%0 Journal Article %J Science %D 2010 %T Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. %A Werren, John H %A Richards, Stephen %A Desjardins, Christopher A %A Niehuis, Oliver %A Gadau, Jürgen %A Colbourne, John K %A Werren, John H %A Richards, Stephen %A Desjardins, Christopher A %A Niehuis, Oliver %A Gadau, Jürgen %A Colbourne, John K %A Beukeboom, Leo W %A Desplan, Claude %A Elsik, Christine G %A Grimmelikhuijzen, Cornelis J P %A Kitts, Paul %A Lynch, Jeremy A %A Murphy, Terence %A Oliveira, Deodoro C S G %A Smith, Christopher D %A van de Zande, Louis %A Worley, Kim C %A Zdobnov, Evgeny M %A Aerts, Maarten %A Albert, Stefan %A Anaya, Victor H %A Anzola, Juan M %A Barchuk, Angel R %A Behura, Susanta K %A Bera, Agata N %A Berenbaum, May R %A Bertossa, Rinaldo C %A Bitondi, Márcia M G %A Bordenstein, Seth R %A Bork, Peer %A Bornberg-Bauer, Erich %A Brunain, Marleen %A Cazzamali, Giuseppe %A Chaboub, Lesley %A Chacko, Joseph %A Chavez, Dean %A Childers, Christopher P %A Choi, Jeong-Hyeon %A Clark, Michael E %A Claudianos, Charles %A Clinton, Rochelle A %A Cree, Andrew G %A Cristino, Alexandre S %A Dang, Phat M %A Darby, Alistair C %A de Graaf, Dirk C %A Devreese, Bart %A Dinh, Huyen H %A Edwards, Rachel %A Elango, Navin %A Elhaik, Eran %A Ermolaeva, Olga %A Evans, Jay D %A Forêt, Sylvain %A Fowler, Gerald R %A Gerlach, Daniel %A Gibson, Joshua D %A Gilbert, Donald G %A Graur, Dan %A Gründer, Stefan %A Hagen, Darren E %A Han, Yi %A Hauser, Frank %A Hultmark, Da %A Hunter, Henry C %A Hurst, Gregory D D %A Jhangian, Shalini N %A Jiang, Huaiyang %A Johnson, Reed M %A Jones, Andrew K %A Junier, Thomas %A Kadowaki, Tatsuhiko %A Kamping, Albert %A Kapustin, Yuri %A Kechavarzi, Bobak %A Kim, Jaebum %A Kim, Jay %A Kiryutin, Boris %A Koevoets, Tosca %A Kovar, Christie L %A Kriventseva, Evgenia V %A Kucharski, Robert %A Lee, Heewook %A Lee, Sandra L %A Lees, Kristin %A Lewis, Lora R %A Loehlin, David W %A Logsdon, John M %A Lopez, Jacqueline A %A Lozado, Ryan J %A Maglott, Donna %A Maleszka, Ryszard %A Mayampurath, Anoop %A Mazur, Danielle J %A McClure, Marcella A %A Moore, Andrew D %A Morgan, Margaret B %A Muller, Jean %A Munoz-Torres, Monica C %A Muzny, Donna M %A Nazareth, Lynne V %A Neupert, Susanne %A Nguyen, Ngoc B %A Nunes, Francis M F %A Oakeshott, John G %A Okwuonu, Geoffrey O %A Pannebakker, Bart A %A Pejaver, Vikas R %A Peng, Zuogang %A Pratt, Stephen C %A Predel, Reinhard %A Pu, Ling-Ling %A Ranson, Hilary %A Raychoudhury, Rhitoban %A Rechtsteiner, Andreas %A Reese, Justin T %A Reid, Jeffrey G %A Riddle, Megan %A Robertson, Hugh M %A Romero-Severson, Jeanne %A Rosenberg, Miriam %A Sackton, Timothy B %A Sattelle, David B %A Schlüns, Helge %A Schmitt, Thomas %A Schneider, Martina %A Schüler, Andreas %A Schurko, Andrew M %A Shuker, David M %A Simões, Zilá L P %A Sinha, Saurabh %A Smith, Zachary %A Solovyev, Victor %A Souvorov, Alexandre %A Springauf, Andreas %A Stafflinger, Elisabeth %A Stage, Deborah E %A Stanke, Mario %A Tanaka, Yoshiaki %A Telschow, Arndt %A Trent, Carol %A Vattathil, Selina %A Verhulst, Eveline C %A Viljakainen, Lumi %A Wanner, Kevin W %A Waterhouse, Robert M %A Whitfield, James B %A Wilkes, Timothy E %A Williamson, Michael %A Willis, Judith H %A Wolschin, Florian %A Wyder, Stefan %A Yamada, Takuji %A Yi, Soojin V %A Zecher, Courtney N %A Zhang, Lan %A Gibbs, Richard A %K Animals %K Arthropods %K Biological Evolution %K DNA Methylation %K DNA Transposable Elements %K Female %K Gene Transfer, Horizontal %K Genes, Insect %K Genetic Speciation %K Genetic Variation %K Genome, Insect %K Host-Parasite Interactions %K Insect Proteins %K Insect Viruses %K Insecta %K Male %K Molecular Sequence Data %K Quantitative Trait Loci %K Recombination, Genetic %K Sequence Analysis, DNA %K Wasp Venoms %K Wasps %K Wolbachia %X

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.

%B Science %V 327 %P 343-8 %8 2010 Jan 15 %G eng %N 5963 %1 https://www.ncbi.nlm.nih.gov/pubmed/20075255?dopt=Abstract %R 10.1126/science.1178028 %0 Journal Article %J Science %D 2009 %T The genome sequence of taurine cattle: a window to ruminant biology and evolution. %A Elsik, Christine G %A Tellam, Ross L %A Worley, Kim C %A Gibbs, Richard A %A Muzny, Donna M %A Weinstock, George M %A Adelson, David L %A Eichler, Evan E %A Elnitski, Laura %A Guigó, Roderic %A Hamernik, Debora L %A Kappes, Steve M %A Lewin, Harris A %A Lynn, David J %A Nicholas, Frank W %A Reymond, Alexandre %A Rijnkels, Monique %A Skow, Loren C %A Zdobnov, Evgeny M %A Schook, Lawrence %A Womack, James %A Alioto, Tyler %A Antonarakis, Stylianos E %A Astashyn, Alex %A Chapple, Charles E %A Chen, Hsiu-Chuan %A Chrast, Jacqueline %A Camara, Francisco %A Ermolaeva, Olga %A Henrichsen, Charlotte N %A Hlavina, Wratko %A Kapustin, Yuri %A Kiryutin, Boris %A Kitts, Paul %A Kokocinski, Felix %A Landrum, Melissa %A Maglott, Donna %A Pruitt, Kim %A Sapojnikov, Victor %A Searle, Stephen M %A Solovyev, Victor %A Souvorov, Alexandre %A Ucla, Catherine %A Wyss, Carine %A Anzola, Juan M %A Gerlach, Daniel %A Elhaik, Eran %A Graur, Dan %A Reese, Justin T %A Edgar, Robert C %A McEwan, John C %A Payne, Gemma M %A Raison, Joy M %A Junier, Thomas %A Kriventseva, Evgenia V %A Eyras, Eduardo %A Plass, Mireya %A Donthu, Ravikiran %A Larkin, Denis M %A Reecy, James %A Yang, Mary Q %A Chen, Lin %A Cheng, Ze %A Chitko-McKown, Carol G %A Liu, George E %A Matukumalli, Lakshmi K %A Song, Jiuzhou %A Zhu, Bin %A Bradley, Daniel G %A Brinkman, Fiona S L %A Lau, Lilian P L %A Whiteside, Matthew D %A Walker, Angela %A Wheeler, Thomas T %A Casey, Theresa %A German, J Bruce %A Lemay, Danielle G %A Maqbool, Nauman J %A Molenaar, Adrian J %A Seo, Seongwon %A Stothard, Paul %A Baldwin, Cynthia L %A Baxter, Rebecca %A Brinkmeyer-Langford, Candice L %A Brown, Wendy C %A Childers, Christopher P %A Connelley, Timothy %A Ellis, Shirley A %A Fritz, Krista %A Glass, Elizabeth J %A Herzig, Carolyn T A %A Iivanainen, Antti %A Lahmers, Kevin K %A Bennett, Anna K %A Dickens, C Michael %A Gilbert, James G R %A Hagen, Darren E %A Salih, Hanni %A Aerts, Jan %A Caetano, Alexandre R %A Dalrymple, Brian %A Garcia, Jose Fernando %A Gill, Clare A %A Hiendleder, Stefan G %A Memili, Erdogan %A Spurlock, Diane %A Williams, John L %A Alexander, Lee %A Brownstein, Michael J %A Guan, Leluo %A Holt, Robert A %A Jones, Steven J M %A Marra, Marco A %A Moore, Richard %A Moore, Stephen S %A Roberts, Andy %A Taniguchi, Masaaki %A Waterman, Richard C %A Chacko, Joseph %A Chandrabose, Mimi M %A Cree, Andy %A Dao, Marvin Diep %A Dinh, Huyen H %A Gabisi, Ramatu Ayiesha %A Hines, Sandra %A Hume, Jennifer %A Jhangiani, Shalini N %A Joshi, Vandita %A Kovar, Christie L %A Lewis, Lora R %A Liu, Yih-Shin %A Lopez, John %A Morgan, Margaret B %A Nguyen, Ngoc Bich %A Okwuonu, Geoffrey O %A Ruiz, San Juana %A Santibanez, Jireh %A Wright, Rita A %A Buhay, Christian %A Ding, Yan %A Dugan-Rocha, Shannon %A Herdandez, Judith %A Holder, Michael %A Sabo, Aniko %A Egan, Amy %A Goodell, Jason %A Wilczek-Boney, Katarzyna %A Fowler, Gerald R %A Hitchens, Matthew Edward %A Lozado, Ryan J %A Moen, Charles %A Steffen, David %A Warren, James T %A Zhang, Jingkun %A Chiu, Readman %A Schein, Jacqueline E %A Durbin, K James %A Havlak, Paul %A Jiang, Huaiyang %A Liu, Yue %A Qin, Xiang %A Ren, Yanru %A Shen, Yufeng %A Song, Henry %A Bell, Stephanie Nicole %A Davis, Clay %A Johnson, Angela Jolivet %A Lee, Sandra %A Nazareth, Lynne V %A Patel, Bella Mayurkumar %A Pu, Ling-Ling %A Vattathil, Selina %A Williams, Rex Lee %A Curry, Stacey %A Hamilton, Cerissa %A Sodergren, Erica %A Wheeler, David A %A Barris, Wes %A Bennett, Gary L %A Eggen, André %A Green, Ronnie D %A Harhay, Gregory P %A Hobbs, Matthew %A Jann, Oliver %A Keele, John W %A Kent, Matthew P %A Lien, Sigbjørn %A McKay, Stephanie D %A McWilliam, Sean %A Ratnakumar, Abhirami %A Schnabel, Robert D %A Smith, Timothy %A Snelling, Warren M %A Sonstegard, Tad S %A Stone, Roger T %A Sugimoto, Yoshikazu %A Takasuga, Akiko %A Taylor, Jeremy F %A Van Tassell, Curtis P %A Macneil, Michael D %A Abatepaulo, Antonio R R %A Abbey, Colette A %A Ahola, Virpi %A Almeida, Iassudara G %A Amadio, Ariel F %A Anatriello, Elen %A Bahadue, Suria M %A Biase, Fernando H %A Boldt, Clayton R %A Carroll, Jeffery A %A Carvalho, Wanessa A %A Cervelatti, Eliane P %A Chacko, Elsa %A Chapin, Jennifer E %A Cheng, Ye %A Choi, Jungwoo %A Colley, Adam J %A de Campos, Tatiana A %A De Donato, Marcos %A Santos, Isabel K F de Miranda %A de Oliveira, Carlo J F %A Deobald, Heather %A Devinoy, Eve %A Donohue, Kaitlin E %A Dovc, Peter %A Eberlein, Annett %A Fitzsimmons, Carolyn J %A Franzin, Alessandra M %A Garcia, Gustavo R %A Genini, Sem %A Gladney, Cody J %A Grant, Jason R %A Greaser, Marion L %A Green, Jonathan A %A Hadsell, Darryl L %A Hakimov, Hatam A %A Halgren, Rob %A Harrow, Jennifer L %A Hart, Elizabeth A %A Hastings, Nicola %A Hernandez, Marta %A Hu, Zhi-Liang %A Ingham, Aaron %A Iso-Touru, Terhi %A Jamis, Catherine %A Jensen, Kirsty %A Kapetis, Dimos %A Kerr, Tovah %A Khalil, Sari S %A Khatib, Hasan %A Kolbehdari, Davood %A Kumar, Charu G %A Kumar, Dinesh %A Leach, Richard %A Lee, Justin C-M %A Li, Changxi %A Logan, Krystin M %A Malinverni, Roberto %A Marques, Elisa %A Martin, William F %A Martins, Natalia F %A Maruyama, Sandra R %A Mazza, Raffaele %A McLean, Kim L %A Medrano, Juan F %A Moreno, Barbara T %A Moré, Daniela D %A Muntean, Carl T %A Nandakumar, Hari P %A Nogueira, Marcelo F G %A Olsaker, Ingrid %A Pant, Sameer D %A Panzitta, Francesca %A Pastor, Rosemeire C P %A Poli, Mario A %A Poslusny, Nathan %A Rachagani, Satyanarayana %A Ranganathan, Shoba %A Razpet, Andrej %A Riggs, Penny K %A Rincon, Gonzalo %A Rodriguez-Osorio, Nelida %A Rodriguez-Zas, Sandra L %A Romero, Natasha E %A Rosenwald, Anne %A Sando, Lillian %A Schmutz, Sheila M %A Shen, Libing %A Sherman, Laura %A Southey, Bruce R %A Lutzow, Ylva Strandberg %A Sweedler, Jonathan V %A Tammen, Imke %A Telugu, Bhanu Prakash V L %A Urbanski, Jennifer M %A Utsunomiya, Yuri T %A Verschoor, Chris P %A Waardenberg, Ashley J %A Wang, Zhiquan %A Ward, Robert %A Weikard, Rosemarie %A Welsh, Thomas H %A White, Stephen N %A Wilming, Laurens G %A Wunderlich, Kris R %A Yang, Jianqi %A Zhao, Feng-Qi %K Alternative Splicing %K Animals %K Animals, Domestic %K Biological Evolution %K Cattle %K Evolution, Molecular %K Female %K Genetic Variation %K Genome %K Humans %K Male %K MicroRNAs %K Molecular Sequence Data %K Proteins %K Sequence Analysis, DNA %K Species Specificity %K Synteny %X

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

%B Science %V 324 %P 522-8 %8 2009 Apr 24 %G eng %N 5926 %1 https://www.ncbi.nlm.nih.gov/pubmed/19390049?dopt=Abstract %R 10.1126/science.1169588 %0 Journal Article %J Nature %D 2008 %T The genome of the model beetle and pest Tribolium castaneum. %A Stephen Richards %A Richard A Gibbs %A Weinstock, George M %A Brown, Susan J %A Denell, Robin %A Beeman, Richard W %A Richard A Gibbs %A Beeman, Richard W %A Brown, Susan J %A Bucher, Gregor %A Friedrich, Markus %A Grimmelikhuijzen, Cornelis J P %A Klingler, Martin %A Lorenzen, Marce %A Stephen Richards %A Roth, Siegfried %A Schröder, Reinhard %A Tautz, Diethard %A Zdobnov, Evgeny M %A Donna M Muzny %A Richard A Gibbs %A Weinstock, George M %A Attaway, Tony %A Bell, Stephanie %A Buhay, Christian J %A Chandrabose, Mimi N %A Chavez, Dean %A Clerk-Blankenburg, Kerstin P %A Cree, Andrew %A Dao, Marvin %A Davis, Clay %A Chacko, Joseph %A Dinh, Huyen %A Dugan-Rocha, Shannon %A Fowler, Gerald %A Garner, Toni T %A Garnes, Jeffrey %A Gnirke, Andreas %A Hawes, Alica %A Hernandez, Judith %A Hines, Sandra %A Holder, Michael %A Hume, Jennifer %A Jhangiani, Shalini N %A Joshi, Vandita %A Ziad Khan %A Jackson, Laronda %A Kovar, Christie %A Kowis, Andrea %A Lee, Sandra %A Lewis, Lora R %A Margolis, Jon %A Morgan, Margaret %A Nazareth, Lynne V %A Nguyen, Ngoc %A Okwuonu, Geoffrey %A Parker, David %A Stephen Richards %A Ruiz, San-Juana %A Santibanez, Jireh %A Savard, Joël %A Steven E Scherer %A Schneider, Brian %A Sodergren, Erica %A Tautz, Diethard %A Vattahil, Selina %A Villasana, Donna %A White, Courtney S %A Wright, Rita %A Park, Yoonseong %A Beeman, Richard W %A Lord, Jeff %A Oppert, Brenda %A Lorenzen, Marce %A Brown, Susan %A Wang, Liangjiang %A Savard, Joël %A Tautz, Diethard %A Stephen Richards %A Weinstock, George %A Richard A Gibbs %A Liu, Yue %A Kim C Worley %A Weinstock, George %A Elsik, Christine G %A Reese, Justin T %A Elhaik, Eran %A Landan, Giddy %A Graur, Dan %A Arensburger, Peter %A Atkinson, Peter %A Beeman, Richard W %A Beidler, Jim %A Brown, Susan J %A Demuth, Jeffery P %A Drury, Douglas W %A Du, Yu-Zhou %A Fujiwara, Haruhiko %A Lorenzen, Marce %A Maselli, Vincenza %A Osanai, Mizuko %A Park, Yoonseong %A Robertson, Hugh M %A Tu, Zhijian %A Wang, Jian-jun %A Wang, Suzhi %A Stephen Richards %A Song, Henry %A Zhang, Lan %A Sodergren, Erica %A Werner, Doreen %A Stanke, Mario %A Morgenstern, Burkhard %A Solovyev, Victor %A Kosarev, Peter %A Brown, Garth %A Chen, Hsiu-Chuan %A Ermolaeva, Olga %A Hlavina, Wratko %A Kapustin, Yuri %A Kiryutin, Boris %A Kitts, Paul %A Maglott, Donna %A Pruitt, Kim %A Sapojnikov, Victor %A Souvorov, Alexandre %A Mackey, Aaron J %A Waterhouse, Robert M %A Wyder, Stefan %A Zdobnov, Evgeny M %A Zdobnov, Evgeny M %A Wyder, Stefan %A Kriventseva, Evgenia V %A Kadowaki, Tatsuhiko %A Bork, Peer %A Aranda, Manuel %A Bao, Riyue %A Beermann, Anke %A Berns, Nicola %A Bolognesi, Renata %A Bonneton, François %A Bopp, Daniel %A Brown, Susan J %A Bucher, Gregor %A Butts, Thomas %A Chaumot, Arnaud %A Denell, Robin E %A Ferrier, David E K %A Friedrich, Markus %A Gordon, Cassondra M %A Jindra, Marek %A Klingler, Martin %A Lan, Que %A Lattorff, H Michael G %A Laudet, Vincent %A von Levetsow, Cornelia %A Liu, Zhenyi %A Lutz, Rebekka %A Lynch, Jeremy A %A da Fonseca, Rodrigo Nunes %A Posnien, Nico %A Reuter, Rolf %A Roth, Siegfried %A Savard, Joël %A Schinko, Johannes B %A Schmitt, Christian %A Schoppmeier, Michael %A Schröder, Reinhard %A Shippy, Teresa D %A Simonnet, Franck %A Marques-Souza, Henrique %A Tautz, Diethard %A Tomoyasu, Yoshinori %A Trauner, Jochen %A Van der Zee, Maurijn %A Vervoort, Michel %A Wittkopp, Nadine %A Wimmer, Ernst A %A Yang, Xiaoyun %A Jones, Andrew K %A Sattelle, David B %A Ebert, Paul R %A Nelson, David %A Scott, Jeffrey G %A Beeman, Richard W %A Muthukrishnan, Subbaratnam %A Kramer, Karl J %A Arakane, Yasuyuki %A Beeman, Richard W %A Zhu, Qingsong %A Hogenkamp, David %A Dixit, Radhika %A Oppert, Brenda %A Jiang, Haobo %A Zou, Zhen %A Marshall, Jeremy %A Elpidina, Elena %A Vinokurov, Konstantin %A Oppert, Cris %A Zou, Zhen %A Evans, Jay %A Lu, Zhiqiang %A Zhao, Picheng %A Sumathipala, Niranji %A Altincicek, Boran %A Vilcinskas, Andreas %A Williams, Michael %A Hultmark, Dan %A Hetru, Charles %A Jiang, Haobo %A Grimmelikhuijzen, Cornelis J P %A Hauser, Frank %A Cazzamali, Giuseppe %A Williamson, Michael %A Park, Yoonseong %A Li, Bin %A Tanaka, Yoshiaki %A Predel, Reinhard %A Neupert, Susanne %A Schachtner, Joachim %A Verleyen, Peter %A Raible, Florian %A Bork, Peer %A Friedrich, Markus %A Walden, Kimberly K O %A Robertson, Hugh M %A Angeli, Sergio %A Forêt, Sylvain %A Bucher, Gregor %A Schuetz, Stefan %A Maleszka, Ryszard %A Wimmer, Ernst A %A Beeman, Richard W %A Lorenzen, Marce %A Tomoyasu, Yoshinori %A Miller, Sherry C %A Grossmann, Daniela %A Bucher, Gregor %K Animals %K Base Composition %K Body Patterning %K Cytochrome P-450 Enzyme System %K DNA Transposable Elements %K Genes, Insect %K Genome, Insect %K Growth and Development %K Humans %K Insecticides %K Neurotransmitter Agents %K Oogenesis %K Phylogeny %K Proteome %K Receptors, G-Protein-Coupled %K Receptors, Odorant %K Repetitive Sequences, Nucleic Acid %K RNA Interference %K Taste %K Telomere %K Tribolium %K Vision, Ocular %X

Tribolium castaneum is a member of the most species-rich eukaryotic order, a powerful model organism for the study of generalized insect development, and an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved the ability to interact with a diverse chemical environment, as shown by large expansions in odorant and gustatory receptors, as well as P450 and other detoxification enzymes. Development in Tribolium is more representative of other insects than is Drosophila, a fact reflected in gene content and function. For example, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, some being expressed in the growth zone crucial for axial elongation in short-germ development. Systemic RNA interference in T. castaneum functions differently from that in Caenorhabditis elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

%B Nature %V 452 %P 949-55 %8 2008 Apr 24 %G eng %N 7190 %1 https://www.ncbi.nlm.nih.gov/pubmed/18362917?dopt=Abstract %R 10.1038/nature06784 %0 Journal Article %J Genome Res %D 2006 %T Community annotation: procedures, protocols, and supporting tools. %A Elsik, Christine G %A Worley, Kim C %A Zhang, Lan %A Milshina, Natalia V %A Jiang, Huaiyang %A Reese, Justin T %A Childs, Kevin L %A Venkatraman, Anand %A Dickens, C Michael %A Weinstock, George M %A Richard A Gibbs %K Animals %K Bees %K Databases, Genetic %K Genome, Human %K Genomics %K Humans %K Models, Genetic %K Molecular Sequence Data %K Sequence Analysis %X

Investigators at the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) and BeeBase organized a community-wide effort to manually annotate the honey bee (Apis mellifera) genome. Although various strategies for manual annotation have been used in the past, the value of dispersed community annotation has not yet been demonstrated. Here we make a case for the merit of dispersed community annotation. We present annotation procedures, standard protocols, and tools used for sequence analysis, data submission, and data management. We also report lessons learned from this dispersed community annotation effort for a metazoan genome.

%B Genome Res %V 16 %P 1329-33 %8 2006 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/17065605?dopt=Abstract %R 10.1101/gr.5580606 %0 Journal Article %J Science %D 2006 %T The genome of the sea urchin Strongylocentrotus purpuratus. %A Sodergren, Erica %A Weinstock, George M %A Davidson, Eric H %A Cameron, R Andrew %A Gibbs, Richard A %A Angerer, Robert C %A Angerer, Lynne M %A Arnone, Maria Ina %A Burgess, David R %A Burke, Robert D %A Coffman, James A %A Dean, Michael %A Elphick, Maurice R %A Ettensohn, Charles A %A Foltz, Kathy R %A Hamdoun, Amro %A Hynes, Richard O %A Klein, William H %A Marzluff, William %A McClay, David R %A Morris, Robert L %A Mushegian, Arcady %A Rast, Jonathan P %A Smith, L Courtney %A Thorndyke, Michael C %A Vacquier, Victor D %A Wessel, Gary M %A Wray, Greg %A Zhang, Lan %A Elsik, Christine G %A Ermolaeva, Olga %A Hlavina, Wratko %A Hofmann, Gretchen %A Kitts, Paul %A Landrum, Melissa J %A Mackey, Aaron J %A Maglott, Donna %A Panopoulou, Georgia %A Poustka, Albert J %A Pruitt, Kim %A Sapojnikov, Victor %A Song, Xingzhi %A Souvorov, Alexandre %A Solovyev, Victor %A Wei, Zheng %A Whittaker, Charles A %A Worley, Kim %A Durbin, K James %A Shen, Yufeng %A Fedrigo, Olivier %A Garfield, David %A Haygood, Ralph %A Primus, Alexander %A Satija, Rahul %A Severson, Tonya %A Gonzalez-Garay, Manuel L %A Jackson, Andrew R %A Milosavljevic, Aleksandar %A Tong, Mark %A Killian, Christopher E %A Livingston, Brian T %A Wilt, Fred H %A Adams, Nikki %A Bellé, Robert %A Carbonneau, Seth %A Cheung, Rocky %A Cormier, Patrick %A Cosson, Bertrand %A Croce, Jenifer %A Fernandez-Guerra, Antonio %A Genevière, Anne-Marie %A Goel, Manisha %A Kelkar, Hemant %A Morales, Julia %A Mulner-Lorillon, Odile %A Robertson, Anthony J %A Goldstone, Jared V %A Cole, Bryan %A Epel, David %A Gold, Bert %A Hahn, Mark E %A Howard-Ashby, Meredith %A Scally, Mark %A Stegeman, John J %A Allgood, Erin L %A Cool, Jonah %A Judkins, Kyle M %A McCafferty, Shawn S %A Musante, Ashlan M %A Obar, Robert A %A Rawson, Amanda P %A Rossetti, Blair J %A Gibbons, Ian R %A Hoffman, Matthew P %A Leone, Andrew %A Istrail, Sorin %A Materna, Stefan C %A Samanta, Manoj P %A Stolc, Viktor %A Tongprasit, Waraporn %A Tu, Qiang %A Bergeron, Karl-Frederik %A Brandhorst, Bruce P %A Whittle, James %A Berney, Kevin %A Bottjer, David J %A Calestani, Cristina %A Peterson, Kevin %A Chow, Elly %A Yuan, Qiu Autumn %A Elhaik, Eran %A Graur, Dan %A Reese, Justin T %A Bosdet, Ian %A Heesun, Shin %A Marra, Marco A %A Schein, Jacqueline %A Anderson, Michele K %A Brockton, Virginia %A Buckley, Katherine M %A Cohen, Avis H %A Fugmann, Sebastian D %A Hibino, Taku %A Loza-Coll, Mariano %A Majeske, Audrey J %A Messier, Cynthia %A Nair, Sham V %A Pancer, Zeev %A Terwilliger, David P %A Agca, Cavit %A Arboleda, Enrique %A Chen, Nansheng %A Churcher, Allison M %A Hallböök, F %A Humphrey, Glen W %A Idris, Mohammed M %A Kiyama, Takae %A Liang, Shuguang %A Mellott, Dan %A Mu, Xiuqian %A Murray, Greg %A Olinski, Robert P %A Raible, Florian %A Rowe, Matthew %A Taylor, John S %A Tessmar-Raible, Kristin %A Wang, D %A Wilson, Karen H %A Yaguchi, Shunsuke %A Gaasterland, Terry %A Galindo, Blanca E %A Gunaratne, Herath J %A Juliano, Celina %A Kinukawa, Masashi %A Moy, Gary W %A Neill, Anna T %A Nomura, Mamoru %A Raisch, Michael %A Reade, Anna %A Roux, Michelle M %A Song, Jia L %A Su, Yi-Hsien %A Townley, Ian K %A Voronina, Ekaterina %A Wong, Julian L %A Amore, Gabriele %A Branno, Margherita %A Brown, Euan R %A Cavalieri, Vincenzo %A Duboc, Véronique %A Duloquin, Louise %A Flytzanis, Constantin %A Gache, Christian %A Lapraz, François %A Lepage, Thierry %A Locascio, Annamaria %A Martinez, Pedro %A Matassi, Giorgio %A Matranga, Valeria %A Range, Ryan %A Rizzo, Francesca %A Röttinger, Eric %A Beane, Wendy %A Bradham, Cynthia %A Byrum, Christine %A Glenn, Tom %A Hussain, Sofia %A Manning, Gerard %A Miranda, Esther %A Thomason, Rebecca %A Walton, Katherine %A Wikramanayke, Athula %A Wu, Shu-Yu %A Xu, Ronghui %A Brown, C Titus %A Chen, Lili %A Gray, Rachel F %A Lee, Pei Yun %A Nam, Jongmin %A Oliveri, Paola %A Smith, Joel %A Muzny, Donna %A Bell, Stephanie %A Chacko, Joseph %A Cree, Andrew %A Curry, Stacey %A Davis, Clay %A Dinh, Huyen %A Dugan-Rocha, Shannon %A Fowler, Jerry %A Gill, Rachel %A Hamilton, Cerrissa %A Hernandez, Judith %A Hines, Sandra %A Hume, Jennifer %A Jackson, Laronda %A Jolivet, Angela %A Kovar, Christie %A Lee, Sandra %A Lewis, Lora %A Miner, George %A Morgan, Margaret %A Nazareth, Lynne V %A Okwuonu, Geoffrey %A Parker, David %A Pu, Ling-Ling %A Thorn, Rachel %A Wright, Rita %K Animals %K Calcification, Physiologic %K Cell Adhesion Molecules %K Complement Activation %K Computational Biology %K Embryonic Development %K Evolution, Molecular %K Gene Expression Regulation, Developmental %K Genes %K Genome %K Immunity, Innate %K Immunologic Factors %K Male %K Nervous System Physiological Phenomena %K Proteins %K Sequence Analysis, DNA %K Signal Transduction %K Strongylocentrotus purpuratus %K Transcription Factors %X

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.

%B Science %V 314 %P 941-52 %8 2006 Nov 10 %G eng %N 5801 %1 https://www.ncbi.nlm.nih.gov/pubmed/17095691?dopt=Abstract %R 10.1126/science.1133609