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1. Transcriptome analysis of the honey bee fungalpathogen, Ascosphaera apis: implications for hostpathogenesis

Author

Cornman, R, Bennett, Anna K, Murray, K, Evans, Jay D, Elsik, Christine G, and Aronstein, Kate

Abstract

AbstractBackgroundWe present a comprehensive transcriptome analysis of the fungus Ascosphaera apis, an economically important pathogen of the Western honey bee (Apis mellifera) that causes chalkbrood disease. Our goals were to further annotate the A. apis reference genome and to identify genes that are candidates for being differentially expressed during host infection versus axenic culture.ResultsWe compared A. apis transcriptome sequence from mycelia grown on liquid or solid media with that dissected from host-infected tissue. 454 pyrosequencing provided 252 Mb of filtered sequence reads from both culture types that were assembled into 10,087 contigs. Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. A phylogeny based on 12 of these protein-coding loci further supported the taxonomic placement of Ascosphaera as sister to the core Onygenales. Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. A novel gene family was identified that has expanded in some ascomycete lineages, but not others. We manually annotated genes with homologs in other fungal genomes that have known relevance to fungal virulence and life history. Functional categories of interest included genes involved in mating-type specification, intracellular signal transduction, and stress response. Computational and manual annotations have been made publicly available on the Bee Pests and Pathogens website.ConclusionsThis comprehensive transcriptome analysis substantially enhances our understanding of the A. apis genome and its expression during infection of honey bee larvae. It also provides resources for future molecular studies of chalkbrood disease and ultimately improved disease management.

Published
2012

2. Earthquake Effects on Employee Transportation

Author

Bennett, Anna K. and Little, David D.

Abstract

The Loma Prieta earthquake of October 17, 1989, had a disastrous impact on surface transportation in the Bay Area. The most tragic effect of the failures in the transportation system was the loss of life in the collapse of the Cypress structure on Interstate 880 in Oakland and of the section of the Bay Bridge. Less dramatic, but disrupting the daily routines of thousands of commuters, were the traffic delays and congestion that occurred in the month that the Bay Bridge and Highway 17 (between Santa Cruz and the South Bay area) were closed for repairs.

Published
1990

3. 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

4. “The Road We Travel”: Developing a co-produced narrative for a photovoice project

Author

Barry, Jennifer, Monahan, Christine, Monahan, Mark, Murphy, Rebecca, Ferguson, Sharon, Lee, Kelley, Bennett, Anna K., Gibbons, Patrick, Higgins, Agnes, Barry, Jennifer, Monahan, Christine, Monahan, Mark, Murphy, Rebecca, Ferguson, Sharon, Lee, Kelley, Bennett, Anna K., Gibbons, Patrick, and Higgins, Agnes

Abstract

4.1 Introduction: PhotoVoice is a participatory methodology in which marginalized communities represent their lived experiences through photography. While the methodology aims to foster partnerships throughout all phases, the literature suggests that in the field of mental health, some phases are often completed without participant involvement. 4.2 Aims: This paper elaborates on how the PhotoVoice method was used to engage service users and family members around their experience of involvement in a co-produced and co-facilitated mental health education intervention, in order to enhance public and policymakers knowledge of the project. 4.3 Methods: Ten participants were recruited and trained in the PhotoVoice method. Participants documented, through photography, their experiences of involvement in the education intervention. Following this, participants came together to co-produce and disseminate the photography exhibition to the public. 4.4 Results: PhotoVoice proved to be a flexible and creative method by which to include marginalized groups. By adhering to the collaborative principles of the methodology, service users and family members can retain decision-making power from the project's inception to its conclusion. 4.5 Implications for Practice: PhotoVoice is ideal for use within mental health nursing as it coincides with the recovery principle of promoting collaborative partnership between service users, family members and clinicians.

Published
2021

7. Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis

Author

Cornman R, Bennett Anna K, Murray K, Evans Jay D, Elsik Christine G, and Aronstein Kate

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background We present a comprehensive transcriptome analysis of the fungus Ascosphaera apis, an economically important pathogen of the Western honey bee (Apis mellifera) that causes chalkbrood disease. Our goals were to further annotate the A. apis reference genome and to identify genes that are candidates for being differentially expressed during host infection versus axenic culture. Results We compared A. apis transcriptome sequence from mycelia grown on liquid or solid media with that dissected from host-infected tissue. 454 pyrosequencing provided 252 Mb of filtered sequence reads from both culture types that were assembled into 10,087 contigs. Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. A phylogeny based on 12 of these protein-coding loci further supported the taxonomic placement of Ascosphaera as sister to the core Onygenales. Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. A novel gene family was identified that has expanded in some ascomycete lineages, but not others. We manually annotated genes with homologs in other fungal genomes that have known relevance to fungal virulence and life history. Functional categories of interest included genes involved in mating-type specification, intracellular signal transduction, and stress response. Computational and manual annotations have been made publicly available on the Bee Pests and Pathogens website. Conclusions This comprehensive transcriptome analysis substantially enhances our understanding of the A. apis genome and its expression during infection of honey bee larvae. It also provides resources for future molecular studies of chalkbrood disease and ultimately improved disease management.

Published
2012
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8. One LTAP strategic plan implemented 57 ways

Author

Bennett, Anna K.

Subjects
United States. Federal Highway Administration -- Transportation policy, Transportation policy -- Analysis, Technical assistance -- Analysis, High speed ground transportation -- Analysis, Business, Engineering and manufacturing industries, Government, Transportation industry, Analysis, Transportation policy
Abstract

The Local Technical Assistance Program (LTAP) has provided training, technical assistance, and technology transfer products to local transportation agencies for the past 15 years. The U.S. Department of Transportation, like [...]

Published
1998

9. Finding the Missing Honey Bee Genes: Lessons Learned From a Genome Upgrade

Author

Elsik, Christine G, Worley, Kim C, Bennett, Anna K, Beye, Martin, Camara, Francisco, Childers, Christopher P, de Graaf, Dirk C, Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D, Foster, Leonard J, Graur, Dan, Guigo, Roderic, HGSC production teams, Hoff, Katharina Jasmin, Holder, Michael E, Hudson, Matthew E, Hunt, Greg, Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L, Ma, Jian, Maleszka, Ryszard, Moritz, Robin FA, Munoz-Torres, Monica C, Murphy, Terence D, Muzny, Donna M, Newsham, Irene F, Reese, Justin T, Robertson, Hugh M, Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M, Van Vaerenbergh, Matthias, Waterhouse, Robert M, Weaver, Daniel B, Whitfield, Charles W, Wu, Yuanqing, Zdobnov, Evgeny M, Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A

Subjects
Apis mellifera, GC content, Gene annotation, Gene prediction, Genome assembly, Genome improvement, Genome sequencing, Repetitive DNA, Transcriptome, fungi
Abstract

Background The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Published
2014

10. 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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11. 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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12. Finding the missing honey bee genes: lessons learned from a genome upgrade

Author

Elsik, Christine G., Worley, Kim C., Bennett, Anna K., Beye, Martin, Camara, Francisco, Childers, Christopher P., de Graaf, Dirk C., Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D., Foster, Leonard J., Graur, Dan, Guigo, Roderic, Hoff, Katharina J., Holder, Michael E., Hudson, Matthew E., Hunt, Greg J., Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L., Ma, Jian, Maleszka, Ryszard, Moritz, Robin F. A., Munoz-Torres, Monica C., Murphy, Terence D., Muzny, Donna M., Newsham, Irene F., Reese, Justin T., Robertson, Hugh M., Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M., Vaerenbergh, Matthias V., Waterhouse, Robert M., Weaver, Daniel B., Whitfield, Charles W., Wu, Yuanqing, Zdobnov, Evgeny M., Zhang, Lan, Zhu, Dianhui, Gibbs, Richard A., Elsik, Christine G., Worley, Kim C., Bennett, Anna K., Beye, Martin, Camara, Francisco, Childers, Christopher P., de Graaf, Dirk C., Debyser, Griet, Deng, Jixin, Devreese, Bart, Elhaik, Eran, Evans, Jay D., Foster, Leonard J., Graur, Dan, Guigo, Roderic, Hoff, Katharina J., Holder, Michael E., Hudson, Matthew E., Hunt, Greg J., Jiang, Huaiyang, Joshi, Vandita, Khetani, Radhika S, Kosarev, Peter, Kovar, Christie L., Ma, Jian, Maleszka, Ryszard, Moritz, Robin F. A., Munoz-Torres, Monica C., Murphy, Terence D., Muzny, Donna M., Newsham, Irene F., Reese, Justin T., Robertson, Hugh M., Robinson, Gene E, Rueppell, Olav, Solovyev, Victor, Stanke, Mario, Stolle, Eckart, Tsuruda, Jennifer M., Vaerenbergh, Matthias V., Waterhouse, Robert M., Weaver, Daniel B., Whitfield, Charles W., Wu, Yuanqing, Zdobnov, Evgeny M., Zhang, Lan, Zhu, Dianhui, and Gibbs, Richard A.

Abstract

BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Published
2014

13. Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis

Author

Cornman, R, Cornman, R, Bennett, Anna K, Murray, K, Evans, Jay D, Elsik, Christine G, Aronstein, Kate, Cornman, R, Cornman, R, Bennett, Anna K, Murray, K, Evans, Jay D, Elsik, Christine G, and Aronstein, Kate

Abstract

BackgroundWe present a comprehensive transcriptome analysis of the fungus Ascosphaera apis, an economically important pathogen of the Western honey bee (Apis mellifera) that causes chalkbrood disease. Our goals were to further annotate the A. apis reference genome and to identify genes that are candidates for being differentially expressed during host infection versus axenic culture.ResultsWe compared A. apis transcriptome sequence from mycelia grown on liquid or solid media with that dissected from host-infected tissue. 454 pyrosequencing provided 252 Mb of filtered sequence reads from both culture types that were assembled into 10,087 contigs. Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. A phylogeny based on 12 of these protein-coding loci further supported the taxonomic placement of Ascosphaera as sister to the core Onygenales. Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. A novel gene family was identified that has expanded in some ascomycete lineages, but not others. We manually annotated genes with homologs in other fungal genomes that have known relevance to fungal virulence and life history. Functional categories of interest included genes involved in mating-type specification, intracellular signal transduction, and stress response. Computational and manual annotations have been made publicly available on the Bee Pests and Pathogens website.ConclusionsThis comprehensive transcriptome analysis substantially enhances our understanding of the A. apis genome and its expression during infection of honey bee larvae. It also provides resources for future molecular studies of chalkbrood disease and ultimately improved disease management.

Published
2012

14. Bovine Genome Database: integrated tools for genome annotation and discovery

Author

Childers, Christopher P., primary, Reese, Justin T., additional, Sundaram, Jaideep P., additional, Vile, Donald C., additional, Dickens, C. Michael, additional, Childs, Kevin L., additional, Salih, Hanni, additional, Bennett, Anna K., additional, Hagen, Darren E., additional, Adelson, David L., additional, and Elsik, Christine G., additional

Published
2010
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15. GMO LABELING--TRUTH BEYOND THE HYPE.

Author

Bennett, Anna K.

Subjects
TRANSGENIC organisms -- Law & legislation, LABELING laws, GENETICS, FEDERAL laws
Abstract

The article offers information on the pros and cons of genetically modified organisms (GMO). One commonly cited reason for GMO labels is that GMO products are harmful to consumers. According to the U.S. Food and Drug Administration, GMO are similar to conventional species which pose no greater risk to health than any conventional species. States are seeking to enact GMO labeling laws is because there are no federal laws that require or reject labeling of GMO.

Published
2013

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