, Candice L, Brown, Wendy C., Caetano, Alexandre R., Carroll, Jeffery A., Carvalho, Wanessa A, Casey, Theresa, Cervelatti, Eliane P., Chacko, Elsa, Chapin, Jennifer E., Cheng, Ye, Childers, Christopher P., Choi, Jungwoo, Colley, Adam J., Connelley, Timothy, de Campos, Tatiana A., De Donato, Marcos, de Miranda Santos, Isabel K.F., de Oliveira, Carlo J.F., Deobald, Heather, Devinoy, Eve, Dickens, Michael C., Donohue, Kaitlin E., Dovc, Peter, Eberlein, Annett, Ellis, Shirley A., Fitzsimmons, Carolyn J., Franzin, Alessandra M., Fritz, Krista, Garcia, Gustavo R., Fernando Garcia, Jose, Genini, Sem, German, Bruce J., Gilbert, James G.R., Gill, Clare A., Gladney, Cody J., Glass, Elizabeth J., Grant, Jason R., Greaser, Marion L., Green, Jonathan A., Hadsell, Darryl L., Hagen, Darren E., Hakimov, Hatam A., Halgren, Rob, Harrow, Jennifer L, Hart, Elizabeth A., Hastings, Nicola, Hernandez, Marta, Herzig, Carolyn T.A., Hiendleder, Stefan G., Hobbs, Matthew, Hu, Zhi-Liang, livanainen, Antti, Ingham, Aaron, Iso-Touru, Terhi, Jamis, Catherine, Jann, Oliver, Jensen, Kirsty, Kapetis, Dimos, Kerr, Tovah, Khalil, Sari S., Khatib, Hasan, Kolbehdari, Davood, Kumar, Charu G., Kumar, Dinesh, Leach, Richard, Lee, Justin C-M, Lemay, Danielle G., Li, Changxi, Liu, George E., Logan, Krystin M., Malinverni, Roberto, Maqbool, Nauman J., Marques, Elisa, Martin, William F., Martins, Natalia F., Maruyama, Sandra R., Mazza, Raffaele, McLean, Kim L, Medrano, Juan F., Memili, Erdogan, Molenaar, Adrian J., Moreno, Barbara T., Moré, Daniela D., Muntean, Carl T., Nandakumar, Hari P., Nogueira, Marcelo F.G., Olsaker, Ingrid, Pant, Sameer D., Panzitta, Francesca, Pastor, Rosemeire C.P., Poli, Mario A., Poslusny, Nathan, Rachagani, Satyanarayana, Ranganathan, Shoba, Razpet, Andrej, Reecy, James, Riggs, Penny K., Rijnkels, Monique, Rincon, Gonzalo, Rodriguez-Osorio, Nelida, Rodriguez-Zas, Sandra L., Romero, Natasha E., Rosenwald, Anne, Sando, Lillian, Schmutz, Sheila M., Seo, Seongwon, Shen, Libing, Sherman, Laura, Skow, Loren C., Southey, Bruce R., Spurlock, Diane, Strandberg Lutzow, Ylva, Sweedler, Jonathan V., Tammen, Imke, Taniguchi, Masaaki, Tellam, Ross L, Telugu, Bhanu Prakash V.L, Urbanski, Jennifer M., Utsunomiya, Yuri T., Verschoor, Chris P., Waardenberg, Ashley J., Walker, Angela, Wang, Zhiquan, Ward, Robert, Weikard, Rosemarie, Welsh, Thomas H., Jr., Wheeler, Thomas T., White, Stephen N., Williams, John L, Wilming, Laurens G., Wunderlich, Kris R., Yang, Jianqi, and Zhao, Feng-Qi
Published: 2009

11. 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., Publica, Waterhouse, Robert, and Universitat de Barcelona
Subjects: 0301 basic medicine, Genome, Insect, Gene Expression, Moth, Computational biology, Biology, Synteny, Biochemistry, Genome, Article, 03 medical and health sciences, 0302 clinical medicine, Manduca, Botany, Animals, Gene family, ddc:576.5, Genomes, Molecular Biology, Gene, Genome size, Innate immunity, Whole genome sequencing, Tobacco hornworm, Genètica animal, Gene Expression Profiling, fungi, Pupa, Sequence Analysis, DNA, biology.organism_classification, Insect biochemistry, Lepidoptera, Gene expression profiling, 030104 developmental biology, Manduca sexta, Larva, Insect Science, Animal genetics, Lepidòpters, Insect, 030217 neurology & neurosurgery
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.&nbsp
Published: 2016

12. 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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13. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

Author: Zhao, Chaoyang, Escalante, Lucio Navarro, Chen, Hang, Benatti, Thiago R., Qu, Jiaxin, Chellapilla, Sanjay, Waterhouse, Robert M., Wheeler, David, Andersson, Martin N., Bao, Riyue, Batterton, Matthew, Behura, Susanta K., Blankenburg, Kerstin P., Caragea, Doina, Carolan, James C., Coyle, Marcus, El-Bouhssini, Mustapha, Francisco, Liezl, Friedrich, Markus, Gill, Navdeep, Grace, Tony, Grimmelikhuijzen, Cornelis J.P., Han, Yi, Hauser, Frank, Herndon, Nicolae, Holder, Michael, Ioannidis, Panagiotis, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N., Johnson, Alisha J., Kalra, Divya, Korchina, Viktoriya, Kovar, Christie, Lara, Fremiet, Lee, Sandra L., Liu, Xuming, Löfstedt, Christer, Mata, Robert, Mathew, Tittu, Muzny, Donna M., Nagar, Swapnil, Nazareth, Lynne V., Okwuonu, Geoffrey, Ongeri, Fiona, Perales, Lora, Peterson, Brittany F., Pu, Ling-Ling, Robertson, Hugh M., Schemerhorn, Brandon J., Scherer, Steven E., Shreve, Jacob T., Simmons, DeNard, Subramanyam, Subhashree, Thornton, Rebecca, Xue, Kun, Weissenberger, George M., Williams, Christie E., Worley, Kim C., Zhu, Dianhui, Zhu, Yiming, Harris, Marion O., Shukle, Richard H., Weren, John H., Zdobnov, Evgeny M., Chen, Ming-Shun, Brown, Susan J., Stuart, Jeffery J., Richards, Stephen, Zhao, Chaoyang, Escalante, Lucio Navarro, Chen, Hang, Benatti, Thiago R., Qu, Jiaxin, Chellapilla, Sanjay, Waterhouse, Robert M., Wheeler, David, Andersson, Martin N., Bao, Riyue, Batterton, Matthew, Behura, Susanta K., Blankenburg, Kerstin P., Caragea, Doina, Carolan, James C., Coyle, Marcus, El-Bouhssini, Mustapha, Francisco, Liezl, Friedrich, Markus, Gill, Navdeep, Grace, Tony, Grimmelikhuijzen, Cornelis J.P., Han, Yi, Hauser, Frank, Herndon, Nicolae, Holder, Michael, Ioannidis, Panagiotis, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N., Johnson, Alisha J., Kalra, Divya, Korchina, Viktoriya, Kovar, Christie, Lara, Fremiet, Lee, Sandra L., Liu, Xuming, Löfstedt, Christer, Mata, Robert, Mathew, Tittu, Muzny, Donna M., Nagar, Swapnil, Nazareth, Lynne V., Okwuonu, Geoffrey, Ongeri, Fiona, Perales, Lora, Peterson, Brittany F., Pu, Ling-Ling, Robertson, Hugh M., Schemerhorn, Brandon J., Scherer, Steven E., Shreve, Jacob T., Simmons, DeNard, Subramanyam, Subhashree, Thornton, Rebecca, Xue, Kun, Weissenberger, George M., Williams, Christie E., Worley, Kim C., Zhu, Dianhui, Zhu, Yiming, Harris, Marion O., Shukle, Richard H., Weren, John H., Zdobnov, Evgeny M., Chen, Ming-Shun, Brown, Susan J., Stuart, Jeffery J., and Richards, Stephen
Abstract: Gall-forming arthropods are highly specialized herbivores that, in combination with their hosts, produce extended phenotypes with unique morphologies [1]. Many are economically important, and others have improved our understanding of ecology and adaptive radiation [2]. However, the mechanisms that these arthropods use to induce plant galls are poorly understood. We sequenced the genome of the Hessian fly (Mayetiola destructor; Diptera: Cecidomyiidae), a plant parasitic gall midge and a pest of wheat (Triticum spp.), with the aim of identifying genic modifications that contribute to its plant-parasitic lifestyle. Among several adaptive modifications, we discovered an expansive reservoir of potential effector proteins. Nearly 5% of the 20,163 predicted gene models matched putative effector gene transcripts present in the M. destructor larval salivary gland. Another 466 putative effectors were discovered among the genes that have no sequence similarities in other organisms. The largest known arthropod gene family (family SSGP-71) was also discovered within the effector reservoir. SSGP-71 proteins lack sequence homologies to other proteins, but their structures resemble both ubiquitin E3 ligases in plants and E3-ligase-mimicking effectors in plant pathogenic bacteria. SSGP-71 proteins and wheat Skp proteins interact in vivo. Mutations in different SSGP-71 genes avoid the effector-triggered immunity that is directed by the wheat resistance genes H6 and H9. Results point to effectors as the agents responsible for arthropod-induced plant gall formation.
Published: 2015

14. 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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15. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

Author: Zhao, Chaoyang, primary, Escalante, Lucio Navarro, additional, Chen, Hang, additional, Benatti, Thiago R., additional, Qu, Jiaxin, additional, Chellapilla, Sanjay, additional, Waterhouse, Robert M., additional, Wheeler, David, additional, Andersson, Martin N., additional, Bao, Riyue, additional, Batterton, Matthew, additional, Behura, Susanta K., additional, Blankenburg, Kerstin P., additional, Caragea, Doina, additional, Carolan, James C., additional, Coyle, Marcus, additional, El-Bouhssini, Mustapha, additional, Francisco, Liezl, additional, Friedrich, Markus, additional, Gill, Navdeep, additional, Grace, Tony, additional, Grimmelikhuijzen, Cornelis J.P., additional, Han, Yi, additional, Hauser, Frank, additional, Herndon, Nicolae, additional, Holder, Michael, additional, Ioannidis, Panagiotis, additional, Jackson, LaRonda, additional, Javaid, Mehwish, additional, Jhangiani, Shalini N., additional, Johnson, Alisha J., additional, Kalra, Divya, additional, Korchina, Viktoriya, additional, Kovar, Christie L., additional, Lara, Fremiet, additional, Lee, Sandra L., additional, Liu, Xuming, additional, Löfstedt, Christer, additional, Mata, Robert, additional, Mathew, Tittu, additional, Muzny, Donna M., additional, Nagar, Swapnil, additional, Nazareth, Lynne V., additional, Okwuonu, Geoffrey, additional, Ongeri, Fiona, additional, Perales, Lora, additional, Peterson, Brittany F., additional, Pu, Ling-Ling, additional, Robertson, Hugh M., additional, Schemerhorn, Brandon J., additional, Scherer, Steven E., additional, Shreve, Jacob T., additional, Simmons, DeNard, additional, Subramanyam, Subhashree, additional, Thornton, Rebecca L., additional, Xue, Kun, additional, Weissenberger, George M., additional, Williams, Christie E., additional, Worley, Kim C., additional, Zhu, Dianhui, additional, Zhu, Yiming, additional, Harris, Marion O., additional, Shukle, Richard H., additional, Werren, John H., additional, Zdobnov, Evgeny M., additional, Chen, Ming-Shun, additional, Brown, Susan J., additional, Stuart, Jeffery J., additional, and Richards, Stephen, additional
Published: 2015
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16. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

Author: Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, Richards, Stephen, Chipman, Ariel D., Ferrier, David E.K., Brena, Carlo, Qu, Jiaxin, Hughes, Daniel S.T., Schröder, Reinhard, Torres-Oliva, Montserrat, Znassi, Nadia, Jiang, Huaiyang, Almeida, Francisca C, Alonso, Claudio R, Apostolou, Zivkos, Aqrawi, Peshtewani, Arthur, Wallace, Barna, Jennifer C J, Blankenburg, Kerstin P, Brites, Daniela, Capella-Gutiérrez, Salvador, Coyle, Marcus, Dearden, Peter K, Du Pasquier, Louis, Duncan, Elizabeth J, Ebert, Dieter, Eibner, Cornelius, Erikson, Galina, Evans, Peter D, Extavour, Cassandra G, Francisco, Liezl, Gabaldón, Toni, Gillis, William J, Goodwin-Horn, Elizabeth A, Green, Jack E, Griffiths-Jones, Sam, Grimmelikhuijzen, Cornelis, Gubbala, Sai, Guigó, Roderic, Han, Yi, Hauser, Frank, Havlak, Paul, Hayden, Luke, Helbing, Sophie, Holder, Michael, Hui, Jerome H L, Hunn, Julia P, Hunnekuhl, Vera S, Jackson, LaRonda, Javaid, Mehwish, Jhangiani, Shalini N, Jiggins, Francis M, Jones, Tamsin E, Kaiser, Tobias S, Kalra, Divya, Kenny, Nathan J, Korchina, Viktoriya, Kovar, Christie L, Kraus, F Bernhard, Lapraz, François, Lee, Sandra L, Lv, Jie, Mandapat, Christigale, Manning, Gerard, Mariotti, Marco, Mata, Robert, Mathew, Tittu, Neumann, Tobias, Newsham, Irene, Ngo, Dinh N, Ninova, Maria, Okwuonu, Geoffrey, Ongeri, Fiona, Palmer, William J, Patil, Shobha, Patraquim, Pedro, Pham, Christopher, Pu, Ling-Ling, Putman, Nicholas H, Rabouille, Catherine, Ramos, Olivia Mendivil, Rhodes, Adelaide C, Robertson, Helen E, Robertson, Hugh M, Ronshaugen, Matthew, Rozas, Julio, Saada, Nehad, Sánchez-Gracia, Alejandro, Scherer, Steven E, Schurko, Andrew M, Siggens, Kenneth W, Simmons, DeNard, Stief, Anna, Stolle, Eckart, Telford, Maximilian J, Tessmar-Raible, Kristin, Thornton, Rebecca, van der Zee, Maurijn, von Haeseler, Arndt, Williams, James M, Willis, Judith H, Wu, Yuanqing, Zou, Xiaoyan, Lawson, Daniel, Muzny, Donna M, Worley, Kim C, Gibbs, Richard A, Akam, Michael, and Richards, Stephen
Abstract: Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific l
Published: 2014

17. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Author: Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., Hunter, Wayne, Richards, Stephen, Gibbs, Richard A., Gerardo, Nicole M., Moran, Nancy, Nakabachi, Atsushi, Stern, David, Tagu, Denis, Wilson, Alex C. C., Muzny, Donna, Kovar, Christie, Cree, Andy, Chacko, Joseph, Chandrabose, Mimi N., Dao, Marvin Diep, Dinh, Huyen H., Gabisi, Ramatu Ayiesha, Hines, Sandra, Hume, Jennifer, Jhangian, Shalini N., Joshi, Vandita, Lewis, Lora R., Liu, Yih-shin, Lopez, John, Morgan, Margaret B., Nguyen, Ngoc Bich, Okwuonu, Geoffrey O., Ruiz, San Juana, Santibanez, Jireh, Wright, Rita A., Fowler, Gerald R., Hitchens, Matthew E., Lozado, Ryan J., Moen, Charles, Steffen, David, Warren, James T., Zhang, Jingkun, Nazareth, Lynne V., Chavez, Dean, Davis, Clay, Lee, Sandra L., Patel, Bella Mayurkumar, Pu, Ling-Ling, Bell, Stephanie N., Johnson, Angela Jolivet, Vattathil, Selina, Williams, Rex L., Jr., Shigenobu, Shuji, Dang, Phat M., Morioka, Mizue, Fukatsu, Takema, Kudo, Toshiaki, Miyagishima, Shin-ya, Jiang, Huaiyang, Worley, Kim C., Legeai, Fabrice, Gauthier, Jean-Pierre, Collin, Olivier, Zhang, Lan, Chen, Hsiu-Chuan, Ermolaeva, Olga, Hlavina, Wratko, Kapustin, Yuri, Kiryutin, Boris, Kitts, Paul, Maglott, Donna, Murphy, Terence, Pruitt, Kim, Sapojnikov, Victor, Souvorov, Alexandre, Thibaud-Nissen, Francoise, Camara, Francisco, Guigo, Roderic, Stanke, Mario, Solovyev, Victor, Kosarev, Peter, Gilbert, Don, Gabaldon, Toni, Huerta-Cepas, Jaime, Marcet-Houben, Marina, Pignatelli, Miguel, Moya, Andres, Rispe, Claude, Ollivier, Morgane, Quesneville, Hadi, Permal, Emmanuelle, Llorens, Carlos, Futami, Ricardo, Hedges, Dale, Robertson, Hugh M., Alioto, Tyler, Mariotti, Marco, Nikoh, Naruo, McCutcheon, John P., Burke, Gaelen, Kamins, Alexandra, Latorre, Amparo, Moran, Nancy A., Ashton, Peter, Calevro, Federica, Charles, Hubert, Colella, Stefano, Douglas, Angela, Jander, Georg, Jones, Derek H., Febvay, Gerard, Kamphuis, Lars G., Kushlan, Philip F., Macdonald, Sandy, Ramsey, John, Schwartz, Julia, Seah, Stuart, Thomas, Gavin, Vellozo, Augusto, Cass, Bodil, Degnan, Patrick, Hurwitz, Bonnie, Leonardo, Teresa, Koga, Ryuichi, Altincicek, Boran, Anselme, Caroline, Atamian, Hagop, Barribeau, Seth M., de Vos, Martin, Duncan, Elizabeth J., Evans, Jay, Ghanim, Murad, Heddi, Abdelaziz, Kaloshian, Isgouhi, Vincent-Monegat, Carole, Parker, Ben J., Perez-Brocal, Vicente, Rahbe, Yvan, Spragg, Chelsea J., Tamames, Javier, Tamarit, Daniel, Tamborindeguy, Cecilia, Vilcinskas, Andreas, Bickel, Ryan D., Brisson, Jennifer A., Butts, Thomas, Chang, Chun-che, Christiaens, Olivier, Davis, Gregory K., Duncan, Elizabeth, Ferrier, David, Iga, Masatoshi, Janssen, Ralf, Lu, Hsiao-Ling, McGregor, Alistair, Miura, Toru, Smagghe, Guy, Smith, James, van der Zee, Maurijn, Velarde, Rodrigo, Wilson, Megan, Dearden, Peter, Edwards, Owain R., Gordon, Karl, Hilgarth, Roland S., Rider, Stanley Dean, Jr., Srinivasan, Dayalan, Walsh, Thomas K., Ishikawa, Asano, Jaubert-Possamai, Stephanie, Fenton, Brian, Huang, Wenting, Rizk, Guillaume, Lavenier, Dominique, Nicolas, Jacques, Smadja, Carole, Zhou, Jing-Jiang, Vieira, Filipe G., He, Xiao-Li, Liu, Renhu, Rozas, Julio, Field, Linda M., Ashton, Peter D., Campbell, Peter, Carolan, James C., Douglas, Angela E., Fitzroy, Carol I. J., Reardon, Karen T., Reeck, Gerald R., Singh, Karam, Wilkinson, Thomas L., Huybrechts, Jurgen, Abdel-latief, Mohatmed, Robichon, Alain, Veenstra, Jan A., Hauser, Frank, Cazzamali, Giuseppe, Schneider, Martina, Williamson, Michael, Stafflinger, Elisabeth, Hansen, Karina K., Grimmelikhuijzen, Cornelis J. P., Price, Daniel R. G., Caillaud, Marina, van Fleet, Eric, Ren, Qinghu, Gatehouse, John A., Brault, Veronique, Monsion, Baptiste, Diaz, Jason, Hunnicutt, Laura, Ju, Ho-Jong, Pechuan, Ximo, Aguilar, Jose, Cortes, Teresa, Ortiz-Rivas, Benjamin, Martinez-Torres, David, Dombrovsky, Aviv, Dale, Richard P., Davies, T. G. Emyr, Williamson, Martin S., Jones, Andrew, Sattelle, David, Williamson, Sally, Wolstenholme, Adrian, Cottret, Ludovic, Sagot, Marie France, Heckel, David G., and Hunter, Wayne
Abstract: Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.
Published: 2010
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18. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Author: Werren, John H, Richards, Stephen, Desjardins, Christopher A, Niehuis, Oliver, Gadau, Jürgen, Colbourne, John K, Beukeboom, Leo W, Desplan, Claude, Elsik, Christine G, Grimmelikhuijzen, Cornelis J P, Kitts, Paul, Lynch, Jeremy A, Murphy, Terence, Oliveira, Deodoro C S G, Smith, Christopher D, van de Zande, Louis, Worley, Kim C, Zdobnov, Evgeny M, Aerts, Maarten, Albert, Stefan, Anaya, Victor H, Anzola, Juan M, Barchuk, Angel R, Behura, Susanta K, Bera, Agata N, Berenbaum, May R, Bertossa, Rinaldo C, Bitondi, Márcia M G, Bordenstein, Seth R, Bork, Peer, Bornberg-Bauer, Erich, Brunain, Marleen, Cazzamali, Giuseppe, Chaboub, Lesley, Chacko, Joseph, Chavez, Dean, Childers, Christopher P, Choi, Jeong-Hyeon, Clark, Michael E, Claudianos, Charles, Clinton, Rochelle A, Cree, Andrew G, Cristino, Alexandre S, Dang, Phat M, Darby, Alistair C, de Graaf, Dirk C, Devreese, Bart, Dinh, Huyen H, Edwards, Rachel, Elango, Navin, Elhaik, Eran, Ermolaeva, Olga, Evans, Jay D, Foret, Sylvain, Fowler, Gerald R, Gerlach, Daniel, Gibson, Joshua D, Gilbert, Donald G, Graur, Dan, Gründer, Stefan, Hagen, Darren E, Han, Yi, Hauser, Frank, Hultmark, Dan, Hunter, Henry C, Hurst, Gregory D D, Jhangian, Shalini N, Jiang, Huaiyang, Johnson, Reed M, Jones, Andrew K, Junier, Thomas, Kadowaki, Tatsuhiko, Kamping, Albert, Kapustin, Yuri, Kechavarzi, Bobak, Kim, Jaebum, Kim, Jay, Kiryutin, Boris, Koevoets, Tosca, Kovar, Christie L, Kriventseva, Evgenia V, Kucharski, Robert, Lee, Heewook, Lee, Sandra L, Lees, Kristin, Lewis, Lora R, Loehlin, David W, Logsdon, John M, Lopez, Jacqueline A, Lozado, Ryan J, Maglott, Donna, Maleszka, Ryszard, Mayampurath, Anoop, Mazur, Danielle J, McClure, Marcella A, Moore, Andrew D, Morgan, Margaret B, Muller, Jean, Munoz-Torres, Monica C, Muzny, Donna M, Nazareth, Lynne V, Neupert, Susanne, Nguyen, Ngoc B, Nunes, Francis M F, Oakeshott, John G, Okwuonu, Geoffrey O, Pannebakker, Bart A, Pejaver, Vikas R, Peng, Zuogang, Pratt, Stephen C, Predel, Reinhard, Pu, Ling-Ling, Ranson, Hilary, Raychoudhury, Rhitoban, Rechtsteiner, Andreas, Reese, Justin T, Reid, Jeffrey G, Riddle, Megan, Robertson, Hugh M, Romero-Severson, Jeanne, Rosenberg, Miriam, Sackton, Timothy B, Sattelle, David B, Schlüns, Helge, Schmitt, Thomas, Schneider, Martina, Schüler, Andreas, Schurko, Andrew M, Shuker, David M, Simões, Zilá L P, Sinha, Saurabh, Smith, Zachary, Solovyev, Victor, Souvorov, Alexandre, Springauf, Andreas, Stafflinger, Elisabeth, Stage, Deborah E, Stanke, Mario, Tanaka, Yoshiaki, Telschow, Arndt, Trent, Carol, Vattathil, Selina, Verhulst, Eveline C, Viljakainen, Lumi, Wanner, Kevin W, Waterhouse, Robert M, Whitfield, James B, Wilkes, Timothy E, Williamson, Michael, Willis, Judith H, Wolschin, Florian, Wyder, Stefan, Yamada, Takuji, Yi, Soojin V, Zecher, Courtney N, Zhang, Lan, Gibbs, Richard A, Werren, John H, Richards, Stephen, Desjardins, Christopher A, Niehuis, Oliver, Gadau, Jürgen, Colbourne, John K, Beukeboom, Leo W, Desplan, Claude, Elsik, Christine G, Grimmelikhuijzen, Cornelis J P, Kitts, Paul, Lynch, Jeremy A, Murphy, Terence, Oliveira, Deodoro C S G, Smith, Christopher D, van de Zande, Louis, Worley, Kim C, Zdobnov, Evgeny M, Aerts, Maarten, Albert, Stefan, Anaya, Victor H, Anzola, Juan M, Barchuk, Angel R, Behura, Susanta K, Bera, Agata N, Berenbaum, May R, Bertossa, Rinaldo C, Bitondi, Márcia M G, Bordenstein, Seth R, Bork, Peer, Bornberg-Bauer, Erich, Brunain, Marleen, Cazzamali, Giuseppe, Chaboub, Lesley, Chacko, Joseph, Chavez, Dean, Childers, Christopher P, Choi, Jeong-Hyeon, Clark, Michael E, Claudianos, Charles, Clinton, Rochelle A, Cree, Andrew G, Cristino, Alexandre S, Dang, Phat M, Darby, Alistair C, de Graaf, Dirk C, Devreese, Bart, Dinh, Huyen H, Edwards, Rachel, Elango, Navin, Elhaik, Eran, Ermolaeva, Olga, Evans, Jay D, Foret, Sylvain, Fowler, Gerald R, Gerlach, Daniel, Gibson, Joshua D, Gilbert, Donald G, Graur, Dan, Gründer, Stefan, Hagen, Darren E, Han, Yi, Hauser, Frank, Hultmark, Dan, Hunter, Henry C, Hurst, Gregory D D, Jhangian, Shalini N, Jiang, Huaiyang, Johnson, Reed M, Jones, Andrew K, Junier, Thomas, Kadowaki, Tatsuhiko, Kamping, Albert, Kapustin, Yuri, Kechavarzi, Bobak, Kim, Jaebum, Kim, Jay, Kiryutin, Boris, Koevoets, Tosca, Kovar, Christie L, Kriventseva, Evgenia V, Kucharski, Robert, Lee, Heewook, Lee, Sandra L, Lees, Kristin, Lewis, Lora R, Loehlin, David W, Logsdon, John M, Lopez, Jacqueline A, Lozado, Ryan J, Maglott, Donna, Maleszka, Ryszard, Mayampurath, Anoop, Mazur, Danielle J, McClure, Marcella A, Moore, Andrew D, Morgan, Margaret B, Muller, Jean, Munoz-Torres, Monica C, Muzny, Donna M, Nazareth, Lynne V, Neupert, Susanne, Nguyen, Ngoc B, Nunes, Francis M F, Oakeshott, John G, Okwuonu, Geoffrey O, Pannebakker, Bart A, Pejaver, Vikas R, Peng, Zuogang, Pratt, Stephen C, Predel, Reinhard, Pu, Ling-Ling, Ranson, Hilary, Raychoudhury, Rhitoban, Rechtsteiner, Andreas, Reese, Justin T, Reid, Jeffrey G, Riddle, Megan, Robertson, Hugh M, Romero-Severson, Jeanne, Rosenberg, Miriam, Sackton, Timothy B, Sattelle, David B, Schlüns, Helge, Schmitt, Thomas, Schneider, Martina, Schüler, Andreas, Schurko, Andrew M, Shuker, David M, Simões, Zilá L P, Sinha, Saurabh, Smith, Zachary, Solovyev, Victor, Souvorov, Alexandre, Springauf, Andreas, Stafflinger, Elisabeth, Stage, Deborah E, Stanke, Mario, Tanaka, Yoshiaki, Telschow, Arndt, Trent, Carol, Vattathil, Selina, Verhulst, Eveline C, Viljakainen, Lumi, Wanner, Kevin W, Waterhouse, Robert M, Whitfield, James B, Wilkes, Timothy E, Williamson, Michael, Willis, Judith H, Wolschin, Florian, Wyder, Stefan, Yamada, Takuji, Yi, Soojin V, Zecher, Courtney N, Zhang, Lan, and Gibbs, Richard A
Abstract: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
Published: 2010
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19. The genome of the sea urchin Strongylocentrotus purpuratus

Author: Sodergren, Erica, Weinstock, George M., Davidson, Eric H., Cameron, R. Andrew, Gibbs, Richard A., Angerer, Robert C., Angerer, Lynne M., Arnone, Maria Ina, Burgess, David R., Burke, Robert D., Coffman, James A., Dean, Michael, Elphick, Maurice R., Ettensohn, Charles A., Foltz, Kathy R., Hamdoun, Amro, Hynes, Richard O., Klein, William H., Marzluff, William, McClay, David R., Morris, Robert L., Mushegian, Arcady, Rast, Jonathan P., Smith, L. Courtney, Thorndyke, Michael C., Vacquier, Victor D., Wessel, Gary M., Wray, Greg, Zhang, Lan, Elsik, Christine G., Ermolaeva, Olga, Hlavina, Wratko, Hofmann, Gretchen, Kitts, Paul, Landrum, Melissa J., Mackey, Aaron J., Maglott, Donna, Panopoulou, Georgia, Poustka, Albert J., Pruitt, Kim, Sapojnikov, Victor, Song, Xingzhi, Souvorov, Alexandre, Solovyev, Victor, Wei, Zheng, Whittaker, Charles A., Worley, Kim, Durbin, K. James, Shen, Yufeng, Fedrigo, Olivier, Garfield, David, Haygood, Ralph, Primus, Alexander, Satija, Rahul, Severson, Tonya, Gonzalez-Garay, Manuel L., Jackson, Andrew R., Milosavljevic, Aleksandar, Tong, Mark, Killian, Christopher E., Livingston, Brian T., Wilt, Fred H., Adams, Nikki, Belle, Robert, Carbonneau, Seth, Cheung, Rocky, Cormier, Patrick, Cosson, Bertrand, Croce, Jenifer, Fernandez-Guerra, Antonio, Geneviere, Anne-Marie, Goel, Manisha, Kelkar, Hemant, Morales, Julia, Mulner-Lorillon, Odile, Robertson, Anthony J., Goldstone, Jared V., Cole, Bryan, Epel, David, Gold, Bert, Hahn, Mark E., Howard-Ashby, Meredith, Scally, Mark, Stegeman, John J., Allgood, Erin L., Cool, Jonah, Judkins, Kyle M., McCafferty, Shawn S., Musante, Ashlan M., Obar, Robert A., Rawson, Amanda P., Rossetti, Blair J., Gibbons, Ian R., Hoffman, Matthew P., Leone, Andrew, Istrail, Sorin, Materna, Stefan C., Samanta, Manoj P., Stolc, Viktor, Tongprasit, Waraporn, Tu, Qiang, Bergeron, Karl-Frederik, Brandhorst, Bruce P., Whittle, James, Berney, Kevin, Bottjer, David J., Calestani, Cristina, Peterson, Kevin, Chow, Elly, Yuan, Qiu Autumn, Elhaik, Eran, Graur, Dan, Reese, Justin T., Bosdet, Ian, Heesun, Shin, Marra, Marco A., Schein, Jacqueline, Anderson, Michele K., Brockton, Virginia, Buckley, Katherine M., Cohen, Avis H., Fugmann, Sebastian D., Hibino, Taku, Loza-Coll, Mariano, Majeske, Audrey J., Messier, Cynthia, Nair, Sham V., Pancer, Zeev, Terwilliger, David P., Agca, Cavit, Arboleda, Enrique, Chen, Nansheng, Churcher, Allison M., Hallböök, Finn, Humphrey, Glen W., Idris, Mohammed M., Kiyama, Takae, Liang, Shuguang, Mellott, Dan, Mu, Xiuqian, Murray, Greg, Olinski, Robert P., Raible, Florian, Rowe, Matthew, Taylor, John S., Tessmar-Raible, Kristin, Wang, D., Wilson, Karen H., Yaguchi, Shunsuke, Gaasterland, Terry, Galindo, Blanca E., Gunaratne, Herath J., Juliano, Celina, Kinukawa, Masashi, Moy, Gary W., Neill, Anna T., Nomura, Mamoru, Raisch, Michael, Reade, Anna, Roux, Michelle M., Song, Jia L., Su, Yi-Hsien, Townley, Ian K., Voronina, Ekaterina, Wong, Julian L., Amore, Gabriele, Branno, Margherita, Brown, Euan R., Cavalieri, Vincenzo, Duboc, Veronique, Duloquin, Louise, Flytzanis, Constantin, Gache, Christian, Lapraz, Francois, Lepage, Thierry, Locascio, Annamaria, Martinez, Pedro, Matassi, Giorgio, Matranga, Valeria, Range, Ryan, Rizzo, Francesca, Roettinger, Eric, Wilson, Karen, Beane, Wendy, Bradham, Cynthia, Byrum, Christine, Glenn, Tom, Hussain, Sofia, Loza, Mariano, Manning, Gerard, Miranda, Esther, Thomason, Rebecca, Walton, Katherine, Wikramanayke, Athula, Whittaker, Charles, Wu, Shu-Yu, Xu, Ronghui, Brown, C. Titus, Chen, Lili, Gray, Rachel F., Lee, Pei Yun, Nam, Jongmin, Oliveri, Paola, Smith, Joel, Muzny, Donna, Bell, Stephanie, Chacko, Joseph, Cree, Andrew, Curry, Stacey, Davis, Clay, Dinh, Huyen, Dugan-Rocha, Shannon, Fowler, Jerry, Gill, Rachel, Hamilton, Cerrissa, Hernandez, Judith, Hines, Sandra, Hume, Jennifer, Jackson, LaRonda, Jolivet, Angela, Kovar, Christie, Lee, Sandra, Lewis, Lora, Miner, George, Morgan, Margaret, Nazareth, Lynne V., Okwuonu, Geoffrey, Parker, David, Pu, Ling-Ling, Thom, Rachel, Wright, Rita, Sodergren, Erica, Weinstock, George M., Davidson, Eric H., Cameron, R. Andrew, Gibbs, Richard A., Angerer, Robert C., Angerer, Lynne M., Arnone, Maria Ina, Burgess, David R., Burke, Robert D., Coffman, James A., Dean, Michael, Elphick, Maurice R., Ettensohn, Charles A., Foltz, Kathy R., Hamdoun, Amro, Hynes, Richard O., Klein, William H., Marzluff, William, McClay, David R., Morris, Robert L., Mushegian, Arcady, Rast, Jonathan P., Smith, L. Courtney, Thorndyke, Michael C., Vacquier, Victor D., Wessel, Gary M., Wray, Greg, Zhang, Lan, Elsik, Christine G., Ermolaeva, Olga, Hlavina, Wratko, Hofmann, Gretchen, Kitts, Paul, Landrum, Melissa J., Mackey, Aaron J., Maglott, Donna, Panopoulou, Georgia, Poustka, Albert J., Pruitt, Kim, Sapojnikov, Victor, Song, Xingzhi, Souvorov, Alexandre, Solovyev, Victor, Wei, Zheng, Whittaker, Charles A., Worley, Kim, Durbin, K. James, Shen, Yufeng, Fedrigo, Olivier, Garfield, David, Haygood, Ralph, Primus, Alexander, Satija, Rahul, Severson, Tonya, Gonzalez-Garay, Manuel L., Jackson, Andrew R., Milosavljevic, Aleksandar, Tong, Mark, Killian, Christopher E., Livingston, Brian T., Wilt, Fred H., Adams, Nikki, Belle, Robert, Carbonneau, Seth, Cheung, Rocky, Cormier, Patrick, Cosson, Bertrand, Croce, Jenifer, Fernandez-Guerra, Antonio, Geneviere, Anne-Marie, Goel, Manisha, Kelkar, Hemant, Morales, Julia, Mulner-Lorillon, Odile, Robertson, Anthony J., Goldstone, Jared V., Cole, Bryan, Epel, David, Gold, Bert, Hahn, Mark E., Howard-Ashby, Meredith, Scally, Mark, Stegeman, John J., Allgood, Erin L., Cool, Jonah, Judkins, Kyle M., McCafferty, Shawn S., Musante, Ashlan M., Obar, Robert A., Rawson, Amanda P., Rossetti, Blair J., Gibbons, Ian R., Hoffman, Matthew P., Leone, Andrew, Istrail, Sorin, Materna, Stefan C., Samanta, Manoj P., Stolc, Viktor, Tongprasit, Waraporn, Tu, Qiang, Bergeron, Karl-Frederik, Brandhorst, Bruce P., Whittle, James, Berney, Kevin, Bottjer, David J., Calestani, Cristina, Peterson, Kevin, Chow, Elly, Yuan, Qiu Autumn, Elhaik, Eran, Graur, Dan, Reese, Justin T., Bosdet, Ian, Heesun, Shin, Marra, Marco A., Schein, Jacqueline, Anderson, Michele K., Brockton, Virginia, Buckley, Katherine M., Cohen, Avis H., Fugmann, Sebastian D., Hibino, Taku, Loza-Coll, Mariano, Majeske, Audrey J., Messier, Cynthia, Nair, Sham V., Pancer, Zeev, Terwilliger, David P., Agca, Cavit, Arboleda, Enrique, Chen, Nansheng, Churcher, Allison M., Hallböök, Finn, Humphrey, Glen W., Idris, Mohammed M., Kiyama, Takae, Liang, Shuguang, Mellott, Dan, Mu, Xiuqian, Murray, Greg, Olinski, Robert P., Raible, Florian, Rowe, Matthew, Taylor, John S., Tessmar-Raible, Kristin, Wang, D., Wilson, Karen H., Yaguchi, Shunsuke, Gaasterland, Terry, Galindo, Blanca E., Gunaratne, Herath J., Juliano, Celina, Kinukawa, Masashi, Moy, Gary W., Neill, Anna T., Nomura, Mamoru, Raisch, Michael, Reade, Anna, Roux, Michelle M., Song, Jia L., Su, Yi-Hsien, Townley, Ian K., Voronina, Ekaterina, Wong, Julian L., Amore, Gabriele, Branno, Margherita, Brown, Euan R., Cavalieri, Vincenzo, Duboc, Veronique, Duloquin, Louise, Flytzanis, Constantin, Gache, Christian, Lapraz, Francois, Lepage, Thierry, Locascio, Annamaria, Martinez, Pedro, Matassi, Giorgio, Matranga, Valeria, Range, Ryan, Rizzo, Francesca, Roettinger, Eric, Wilson, Karen, Beane, Wendy, Bradham, Cynthia, Byrum, Christine, Glenn, Tom, Hussain, Sofia, Loza, Mariano, Manning, Gerard, Miranda, Esther, Thomason, Rebecca, Walton, Katherine, Wikramanayke, Athula, Whittaker, Charles, Wu, Shu-Yu, Xu, Ronghui, Brown, C. Titus, Chen, Lili, Gray, Rachel F., Lee, Pei Yun, Nam, Jongmin, Oliveri, Paola, Smith, Joel, Muzny, Donna, Bell, Stephanie, Chacko, Joseph, Cree, Andrew, Curry, Stacey, Davis, Clay, Dinh, Huyen, Dugan-Rocha, Shannon, Fowler, Jerry, Gill, Rachel, Hamilton, Cerrissa, Hernandez, Judith, Hines, Sandra, Hume, Jennifer, Jackson, LaRonda, Jolivet, Angela, Kovar, Christie, Lee, Sandra, Lewis, Lora, Miner, George, Morgan, Margaret, Nazareth, Lynne V., Okwuonu, Geoffrey, Parker, David, Pu, Ling-Ling, Thom, Rachel, and Wright, Rita
Abstract: We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
Published: 2006
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20. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

Author: Gibbs, Richard A., primary, Rogers, Jeffrey, additional, Katze, Michael G., additional, Bumgarner, Roger, additional, Weinstock, George M., additional, Mardis, Elaine R., additional, Remington, Karin A., additional, Strausberg, Robert L., additional, Venter, J. Craig, additional, Wilson, Richard K., additional, Batzer, Mark A., additional, Bustamante, Carlos D., additional, Eichler, Evan E., additional, Hahn, Matthew W., additional, Hardison, Ross C., additional, Makova, Kateryna D., additional, Miller, Webb, additional, Milosavljevic, Aleksandar, additional, Palermo, Robert E., additional, Siepel, Adam, additional, Sikela, James M., additional, Attaway, Tony, additional, Bell, Stephanie, additional, Bernard, Kelly E., additional, Buhay, Christian J., additional, Chandrabose, Mimi N., additional, Dao, Marvin, additional, Davis, Clay, additional, Delehaunty, Kimberly D., additional, Ding, Yan, additional, Dinh, Huyen H., additional, Dugan-Rocha, Shannon, additional, Fulton, Lucinda A., additional, Gabisi, Ramatu Ayiesha, additional, Garner, Toni T., additional, Godfrey, Jennifer, additional, Hawes, Alicia C., additional, Hernandez, Judith, additional, Hines, Sandra, additional, Holder, Michael, additional, Hume, Jennifer, additional, Jhangiani, Shalini N., additional, Joshi, Vandita, additional, Khan, Ziad Mohid, additional, Kirkness, Ewen F., additional, Cree, Andrew, additional, Fowler, R. Gerald, additional, Lee, Sandra, additional, Lewis, Lora R., additional, Li, Zhangwan, additional, Liu, Yih-shin, additional, Moore, Stephanie M., additional, Muzny, Donna, additional, Nazareth, Lynne V., additional, Ngo, Dinh Ngoc, additional, Okwuonu, Geoffrey O., additional, Pai, Grace, additional, Parker, David, additional, Paul, Heidie A., additional, Pfannkoch, Cynthia, additional, Pohl, Craig S., additional, Rogers, Yu-Hui, additional, Ruiz, San Juana, additional, Sabo, Aniko, additional, Santibanez, Jireh, additional, Schneider, Brian W., additional, Smith, Scott M., additional, Sodergren, Erica, additional, Svatek, Amanda F., additional, Utterback, Teresa R., additional, Vattathil, Selina, additional, Warren, Wesley, additional, White, Courtney Sherell, additional, Chinwalla, Asif T., additional, Feng, Yucheng, additional, Halpern, Aaron L., additional, Hillier, LaDeana W., additional, Huang, Xiaoqiu, additional, Minx, Pat, additional, Nelson, Joanne O., additional, Pepin, Kymberlie H., additional, Qin, Xiang, additional, Sutton, Granger G., additional, Venter, Eli, additional, Walenz, Brian P., additional, Wallis, John W., additional, Worley, Kim C., additional, Yang, Shiaw-Pyng, additional, Jones, Steven M., additional, Marra, Marco A., additional, Rocchi, Mariano, additional, Schein, Jacqueline E., additional, Baertsch, Robert, additional, Clarke, Laura, additional, Csürös, Miklós, additional, Glasscock, Jarret, additional, Harris, R. Alan, additional, Havlak, Paul, additional, Jackson, Andrew R., additional, Jiang, Huaiyang, additional, Liu, Yue, additional, Messina, David N., additional, Shen, Yufeng, additional, Song, Henry Xing-Zhi, additional, Wylie, Todd, additional, Zhang, Lan, additional, Birney, Ewan, additional, Han, Kyudong, additional, Konkel, Miriam K., additional, Lee, Jungnam, additional, Smit, Arian F. A., additional, Ullmer, Brygg, additional, Wang, Hui, additional, Xing, Jinchuan, additional, Burhans, Richard, additional, Cheng, Ze, additional, Karro, John E., additional, Ma, Jian, additional, Raney, Brian, additional, She, Xinwei, additional, Cox, Michael J., additional, Demuth, Jeffery P., additional, Dumas, Laura J., additional, Han, Sang-Gook, additional, Hopkins, Janet, additional, Karimpour-Fard, Anis, additional, Kim, Young H., additional, Pollack, Jonathan R., additional, Vinar, Tomas, additional, Addo-Quaye, Charles, additional, Degenhardt, Jeremiah, additional, Denby, Alexandra, additional, Hubisz, Melissa J., additional, Indap, Amit, additional, Kosiol, Carolin, additional, Lahn, Bruce T., additional, Lawson, Heather A., additional, Marklein, Alison, additional, Nielsen, Rasmus, additional, Vallender, Eric J., additional, Clark, Andrew G., additional, Ferguson, Betsy, additional, Hernandez, Ryan D., additional, Hirani, Kashif, additional, Kehrer-Sawatzki, Hildegard, additional, Kolb, Jessica, additional, Patil, Shobha, additional, Pu, Ling-Ling, additional, Ren, Yanru, additional, Smith, David Glenn, additional, Wheeler, David A., additional, Schenck, Ian, additional, Ball, Edward V., additional, Chen, Rui, additional, Cooper, David N., additional, Giardine, Belinda, additional, Hsu, Fan, additional, Kent, W. James, additional, Lesk, Arthur, additional, Nelson, David L., additional, O'Brien, William E., additional, Prüfer, Kay, additional, Stenson, Peter D., additional, Wallace, James C., additional, Ke, Hui, additional, Liu, Xiao-Ming, additional, Wang, Peng, additional, Xiang, Andy Peng, additional, Yang, Fan, additional, Barber, Galt P., additional, Haussler, David, additional, Karolchik, Donna, additional, Kern, Andy D., additional, Kuhn, Robert M., additional, Smith, Kayla E., additional, and Zwieg, Ann S., additional
Published: 2007
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21. The Genome of the Sea Urchin Strongylocentrotus purpuratus

Author: Sodergren, Erica, primary, Weinstock, George M., additional, Davidson, Eric H, additional, Cameron, R. Andrew, additional, Gibbs, Richard A., additional, Angerer, Robert C., additional, Angerer, Lynne M., additional, Arnone, Maria Ina, additional, Burgess, David R., additional, Burke, Robert D., additional, Coffman, James A., additional, Dean, Michael, additional, Elphick, Maurice R., additional, Ettensohn, Charles A., additional, Foltz, Kathy R., additional, Hamdoun, Amro, additional, Hynes, Richard O., additional, Klein, William H., additional, Marzluff, William, additional, McClay, David R., additional, Morris, Robert L., additional, Mushegian, Arcady, additional, Rast, Jonathan P., additional, Smith, L. Courtney, additional, Thorndyke, Michael C., additional, Vacquier, Victor D., additional, Wessel, Gary M., additional, Wray, Greg, additional, Zhang, Lan, additional, Elsik, Christine G., additional, Ermolaeva, Olga, additional, Hlavina, Wratko, additional, Hofmann, Gretchen, additional, Kitts, Paul, additional, Landrum, Melissa J., additional, Mackey, Aaron J., additional, Maglott, Donna, additional, Panopoulou, Georgia, additional, Poustka, Albert J., additional, Pruitt, Kim, additional, Sapojnikov, Victor, additional, Song, Xingzhi, additional, Souvorov, Alexandre, additional, Solovyev, Victor, additional, Wei, Zheng, additional, Whittaker, Charles A., additional, Worley, Kim, additional, Durbin, K. James, additional, Shen, Yufeng, additional, Fedrigo, Olivier, additional, Garfield, David, additional, Haygood, Ralph, additional, Primus, Alexander, additional, Satija, Rahul, additional, Severson, Tonya, additional, Gonzalez-Garay, Manuel L., additional, Jackson, Andrew R., additional, Milosavljevic, Aleksandar, additional, Tong, Mark, additional, Killian, Christopher E., additional, Livingston, Brian T., additional, Wilt, Fred H., additional, Adams, Nikki, additional, BelleÌ, Robert, additional, Carbonneau, Seth, additional, Cheung, Rocky, additional, Cormier, Patrick, additional, Cosson, Bertrand, additional, Croce, Jenifer, additional, Fernandez-Guerra, Antonio, additional, GenevieÌre, Anne-Marie, additional, Goel, Manisha, additional, Kelkar, Hemant, additional, Morales, Julia, additional, Mulner-Lorillon, Odile, additional, Robertson, Anthony J., additional, Goldstone, Jared V., additional, Cole, Bryan, additional, Epel, David, additional, Gold, Bert, additional, Hahn, Mark E., additional, Howard-Ashby, Meredith, additional, Scally, Mark, additional, Stegeman, John J., additional, Allgood, Erin L., additional, Cool, Jonah, additional, Judkins, Kyle M., additional, McCafferty, Shawn S., additional, Musante, Ashlan M., additional, Obar, Robert A., additional, Rawson, Amanda P., additional, Rossetti, Blair J., additional, Gibbons, Ian R., additional, Hoffman, Matthew P., additional, Leone, Andrew, additional, Istrail, Sorin, additional, Materna, Stefan C., additional, Samanta, Manoj P., additional, Stolc, Viktor, additional, Tongprasit, Waraporn, additional, Tu, Qiang, additional, Bergeron, Karl-Frederik, additional, Brandhorst, Bruce P., additional, Whittle, James, additional, Berney, Kevin, additional, Bottjer, David J., additional, Calestani, Cristina, additional, Peterson, Kevin, additional, Chow, Elly, additional, Yuan, Qiu Autumn, additional, Elhaik, Eran, additional, Graur, Dan, additional, Reese, Justin T., additional, Bosdet, Ian, additional, Heesun, Shin, additional, Marra, Marco A., additional, Schein, Jacqueline, additional, Anderson, Michele K., additional, Brockton, Virginia, additional, Buckley, Katherine M., additional, Cohen, Avis H., additional, Fugmann, Sebastian D., additional, Hibino, Taku, additional, Loza-Coll, Mariano, additional, Majeske, Audrey J., additional, Messier, Cynthia, additional, Nair, Sham V., additional, Pancer, Zeev, additional, Terwilliger, David P., additional, Agca, Cavit, additional, Arboleda, Enrique, additional, Chen, Nansheng, additional, Churcher, Allison M., additional, HallboÌoÌk, F., additional, Humphrey, Glen W., additional, Idris, Mohammed M., additional, Kiyama, Takae, additional, Liang, Shuguang, additional, Mellott, Dan, additional, Mu, Xiuqian, additional, Murray, Greg, additional, Olinski, Robert P., additional, Raible, Florian, additional, Rowe, Matthew, additional, Taylor, John S., additional, Tessmar-Raible, Kristin, additional, Wang, D., additional, Wilson, Karen H., additional, Yaguchi, Shunsuke, additional, Gaasterland, Terry, additional, Galindo, Blanca E., additional, Gunaratne, Herath J., additional, Juliano, Celina, additional, Kinukawa, Masashi, additional, Moy, Gary W., additional, Neill, Anna T., additional, Nomura, Mamoru, additional, Raisch, Michael, additional, Reade, Anna, additional, Roux, Michelle M., additional, Song, Jia L., additional, Su, Yi-Hsien, additional, Townley, Ian K., additional, Voronina, Ekaterina, additional, Wong, Julian L., additional, Amore, Gabriele, additional, Branno, Margherita, additional, Brown, Euan R., additional, Cavalieri, Vincenzo, additional, Duboc, VeÌronique, additional, Duloquin, Louise, additional, Flytzanis, Constantin, additional, Gache, Christian, additional, Lapraz, FrancÌ§ois, additional, Lepage, Thierry, additional, Locascio, Annamaria, additional, Martinez, Pedro, additional, Matassi, Giorgio, additional, Matranga, Valeria, additional, Range, Ryan, additional, Rizzo, Francesca, additional, RoÌttinger, Eric, additional, Beane, Wendy, additional, Bradham, Cynthia, additional, Byrum, Christine, additional, Glenn, Tom, additional, Hussain, Sofia, additional, Manning, Gerard, additional, Miranda, Esther, additional, Thomason, Rebecca, additional, Walton, Katherine, additional, Wikramanayke, Athula, additional, Wu, Shu-Yu, additional, Xu, Ronghui, additional, Brown, C. Titus, additional, Chen, Lili, additional, Gray, Rachel F., additional, Lee, Pei Yun, additional, Nam, Jongmin, additional, Oliveri, Paola, additional, Smith, Joel, additional, Muzny, Donna, additional, Bell, Stephanie, additional, Chacko, Joseph, additional, Cree, Andrew, additional, Curry, Stacey, additional, Davis, Clay, additional, Dinh, Huyen, additional, Dugan-Rocha, Shannon, additional, Fowler, Jerry, additional, Gill, Rachel, additional, Hamilton, Cerrissa, additional, Hernandez, Judith, additional, Hines, Sandra, additional, Hume, Jennifer, additional, Jackson, LaRonda, additional, Jolivet, Angela, additional, Kovar, Christie, additional, Lee, Sandra, additional, Lewis, Lora, additional, Miner, George, additional, Morgan, Margaret, additional, Nazareth, Lynne V., additional, Okwuonu, Geoffrey, additional, Parker, David, additional, Pu, Ling-Ling, additional, Thorn, Rachel, additional, and Wright, Rita, additional
Published: 2006
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22. [Resveratrol attenuates cardiac function impairment in plateau hypobaric hypoxia rats].

Author: Xu HB, Song XN, Yan CQ, Wang GR, Pu LL, Wang ZR, Wang XX, Chen ZL, and Liu WL
Subjects: Animals, Rats, Resveratrol, Hypoxia, Oxygen, Hypertrophy, Superoxide Dismutase, Antioxidants, Altitude Sickness
Abstract: Objective: To study the protective effects of resveratrol (RSV) on cardiac function in rats with high altitude hypobaric hypoxia and its mechanisms. Methods: Thirty-six rats were randomly divided into control group, hypobaric hypoxia group (HH) and hypobaric hypoxia + RSV group (HH+RSV) according to the random number, 12 rats in each group. Rats in the HH and HH+RSV groups were subjected to chronic long-term high altitude hypobaric hypoxia intervention for 8 weeks in a hypobaric chamber at a simulated altitude of 6 000 m for 20 h / d. The rats of HH + RSV were fed with RSV at a dose of 400 mg/(kg·d). The rats were tested once a week for body weight and twice a week for food intake. Before execution, the rats were tested by blood cell analyzer for routine blood parameters and echocardiogram for cardiac function parameters in each group. The routine blood indexes of each group were measured by blood cell analyzer, the cardiac function indexes of each group were measured by echocardiography, myocardial hypertrophy was evaluated by HE staining, myocardial tissue reactive oxygen levels were evaluated by dihydroethidium (DHE) staining. Oxidative stress was evaluated by serum and myocardial tissue total antioxidant capacity (T-AOC), superoxide dismutase activity (SOD) and malondialdehyde (MDA) content. Results: Compared with the C group, the body mass and food intake of rats were decreased significantly ( P ＜0.05) in HH group, while compared with the C group, RSV had no significant effects on the body mass and food intake of rats in the HH+RSV group ( P ＞0.05). Compared with the C group, the levels of erythrocytes and hemoglobin of rats in the HH group were increased significantly ( P ＜0.05), while the platelet concentration was decreased significantly( P ＜0.05); compared with the HH group, the erythrocyte and hemoglobin levels were decreased significantly ( P ＜0.05) and platelet concentration was increased significantly( P ＜0.05) in rats of the HH+RSV group. Compared with the C group, the cardiac coefficient, myocardial fiber diameter and thickness were significantly increased in the HH group ( P ＜0.05); compared with the HH group, the cardiac coefficient and myocardial fiber thickness were significantly decreased in the HH+RSV group ( P ＜0.05). Echocardiographic analysis showed a significant increase in ventricular wall thickness ( P ＜0.05) and a significant decrease in ejection fraction and cardiac output ( P ＜0.05) in the HH group compared with the C group, and a significant decrease in ventricular wall thickness and a significant improvement in cardiac function ( P ＜0.05) in the HH+RSV group compared with the HH group. The results of DHE staining showed that myocardial tissue reactive oxygen levels were increased significantly in the HH group compared with the C group ( P ＜0.05); myocardial tissue reactive oxygen levels were significantly restored in the HH+RSV group compared with the HH group ( P ＜0.05). The oxidative/antioxidant results showed that the serum and myocardial T-AOC and SOD activities were decreased significantly ( P ＜0.05) and the MDA level was increased significantly ( P ＜0.05) in the HH group compared with the C group; the serum and myocardial T-AOC and SOD activities were increased significantly ( P ＜0.05) and the MDA level was decreased significantly( P ＜0.05) in the HH+RSV group compared with the HH group. Conclusion: Long-term plateau hypobaric hypoxia exposure leads to myocardial hypertrophy and reduced cardiac function in rats. Resveratrol intervention significantly improves myocardial hypertrophy and cardiac function in rats caused by altitude hypobaric hypoxia exposure, which is closely related to reducing of reactive oxygen species and improving myocardial oxidative stress levels.
Published: 2022
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23. [Construction and evaluation of a gradient stress model of PC12 cells induced by corticosterone].

Author: Li MZ, Xu LF, Chen ZL, Wang XX, Pu LL, Liu WL, and Wang TH
Subjects: Animals, Cell Survival, PC12 Cells, Rats, Superoxide Dismutase, Corticosterone pharmacology, NAD pharmacology
Abstract: Objective: A gradient stress model of PC12 cells induced by corticosterone was established to provide a basis for the evaluation and regulation of cell stress. Methods: The effect of corticosterone on cell viability was observed by measuring PC12 cell viability at different concentrations of corticosterone (0~1 000 μmol/L) after different intervention times (8~48 h) to screen the cell models for optimal intervention conditions. Key stress indicators (MDA, SOD, NADH, LDH) were measured spectrophotometrically and microscopically to evaluate the models. Results: When the concentration of corticosterone was below 200 μmol/L and the intervention time was 12 h, the cell viability was below half inactivation rate, which could reduce the confounding factors due to the decrease of cell viability in each group. Compared with the blank control group, corticosterone increased the levels of MDA, NADH and LDH,and decreased the levels of SOD in the model group in a concentration-dependent manner ( P ＜0.01), which was consistent with the construction of the gradient stress model. Conclusion: A gradient stress injury model of PC12 cells was successfully established, with intervention concentrations of 0 μmol/L, 25 μmol/L, 50 μmol/L, 100 μmol/L, 150 μmol/L and 200 μmol/L corticosterone at an intervention time of 12 h. The degree of stress injury of the cell model was increased gradually, which could be used as a basis and object for conducting cell stress injury assessment and regulation experiments.
Published: 2022
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24. [Effects of MAPKs inhibitors on GSH metabolic enzymes in rat hepatocytes].

Author: Gao WN, Pu LL, Wei JY, Xin ZH, Wang YW, Shi TL, Li T, and Guo CJ
Subjects: Animals, Cells, Cultured, Hepatocytes drug effects, Rats, Enzyme Inhibitors pharmacology, Glutathione metabolism, Hepatocytes enzymology, JNK Mitogen-Activated Protein Kinases antagonists & inhibitors, Mitogen-Activated Protein Kinases antagonists & inhibitors
Abstract: Objective: To investigate the effects of mitogen-activated protein kinases (MAPKs) inhibitors on glutathione (GSH) metabolism, and to explore the pathway related to GSH metabolism., Methods: BRL rat hepatocytes were treated by c-Jun NH2-terminal kinase (JNK),p38, and extracellular signal-regulated kinase 1/2 (ERK1/2) inhibitors:SP600125, SB203580 and PD98659, respectively, for 24 h. MTT method was used to measure hepatocytes viability. The content of GSH was determined by high performance liquid chromatography. The protein expressions of JNK and phosphorylated JNK (p-JNK) was tested by Luminex method. Activities of GSH metabolic enzymes were detected by commercial kits., Results: Hepatocytes vitality was inhibited when the concentrations of SP600125, SB203580 and PD98659 were higher than 10 μ mol/L, 20 μ mol/L, and 40 μ mol/L, respectively; SP600125 decreased the content of GSH in hepatocytes, while SB203580 and PD98659 had no effect. SP600125 reduced p-JNK protein expression, and enhanced GSH-Px activity significantly., Conclusions: JNK MAPK pathway takes part in the GSH metabolism in hepatocytes.
Published: 2017
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25. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

Author: Kanost MR, Arrese EL, Cao X, Chen YR, Chellapilla S, Goldsmith MR, Grosse-Wilde E, Heckel DG, Herndon N, Jiang H, Papanicolaou A, Qu J, Soulages JL, Vogel H, Walters J, Waterhouse RM, Ahn SJ, Almeida FC, An C, Aqrawi P, Bretschneider A, Bryant WB, Bucks S, Chao H, Chevignon G, Christen JM, Clarke DF, Dittmer NT, Ferguson LCF, Garavelou S, Gordon KHJ, Gunaratna RT, Han Y, Hauser F, He Y, Heidel-Fischer H, Hirsh A, Hu Y, Jiang H, Kalra D, Klinner C, König C, Kovar C, Kroll AR, Kuwar SS, Lee SL, Lehman R, Li K, Li Z, Liang H, Lovelace S, Lu Z, Mansfield JH, McCulloch KJ, Mathew T, Morton B, Muzny DM, Neunemann D, Ongeri F, Pauchet Y, Pu LL, Pyrousis I, Rao XJ, Redding A, Roesel C, Sanchez-Gracia A, Schaack S, Shukla A, Tetreau G, Wang Y, Xiong GH, Traut W, Walsh TK, Worley KC, Wu D, Wu W, Wu YQ, Zhang X, Zou Z, Zucker H, Briscoe AD, Burmester T, Clem RJ, Feyereisen R, Grimmelikhuijzen CJP, Hamodrakas SJ, Hansson BS, Huguet E, Jermiin LS, Lan Q, Lehman HK, Lorenzen M, Merzendorfer H, Michalopoulos I, Morton DB, Muthukrishnan S, Oakeshott JG, Palmer W, Park Y, Passarelli AL, Rozas J, Schwartz LM, Smith W, Southgate A, Vilcinskas A, Vogt R, Wang P, Werren J, Yu XQ, Zhou JJ, Brown SJ, Scherer SE, Richards S, and Blissard GW
Subjects: Animals, Gene Expression Profiling, Larva genetics, Larva growth & development, Manduca growth & development, Pupa genetics, Pupa growth & development, Sequence Analysis, DNA, Synteny, Gene Expression, Genome, Insect, Manduca genetics
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., (Copyright © 2016 Elsevier Ltd. All rights reserved.)
Published: 2016
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26. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Author: Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, and Gibbs RA
Subjects: Animals, Arthropods parasitology, DNA Methylation, DNA Transposable Elements, Female, Gene Transfer, Horizontal, Genes, Insect, Genetic Speciation, Genetic Variation, Host-Parasite Interactions, Insect Proteins genetics, Insect Proteins metabolism, Insect Viruses genetics, Insecta genetics, Male, Molecular Sequence Data, Quantitative Trait Loci, Recombination, Genetic, Sequence Analysis, DNA, Wasp Venoms chemistry, Wasp Venoms toxicity, Wasps physiology, Wolbachia genetics, Biological Evolution, Genome, Insect, Wasps genetics
Abstract: We report here genome sequences and comparative analyses of three closely related parasitoid wasps: Nasonia vitripennis, N. giraulti, and N. longicornis. Parasitoids are important regulators of arthropod populations, including major agricultural pests and disease vectors, and Nasonia is an emerging genetic model, particularly for evolutionary and developmental genetics. Key findings include the identification of a functional DNA methylation tool kit; hymenopteran-specific genes including diverse venoms; lateral gene transfers among Pox viruses, Wolbachia, and Nasonia; and the rapid evolution of genes involved in nuclear-mitochondrial interactions that are implicated in speciation. Newly developed genome resources advance Nasonia for genetic research, accelerate mapping and cloning of quantitative trait loci, and will ultimately provide tools and knowledge for further increasing the utility of parasitoids as pest insect-control agents.
Published: 2010
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26 results on '"Pu, Ling-Ling"'

1. Isoquercitrin attenuates the osteoclast-mediated bone loss in rheumatoid arthritis via the Nrf2/ROS/NF-κB pathway

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

3. Isoquercitrin attenuates the osteoclast-mediated bone loss in rheumatoid arthritis via the Nrf2/ROS/NF-κB pathway

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

5. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

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

7. The Drosophila melanogaster Genetic Reference Panel.

8. Insights into social insects from the genome of the honeybee Apis mellifera

9. The finished DNA sequence of human chromosome 12

10. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

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

12. The genomes of two key bumblebee species with primitive eusocial organization

13. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

14. The genomes of two key bumblebee species with primitive eusocial organization

15. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

16. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

17. Genome Sequence of the Pea Aphid Acyrthosiphon pisum

18. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

19. The genome of the sea urchin Strongylocentrotus purpuratus

20. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

21. The Genome of the Sea Urchin Strongylocentrotus purpuratus

22. [Resveratrol attenuates cardiac function impairment in plateau hypobaric hypoxia rats].

23. [Construction and evaluation of a gradient stress model of PC12 cells induced by corticosterone].

24. [Effects of MAPKs inhibitors on GSH metabolic enzymes in rat hepatocytes].

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

26. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

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26 results on '"Pu, Ling-Ling"'

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