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2. Hemichordate genomes and deuterostome origins.

Author

Simakov, Oleg, Kawashima, Takeshi, Marlétaz, Ferdinand, Jenkins, Jerry, Koyanagi, Ryo, Mitros, Therese, Hisata, Kanako, Bredeson, Jessen, Shoguchi, Eiichi, Gyoja, Fuki, Yue, Jia-Xing, Chen, Yi-Chih, Freeman, Robert M, Sasaki, Akane, Hikosaka-Katayama, Tomoe, Sato, Atsuko, Fujie, Manabu, Baughman, Kenneth W, Levine, Judith, Gonzalez, Paul, Cameron, Christopher, Fritzenwanker, Jens H, Pani, Ariel M, Goto, Hiroki, Kanda, Miyuki, Arakaki, Nana, Yamasaki, Shinichi, Qu, Jiaxin, Cree, Andrew, Ding, Yan, Dinh, Huyen H, Dugan, Shannon, Holder, Michael, Jhangiani, Shalini N, Kovar, Christie L, Lee, Sandra L, Lewis, Lora R, Morton, Donna, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Chen, Rui, Richards, Stephen, Muzny, Donna M, Gillis, Andrew, Peshkin, Leonid, Wu, Michael, Humphreys, Tom, Su, Yi-Hsien, Putnam, Nicholas H, Schmutz, Jeremy, Fujiyama, Asao, Yu, Jr-Kai, Tagawa, Kunifumi, Worley, Kim C, Gibbs, Richard A, Kirschner, Marc W, Lowe, Christopher J, Satoh, Noriyuki, Rokhsar, Daniel S, and Gerhart, John

Subjects
Animals, Chordata, Nonvertebrate, Echinodermata, Transforming Growth Factor beta, Evolution, Molecular, Phylogeny, Signal Transduction, Conserved Sequence, Synteny, Multigene Family, Genome, Chordata, Nonvertebrate, Evolution, Molecular, General Science & Technology
Abstract

Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Published
2015

3. A high-resolution map of human evolutionary constraint using 29 mammals.

Author

Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F, Parker, Brian J, Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D, Lowe, Craig B, Holloway, Alisha K, Clamp, Michele, Gnerre, Sante, Alföldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B, Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J, Rasmussen, Matthew D, Robinson, Jim, Stark, Alexander, Vilella, Albert J, Wen, Jiayu, Xie, Xiaohui, Zody, Michael C, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin, Jen, Bloom, Toby, Chin, Chee Whye, Heiman, Dave, Nicol, Robert, Nusbaum, Chad, Young, Sarah, Wilkinson, Jane, Worley, Kim C, Kovar, Christie L, Muzny, Donna M, Gibbs, Richard A, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree, Andrew, Dihn, Huyen H, Fowler, Gerald, Jhangiani, Shalili, Joshi, Vandita, Lee, Sandra, Lewis, Lora R, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Warren, Wesley C, Mardis, Elaine R, Weinstock, George M, Wilson, Richard K, Genome Institute at Washington University, Delehaunty, Kim, Dooling, David, Fronik, Catrina, Fulton, Lucinda, Fulton, Bob, Graves, Tina, Minx, Patrick, Sodergren, Erica, Birney, Ewan, Margulies, Elliott H, Herrero, Javier, Green, Eric D, Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S, Pedersen, Jakob S, Lander, Eric S, and Kellis, Manolis

Subjects
Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Animals, Mammals, Humans, Disease, RNA, Sequence Alignment, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Phylogeny, Genome, Genome, Human, Exons, Health, Selection, Genetic, Molecular Sequence Annotation, Sequence Analysis, DNA, Evolution, Molecular, Human, Selection, Genetic, General Science & Technology
Abstract

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

Published
2011

4. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

Author

McLendon, Roger, Friedman, Allan, Bigner, Darrell, Van Meir, Erwin G, Brat, Daniel J, M. Mastrogianakis, Gena, Olson, Jeffrey J, Mikkelsen, Tom, Lehman, Norman, Aldape, Ken, Alfred Yung, WK, Bogler, Oliver, VandenBerg, Scott, Berger, Mitchel, Prados, Michael, Muzny, Donna, Morgan, Margaret, Scherer, Steve, Sabo, Aniko, Nazareth, Lynn, Lewis, Lora, Hall, Otis, Zhu, Yiming, Ren, Yanru, Alvi, Omar, Yao, Jiqiang, Hawes, Alicia, Jhangiani, Shalini, Fowler, Gerald, San Lucas, Anthony, Kovar, Christie, Cree, Andrew, Dinh, Huyen, Santibanez, Jireh, Joshi, Vandita, Gonzalez-Garay, Manuel L, Miller, Christopher A, Milosavljevic, Aleksandar, Donehower, Larry, Wheeler, David A, Gibbs, Richard A, Cibulskis, Kristian, Sougnez, Carrie, Fennell, Tim, Mahan, Scott, Wilkinson, Jane, Ziaugra, Liuda, Onofrio, Robert, Bloom, Toby, Nicol, Rob, Ardlie, Kristin, Baldwin, Jennifer, Gabriel, Stacey, Lander, Eric S, Ding, Li, Fulton, Robert S, McLellan, Michael D, Wallis, John, Larson, David E, Shi, Xiaoqi, Abbott, Rachel, Fulton, Lucinda, Chen, Ken, Koboldt, Daniel C, Wendl, Michael C, Meyer, Rick, Tang, Yuzhu, Lin, Ling, Osborne, John R, Dunford-Shore, Brian H, Miner, Tracie L, Delehaunty, Kim, Markovic, Chris, Swift, Gary, Courtney, William, Pohl, Craig, Abbott, Scott, Hawkins, Amy, Leong, Shin, Haipek, Carrie, Schmidt, Heather, Wiechert, Maddy, Vickery, Tammi, Scott, Sacha, Dooling, David J, Chinwalla, Asif, Weinstock, George M, Mardis, Elaine R, Wilson, Richard K, Getz, Gad, Winckler, Wendy, Verhaak, Roel GW, Lawrence, Michael S, O’Kelly, Michael, Robinson, Jim, Alexe, Gabriele, Beroukhim, Rameen, Carter, Scott, Chiang, Derek, and Gould, Josh

Subjects
Cancer, Human Genome, Genetic Testing, Brain Cancer, Genetics, Brain Disorders, Biotechnology, Rare Diseases, Aetiology, 2.1 Biological and endogenous factors, Adolescent, Adult, Aged, Aged, 80 and over, Brain Neoplasms, DNA Methylation, DNA Modification Methylases, DNA Repair, DNA Repair Enzymes, Female, Gene Dosage, Gene Expression Regulation, Neoplastic, Genes, Tumor Suppressor, Genes, erbB-1, Genome, Human, Genomics, Glioblastoma, Humans, Male, Middle Aged, Models, Molecular, Mutation, Neurofibromin 1, Phosphatidylinositol 3-Kinases, Protein Structure, Tertiary, Retrospective Studies, Signal Transduction, Tumor Suppressor Proteins, Cancer Genome Atlas Research Network, General Science & Technology
Abstract

Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas (TCGA) pilot project aims to assess the value of large-scale multi-dimensional analysis of these molecular characteristics in human cancer and to provide the data rapidly to the research community. Here we report the interim integrative analysis of DNA copy number, gene expression and DNA methylation aberrations in 206 glioblastomas--the most common type of adult brain cancer--and nucleotide sequence aberrations in 91 of the 206 glioblastomas. This analysis provides new insights into the roles of ERBB2, NF1 and TP53, uncovers frequent mutations of the phosphatidylinositol-3-OH kinase regulatory subunit gene PIK3R1, and provides a network view of the pathways altered in the development of glioblastoma. Furthermore, integration of mutation, DNA methylation and clinical treatment data reveals a link between MGMT promoter methylation and a hypermutator phenotype consequent to mismatch repair deficiency in treated glioblastomas, an observation with potential clinical implications. Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer.

Published
2008

7. Gibbon genome and the fast karyotype evolution of small apes

Author

Carbone, Lucia, Alan Harris, R., Gnerre, Sante, Veeramah, Krishna R., Lorente-Galdos, Belen, Huddleston, John, Meyer, Thomas J., Herrero, Javier, Roos, Christian, Aken, Bronwen, Anaclerio, Fabio, Archidiacono, Nicoletta, Baker, Carl, Barrell, Daniel, Batzer, Mark A., Beal, Kathryn, Blancher, Antoine, Bohrson, Craig L., Brameier, Markus, Campbell, Michael S., Capozzi, Oronzo, Casola, Claudio, Chiatante, Giorgia, Cree, Andrew, Damert, Annette, de Jong, Pieter J., Dumas, Laura, Fernandez-Callejo, Marcos, Flicek, Paul, Fuchs, Nina V., Gut, Ivo, Gut, Marta, Hahn, Matthew W., Hernandez-Rodriguez, Jessica, Hillier, LaDeana W., Hubley, Robert, Ianc, Bianca, Izsvák, Zsuzsanna, Jablonski, Nina G., Johnstone, Laurel M., Karimpour-Fard, Anis, Konkel, Miriam K., Kostka, Dennis, Lazar, Nathan H., Lee, Sandra L., Lewis, Lora R., Liu, Yue, Locke, Devin P., Mallick, Swapan, Mendez, Fernando L., Muffato, Matthieu, Nazareth, Lynne V., Nevonen, Kimberly A., O’Bleness, Majesta, Ochis, Cornelia, Odom, Duncan T., Pollard, Katherine S., Quilez, Javier, Reich, David, Rocchi, Mariano, Schumann, Gerald G., Searle, Stephen, Sikela, James M., Skollar, Gabriella, Smit, Arian, Sonmez, Kemal, Hallers, Boudewijn ten, Terhune, Elizabeth, Thomas, Gregg W. C., Ullmer, Brygg, Ventura, Mario, Walker, Jerilyn A., Wall, Jeffrey D., Walter, Lutz, Ward, Michelle C., Wheelan, Sarah J., Whelan, Christopher W., White, Simon, Wilhelm, Larry J., Woerner, August E., Yandell, Mark, Zhu, Baoli, Hammer, Michael F., Marques-Bonet, Tomas, Eichler, Evan E., Fulton, Lucinda, Fronick, Catrina, Muzny, Donna M., Warren, Wesley C., Worley, Kim C., Rogers, Jeffrey, Wilson, Richard K., and Gibbs, Richard A.

Published
2014
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9. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

Author

Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Graves, Tina, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Buhay, Christian J., Kremitzki, Colin, Wang, Qiaoyan, Shen, Hua, Holder, Michael, Villasana, Donna, Nazareth, Lynne V., Cree, Andrew, Courtney, Laura, Veizer, Joelle, Kotkiewicz, Holland, Cho, Ting-Jan, Koutseva, Natalia, Rozen, Steve, Muzny, Donna M., Warren, Wesley C., Gibbs, Richard A., Wilson, Richard K., and Page, David C.

Subjects
Rhesus monkey -- Genetic aspects, Chimpanzees -- Genetic aspects, Human genetics -- Research, Human chromosomes -- Properties, Y chromosome -- Properties, Evolutionary genetics -- Research, Chromosome mapping -- Methods, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200-300 million years (1-3). The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes' genes owing to genetic decay (4,5). This evolutionary decay was driven by a series of five 'stratification' events. Each event suppressed X-Y crossing over within a chromosome segment or 'stratum', incorporated that segment into the MSY and subjected its genes to the erosive forces that attend the absence of crossing over (2,6). The last of these events occurred 30 million years ago, 5 million years before the human and Old World monkey lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome (7-10), remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage. To investigate this question, we sequenced the MSY of the rhesus macaque, an Old World monkey, and compared it to the human MSY. We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. In the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 million years ago. Likewise, the rhesus MSY has not lost any older genes (from strata 1-4) during the past 25 million years, despite its major structural differences to the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection., The human Y chromosome no longer engages in crossing over with its once-identical partner, the X chromosome, except in its pseudoautosomal regions. During evolution, X-Y crossing over was suppressed in [...]

Published
2012
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11. 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, Nelson, David, Kucherlapati, Raju, Weinstock, George, and Gibbs, Richard A.

Published
2006
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12. The DNA sequence, annotation and analysis of human chromosome 3

Author

Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, Sudbrak, Ralf, 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., Morgan, Margaret B., Nazareth, Lynne V., Scott, Graham, Sodergren, Erica, Song, Xing-Zhi, Steffen, David, Wei, Sharon, Wheeler, David A., Wright, Mathew W., Worley, Kim C., Yuan, Ye, Zhang, Zhengdong, Adams, Charles Q., Ansari-Lari, M. Ali, Ayele, Mulu, Brown, Mary J., Chen, Guan, Chen, Zhijian, Clendenning, James, Clerc-Blankenburg, Kerstin P., Chen, Runsheng, Chen, Zhu, Davis, Clay, Delgado, Oliver, Dinh, Huyen H., Dong, Wei, Draper, Heather, Ernst, Stephen, Fu, Gang, Gonzalez-Garay, Manuel L., Garcia, Dawn K., Gillett, Will, Gu, Jun, Hao, Bailin, Haugen, Eric, Havlak, Paul, He, Xin, Hennig, Steffen, Hu, Songnian, Huang, Wei, Jackson, Laronda R., Jacob, Leni S., Kelly, Susan H., Kube, Michael, Levy, Ruth, Li, Zhangwan, Liu, Bin, Liu, Jing, Liu, Wen, Lu, Jing, Maheshwari, Manjula, Nguyen, Bao-Viet, Okwuonu, Geoffrey O., Palmeiri, Anthony, Pasternak, Shiran, Perez, Lesette M., Phelps, Karen A., Plopper, Farah J. H., Qiang, Boqin, Raymond, Christopher, Rodriguez, Ruben, Saenphimmachak, Channakhone, Santibanez, Jireh, Shen, Hua, Shen, Yan, Subramanian, Sandhya, Tabor, Paul E., Verduzco, Daniel, Waldron, Lenee, Wang, Jian, Wang, Jun, Wang, Qiaoyan, Williams, Gabrielle A., Wong, Gane K.-S., Yao, Zhijian, Zhang, JingKun, Zhang, Xiuqing, Zhao, Guoping, Zhou, Jianling, Zhou, Yang, contributors, further, Nelson, David, Lehrach, Hans, Reinhardt, Richard, Naylor, Susan L., Yang, Huanming, Olson, Maynard, Weinstock, George, and Gibbs, Richard A.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Donna M. Muzny [1]; Steven E. Scherer (corresponding author) [1]; Rajinder Kaul [2]; Jing Wang [3]; Jun Yu [3]; Ralf Sudbrak [4, 5]; Christian J. Buhay [1]; Rui Chen [...]

Published
2006
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13. The DNA sequence of the human X chromosome

Author

Ross, Mark T., Grafham, Darren V., Coffey, Alison J., Scherer, Steven, McLay, Kirsten, Muzny, Donna, Platzer, Matthias, Howell, Gareth R., Burrows, Christine, Bird, Christine P., Frankish, Adam, Lovell, Frances L., Howe, Kevin L., Ashurst, Jennifer L., Fulton, Robert S., Sudbrak, Ralf, Wen, Gaiping, Jones, Matthew C., Hurles, Matthew E., Andrews, T. Daniel, Scott, Carol E., Searle, Stephen, Ramser, Juliane, Whittaker, Adam, Deadman, Rebecca, Carter, Nigel P., Hunt, Sarah E., Chen, Rui, Cree, Andrew, Gunaratne, Preethi, Havlak, Paul, Hodgson, Anne, Metzker, Michael L., Richards, Stephen, Scott, Graham, Steffen, David, Sodergren, Erica, Wheeler, David A., Worley, Kim C., Ainscough, Rachael, Ambrose, Kerrie D., Ansari-Lari, M. Ali, Aradhya, Swaroop, Ashwell, Robert I. S., Babbage, Anne K., Bagguley, Claire L., Ballabio, Andrea, Banerjee, Ruby, Barker, Gary E., Barlow, Karen F., Barrett, Ian P., Bates, Karen N., Beare, David M., Beasley, Helen, Beasley, Oliver, Beck, Alfred, Bethel, Graeme, Blechschmidt, Karin, Brady, Nicola, Bray-Allen, Sarah, Bridgeman, Anne M., Brown, Andrew J., Brown, Mary J., Bonnin, David, Bruford, Elspeth A., Buhay, Christian, Burch, Paula, Burford, Deborah, Burgess, Joanne, Burrill, Wayne, Burton, John, Bye, Jackie M., Carder, Carol, Carrel, Laura, Chako, Joseph, Chapman, Joanne C., Chavez, Dean, Chen, Ellson, Chen, Guan, Chen, Yuan, Chen, Zhijian, Chinault, Craig, Ciccodicola, Alfredo, Clark, Sue Y., Clarke, Graham, Clee, Chris M., Clegg, Sheila, Clerc-Blankenburg, Kerstin, Clifford, Karen, Cobley, Vicky, Cole, Charlotte G., Conquer, Jen S., Corby, Nicole, Connor, Richard E., David, Robert, Davies, Joy, Davis, Clay, Davis, John, Delgado, Oliver, DeShazo, Denise, Dhami, Pawandeep, Ding, Yan, Dinh, Huyen, Dodsworth, Steve, Draper, Heather, Dugan-Rocha, Shannon, Dunham, Andrew, Dunn, Matthew, Durbin, K. James, Dutta, Ireena, Eades, Tamsin, Ellwood, Matthew, Emery-Cohen, Alexandra, Errington, Helen, Evans, Kathryn L., Faulkner, Louisa, Francis, Fiona, Frankland, John, Fraser, Audrey E., Galgoczy, Petra, Gilbert, James, Gill, Rachel, Glockner, Gernot, Gregory, Simon G., Gribble, Susan, Griffiths, Coline, Grocock, Russell, Gu, Yanghong, Gwilliam, Rhian, Hamilton, Cerissa, Hart, Elizabeth A., Hawes, Alicia, Heath, Paul D., Heitmann, Katja, Hennig, Steffen, Hernandez, Judith, Hinzmann, Bernd, Ho, Sarah, Hoffs, Michael, Howden, Phillip J., Huckle, Elizabeth J., Hume, Jennifer, Hunt, Paul J., Hunt, Adrienne R., Isherwood, Judith, Jacob, Leni, Johnson, David, Jones, Sally, de Jong, Pieter J., Joseph, Shirin S., Keenan, Stephen, Kelly, Susan, Kershaw, Joanne K., Khan, Ziad, Kioschis, Petra, Klages, Sven, Knights, Andrew J., Kosiura, Anna, Kovar-Smith, Christie, Laird, Gavin K., Langford, Cordelia, Lawlor, Stephanie, Leversha, Margaret, Lewis, Lora, Liu, Wen, Lloyd, Christine, Lloyd, David M., Loulseged, Hermela, Loveland, Jane E., Lovell, Jamieson D., Lozado, Ryan, Lu, Jing, Lyne, Rachael, Ma, Jie, Maheshwari, Manjula, Matthews, Lucy H., McDowall, Jennifer, McLaren, Stuart, McMurray, Amanda, Meidl, Patrick, Meitinger, Thomas, Milne, Sarah, Miner, George, Mistry, Shailesh L., Morgan, Margaret, Morris, Sidney, Muller, Ines, Mullikin, James C., Nguyen, Ngoc, Nordsiek, Gabriele, Nyakatura, Gerald, O'Dell, Christopher N., Okwuonu, Geoffery, Palmer, Sophie, Pandian, Richard, Parker, David, Parrish, Julia, Pasternak, Shiran, Patel, Dina, Pearce, Alex V., Pearson, Danita M., Pelan, Sarah E., Perez, Lesette, Porter, Keith M., Ramsey, Yvonne, Reichwald, Kathrin, Rhodes, Susan, Ridler, Kerry A., Schlessinger, David, Schueler, Mary G., Sehra, Harminder K., Shaw-Smith, Charles, Shen, Hua, Sheridan, Elizabeth M., Shownkeen, Ratna, Skuce, Carl D., Smith, Michelle L., Sotheran, Elizabeth C., Steingruber, Helen E., Steward, Charles A., Storey, Roy, Swann, R. Mark, Swarbreck, David, Tabor, Paul E., Taudien, Stefan, Taylor, Tineace, Teague, Brian, Thomas, Karen, Thorpe, Andrea, Timms, Kirsten, Tracey, Alan, Trevanion, Steve, Tromans, Anthony C., d'Urso, Michele, Verduzco, Daniel, Villasana, Donna, Waldron, Lenee, Wall, Melanie, Wang, Qiaoyan, Warren, James, Warry, Georgina L., Wei, Xuehong, West, Anthony, Whitehead, Siobhan L., Whiteley, Mathew N., Wilkinson, Jane E., Willey, David L., Williams, Gabrielle, Williams, Leanne, Williamson, Angela, Williamson, Helen, Wilming, Laurens, Woodmansey, Rebecca L., Wray, Paul W., Yen, Jennifer, Zhang, Jingkun, Zhou, Jianling, Zoghbi, Huda, Zorilla, Sara, Buck, David, Reinhardt, Richard, Poustka, Annemarie, Rosenthal, Andre, Lehrach, Hans, Meindl, Alfons, Minx, Patrick J., Hillier, LaDeana W., Willard, Huntington F., Wilson, Richard K., Waterston, Robert H., Rice, Catherine M., Vaudin, Mark, Coulson, Alan, Nelson, David L., Weinstock, George, Sulston, John E., Durbin, Richard, Hubbard, Tim, Gibbs, Richard A., Beck, Stephan, Rogers, Jane, and Bentley, David R.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Mark T. Ross (corresponding author) [1]; Darren V. Grafham [1]; Alison J. Coffey [1]; Steven Scherer [2]; Kirsten McLay [1]; Donna Muzny [2]; Matthias Platzer [3]; Gareth R. Howell [...]

Published
2005
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14. Pooled genomic indexing of rhesus macaque

Author

Milosavljevic, Aleksandar, Jackson, Andrew R., Sodergren, Erica A., Harris, Ronald A., Kalafus, Ken J., Csuros, Miklos, Dai, Weilie, Cree, Andrew, Hodgson, Anne, Zhu, Baolo, Gibbs, Richard A., Weinstock, George M., and Pieter J. de Jong

Subjects
Chromosome mapping -- Research, Nucleotide sequencing -- Research, Macaques -- Genetic aspects, Health
Abstract

Pooled genomic indexing (PGI) is a method for mapping collections of bacterial chromosome (BAC) clones between species by using a combination of clone pooling and DNA sequencing. The method could be used to map a total of 3858 BAC clones covering -24% of the rhesus macaque genome onto 4178 homologous loci in the human genome.

Published
2005

18. Hemichordate genomes and deuterostome origins

Author

Kanda, Miyuki, Yamasaki, Shinichi, Fujie, Manabu, Levine, Judith, Sasaki, Akane, Dinh, Huyen H., Cameron, Christopher, Pani, Ariel M., Freeman, Robert M., Cree, Andrew, Hisata, Kanako, Simakov, Oleg, Sato, Atsuko, Gyoja, Fuki, Goto, Hiroki, Gonzalez, Paul, Hikosaka-Katayama, Tomoe, Shoguchi, Eiichi, Qu, Jiaxin, Dugan, Shannon, Mitros, Therese, Chen, Yi-Chih, Marlétaz, Ferdinand, Baughman, Kenneth W., Jenkins, Jerry, Fritzenwanker, Jens H., Bredeson, Jessen, Kawashima, Takeshi, Yue, Jia-Xing, Ding, Yan, Arakaki, Nana, and Koyanagi, Ryo

Abstract

Acorn worms, also known as enteropneust (literally, ‘gut-breathing’) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal ‘gill’ slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Published
2015
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19. Hemichordate genomes and deuterostome origins.

Author

Hisata, Kanako, Hisata, Kanako, Bredeson, Jessen, Shoguchi, Eiichi, Gyoja, Fuki, Yue, Jia-Xing, Chen, Yi-Chih, Freeman, Robert, Sasaki, Akane, Hikosaka-Katayama, Tomoe, Sato, Atsuko, Fujie, Manabu, Baughman, Kenneth, Levine, Judith, Gonzalez, Paul, Cameron, Christopher, Fritzenwanker, Jens, Pani, Ariel, Goto, Hiroki, Kanda, Miyuki, Arakaki, Nana, Yamasaki, Shinichi, Qu, Jiaxin, Cree, Andrew, Ding, Yan, Dinh, Huyen, Dugan, Shannon, Holder, Michael, Jhangiani, Shalini, Kovar, Christie, Lee, Sandra, Lewis, Lora, Morton, Donna, Nazareth, Lynne, Okwuonu, Geoffrey, Santibanez, Jireh, Chen, Rui, Richards, Stephen, Muzny, Donna, Gillis, Andrew, Peshkin, Leonid, Wu, Michael, Humphreys, Tom, Su, Yi-Hsien, Putnam, Nicholas, Schmutz, Jeremy, Fujiyama, Asao, Yu, Jr-Kai, Tagawa, Kunifumi, Simakov, Oleg, Kawashima, Takeshi, Marlétaz, Ferdinand, Jenkins, Jerry, Koyanagi, Ryo, Worley, Kim, Gibbs, Richard, Kirschner, Marc, Lowe, Christopher, Satoh, Noriyuki, Gerhart, John, Rokhsar, Daniel, Mitros, Therese, Hisata, Kanako, Hisata, Kanako, Bredeson, Jessen, Shoguchi, Eiichi, Gyoja, Fuki, Yue, Jia-Xing, Chen, Yi-Chih, Freeman, Robert, Sasaki, Akane, Hikosaka-Katayama, Tomoe, Sato, Atsuko, Fujie, Manabu, Baughman, Kenneth, Levine, Judith, Gonzalez, Paul, Cameron, Christopher, Fritzenwanker, Jens, Pani, Ariel, Goto, Hiroki, Kanda, Miyuki, Arakaki, Nana, Yamasaki, Shinichi, Qu, Jiaxin, Cree, Andrew, Ding, Yan, Dinh, Huyen, Dugan, Shannon, Holder, Michael, Jhangiani, Shalini, Kovar, Christie, Lee, Sandra, Lewis, Lora, Morton, Donna, Nazareth, Lynne, Okwuonu, Geoffrey, Santibanez, Jireh, Chen, Rui, Richards, Stephen, Muzny, Donna, Gillis, Andrew, Peshkin, Leonid, Wu, Michael, Humphreys, Tom, Su, Yi-Hsien, Putnam, Nicholas, Schmutz, Jeremy, Fujiyama, Asao, Yu, Jr-Kai, Tagawa, Kunifumi, Simakov, Oleg, Kawashima, Takeshi, Marlétaz, Ferdinand, Jenkins, Jerry, Koyanagi, Ryo, Worley, Kim, Gibbs, Richard, Kirschner, Marc, Lowe, Christopher, Satoh, Noriyuki, Gerhart, John, Rokhsar, Daniel, and Mitros, Therese

Abstract

Acorn worms, also known as enteropneust (literally, gut-breathing) hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal gill slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.

Published
2015

20. Results of the 2014 SRS Survey on PJK/PJF

Author

Scheer, Justin K., primary, Fakurnejad, Shayan, additional, Lau, Darryl, additional, Daubs, Michael D., additional, Coe, Jeffrey D., additional, Paonessa, Kenneth J., additional, LaGrone, Michael O., additional, Amaral, Rodrigo A., additional, Trobisch, Per D., additional, Lee, Jung-Hee, additional, Fabris-Monterumici, Daniel, additional, Anand, Neel, additional, Cree, Andrew K., additional, Hart, Robert A., additional, Hey, Lloyd A., additional, and Ames, Christopher P., additional

Published
2015
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23. Proximal Junctional Kyphosis and Failure After Spinal Deformity Surgery

Author

Lau, Darryl, primary, Clark, Aaron J., additional, Scheer, Justin K., additional, Daubs, Michael D., additional, Coe, Jeffrey D., additional, Paonessa, Kenneth J., additional, LaGrone, Michael O., additional, Kasten, Michael D., additional, Amaral, Rodrigo A., additional, Trobisch, Per D., additional, Lee, Jung-Hee, additional, Fabris-Monterumici, Daniel, additional, Anand, Neel, additional, Cree, Andrew K., additional, Hart, Robert A., additional, Hey, Lloyd A., additional, and Ames, Christopher P., additional

Published
2014
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25. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes

Author

Massachusetts Institute of Technology. Department of Biology, Whitehead Institute for Biomedical Research, Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Cho, Ting-Jan, Koutseva, Natalia, Rozen, Steve, Page, David C., Graves, Tina, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Buhay, Christian J., Kremitzki, Colin, Wang, Qiaoyan, Shen, Hua, Holder, Michael, Villasana, Donna, Nazareth, Lynne V., Cree, Andrew, Courtney, Laura, Veizer, Joelle, Kotkiewicz, Holland, Muzny, Donna M., Warren2, Wesley C., Gibbs, Richard A., Wilson, Richard K., Page, David C, Massachusetts Institute of Technology. Department of Biology, Whitehead Institute for Biomedical Research, Hughes, Jennifer F., Skaletsky, Helen, Brown, Laura G., Pyntikova, Tatyana, Cho, Ting-Jan, Koutseva, Natalia, Rozen, Steve, Page, David C., Graves, Tina, Fulton, Robert S., Dugan, Shannon, Ding, Yan, Buhay, Christian J., Kremitzki, Colin, Wang, Qiaoyan, Shen, Hua, Holder, Michael, Villasana, Donna, Nazareth, Lynne V., Cree, Andrew, Courtney, Laura, Veizer, Joelle, Kotkiewicz, Holland, Muzny, Donna M., Warren2, Wesley C., Gibbs, Richard A., Wilson, Richard K., and Page, David C

Abstract

The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200–300 million years[superscript 1, 2, 3]. The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes’ genes owing to genetic decay[superscript 4, 5]. This evolutionary decay was driven by a series of five ‘stratification’ events. Each event suppressed X–Y crossing over within a chromosome segment or ‘stratum’, incorporated that segment into the MSY and subjected its genes to the erosive forces that attend the absence of crossing over[superscript 2, 6]. The last of these events occurred 30 million years ago, 5 million years before the human and Old World monkey lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome[superscript 7, 8, 9, 10], remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the Old World monkey lineage. To investigate this question, we sequenced the MSY of the rhesus macaque, an Old World monkey, and compared it to the human MSY. We discovered that during the last 25 million years MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. In the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 million years ago. Likewise, the rhesus MSY has not lost any older genes (from strata 1–4) during the past 25 million years, despite its major structural differences to the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection.

Published
2012

26. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, Levchenko, Tanya, Renfree, Marilyn B., Papenfuss, Anthony T., Deakin, Janine E., Lindsay, James, Heider, Thomas, Belov, Katherine, Rens, Willem, Waters, Paul D., Pharo, Elizabeth A., Shaw, Geoff, Wong, Emily S. W., Gibbs, Richard A, Cooper, Desmond W, Speed, Terence P, Fujiyama, Asao, Graves, Jennifer A. M., O'Neill, Rachel J., Pask, Andrew J., Forrest, Susan M., Worley, Kim C., Lefèvre, Christophe M., Nicholas, Kevin R., Kuroki, Yoko, Wakefield, Matthew J., Zenger, Kyall R., Wang, Chenwei, Ferguson-Smith, Malcolm, Nicholas, Frank W., Hickford, Danielle, Yu, Hongshi, Short, Kirsty R., Siddle, Hannah V., Frankenberg, Stephen R., Chew, Keng, Menzies, Brandon R., Stringer, Jessica M., Suzuki, Shunsuke, Hore, Timothy A., Delbridge, Margaret L., Mohammadi, Amir, Schneider, Nanette Y., Hu, Yanqiu, O'Hara, William, Al Nadaf, Shafagh, Wu, Chen, Feng, Zhi-Ping, Cocks, Benjamin G., Wang, Jianghui, Flicek, Paul, Searle, Stephen M. J., Fairley, Susan, Beal, Kathryn, Herrero, Javier, Carone, Dawn M., Suzuki, Yutaka, Sugano, Sumio, Toyoda, Atsushi, Sakaki, Yoshiyuki, Kondo, Shinji, Nishida, Yuichiro, Tatsumoto, Shoji, Mandiou, Ion, Hsu, Arthur, McColl, Kaighin A., Lansdell, Benjamin, Weinstock, George, Kuczek, Elizabeth, McGrath, Annette, Wilson, Peter, Men, Artem, Hazar-Rethinam, Mehlika, Hall, Allison, Davis, John, Wood, David, Williams, Sarah, Sundaravadanam, Yogi, Muzny, Donna M, Jhangiani, Shalini N, Lewis, Lora R, Morgan, Margaret B, Okwuonu, Geoffrey O, Ruiz, San, Santibanez, Jireh, Nazareth, Lynne, Cree, Andrew, Fowler, Gerald, Kovar, Christie L, Dinh, Huyen H, Joshi, Vandita, Jing, Chyn, Lara, Fremiet, Thornton, Rebecca, Chen, Lei, Deng, Jixin, Liu, Yue, Shen, Joshua Y, Song, Xing-Zhi, Edson, Janette, Troon, Carmen, Thomas, Daniel, Stephens, Amber, Yapa, Lankesha, and Levchenko, Tanya

Abstract

BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Published
2011

27. 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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28. The genome of the model beetle and pest Tribolium castaneum.

Author

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

Abstract

Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.

Published
2008

29. Evolutionary and biomedical insights from the rhesus macaque genome

Author

Gibbs, Richard A, Rogers, Jeffrey, Katze, Michael G, Bumgarner, Roger, Weinstock, George M, Mardis, Elaine R, Remington, Karin A, Strausberg, Robert L, Venter, J Craig, Wilson, Richard K, Batzer, Mark A, Bustamante, Carlos D, Eichler, Evan E, Hahn, Matthew W, Hardison, Ross C, Makova, Kateryna D, Miller, Webb, Milosavljevic, Aleksandar, Palermo, Robert E, Siepel, Adam, Sikela, James M, Attaway, Tony, Bell, Stephanie, Bernard, Kelly E, Buhay, Christian J, Chandrabose, Mimi N, Dao, Marvin, Davis, Clay, Delehaunty, Kimberly D, Ding, Yan, Dinh, Huyen H, Dugan-Rocha, Shannon, Fulton, Lucinda A, Gabisi, Ramatu Ayiesha, Garner, Toni T, Godfrey, Jennifer, Hawes, Alicia C, Hernandez, Judith, Hines, Sandra, Holder, Michael, Hume, Jennifer, Jhangiani, Shalini N, Joshi, Vandita, Khan, Ziad Mohid, Kirkness, Ewen F, Cree, Andrew, Fowler, R Gerald, Lee, Sandra, Lewis, Lora R, Nielsen, Rasmus, Gibbs, Richard A, Rogers, Jeffrey, Katze, Michael G, Bumgarner, Roger, Weinstock, George M, Mardis, Elaine R, Remington, Karin A, Strausberg, Robert L, Venter, J Craig, Wilson, Richard K, Batzer, Mark A, Bustamante, Carlos D, Eichler, Evan E, Hahn, Matthew W, Hardison, Ross C, Makova, Kateryna D, Miller, Webb, Milosavljevic, Aleksandar, Palermo, Robert E, Siepel, Adam, Sikela, James M, Attaway, Tony, Bell, Stephanie, Bernard, Kelly E, Buhay, Christian J, Chandrabose, Mimi N, Dao, Marvin, Davis, Clay, Delehaunty, Kimberly D, Ding, Yan, Dinh, Huyen H, Dugan-Rocha, Shannon, Fulton, Lucinda A, Gabisi, Ramatu Ayiesha, Garner, Toni T, Godfrey, Jennifer, Hawes, Alicia C, Hernandez, Judith, Hines, Sandra, Holder, Michael, Hume, Jennifer, Jhangiani, Shalini N, Joshi, Vandita, Khan, Ziad Mohid, Kirkness, Ewen F, Cree, Andrew, Fowler, R Gerald, Lee, Sandra, Lewis, Lora R, and Nielsen, Rasmus

Abstract

Udgivelsesdato: 2007-Apr-13, The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

Published
2007

31. 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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32. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B, primary, Papenfuss, Anthony T, additional, Deakin, Janine E, additional, Lindsay, James, additional, Heider, Thomas, additional, Belov, Katherine, additional, Rens, Willem, additional, Waters, Paul D, additional, Pharo, Elizabeth A, additional, Shaw, Geoff, additional, Wong, Emily SW, additional, Lefèvre, Christophe M, additional, Nicholas, Kevin R, additional, Kuroki, Yoko, additional, Wakefield, Matthew J, additional, Zenger, Kyall R, additional, Wang, Chenwei, additional, Ferguson-Smith, Malcolm, additional, Nicholas, Frank W, additional, Hickford, Danielle, additional, Yu, Hongshi, additional, Short, Kirsty R, additional, Siddle, Hannah V, additional, Frankenberg, Stephen R, additional, Chew, Keng Y, additional, Menzies, Brandon R, additional, Stringer, Jessica M, additional, Suzuki, Shunsuke, additional, Hore, Timothy A, additional, Delbridge, Margaret L, additional, Patel, Hardip, additional, Mohammadi, Amir, additional, Schneider, Nanette Y, additional, Hu, Yanqiu, additional, O'Hara, William, additional, Al Nadaf, Shafagh, additional, Wu, Chen, additional, Feng, Zhi-Ping, additional, Cocks, Benjamin G, additional, Wang, Jianghui, additional, Flicek, Paul, additional, Searle, Stephen MJ, additional, Fairley, Susan, additional, Beal, Kathryn, additional, Herrero, Javier, additional, Carone, Dawn M, additional, Suzuki, Yutaka, additional, Sugano, Sumio, additional, Toyoda, Atsushi, additional, Sakaki, Yoshiyuki, additional, Kondo, Shinji, additional, Nishida, Yuichiro, additional, Tatsumoto, Shoji, additional, Mandiou, Ion, additional, Hsu, Arthur, additional, McColl, Kaighin A, additional, Lansdell, Benjamin, additional, Weinstock, George, additional, Kuczek, Elizabeth, additional, McGrath, Annette, additional, Wilson, Peter, additional, Men, Artem, additional, Hazar-Rethinam, Mehlika, additional, Hall, Allison, additional, Davis, John, additional, Wood, David, additional, Williams, Sarah, additional, Sundaravadanam, Yogi, additional, Muzny, Donna M, additional, Jhangiani, Shalini N, additional, Lewis, Lora R, additional, Morgan, Margaret B, additional, Okwuonu, Geoffrey O, additional, Ruiz, San J, additional, Santibanez, Jireh, additional, Nazareth, Lynne, additional, Cree, Andrew, additional, Fowler, Gerald, additional, Kovar, Christie L, additional, Dinh, Huyen H, additional, Joshi, Vandita, additional, Jing, Chyn, additional, Lara, Fremiet, additional, Thornton, Rebecca, additional, Chen, Lei, additional, Deng, Jixin, additional, Liu, Yue, additional, Shen, Joshua Y, additional, Song, Xing-Zhi, additional, Edson, Janette, additional, Troon, Carmen, additional, Thomas, Daniel, additional, Stephens, Amber, additional, Yapa, Lankesha, additional, Levchenko, Tanya, additional, Gibbs, Richard A, additional, Cooper, Desmond W, additional, Speed, Terence P, additional, Fujiyama, Asao, additional, M Graves, Jennifer A, additional, O'Neill, Rachel J, additional, Pask, Andrew J, additional, Forrest, Susan M, additional, and Worley, Kim C, additional

Published
2011
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33. Deep resequencing reveals excess rare recent variants consistent with explosive population growth

Author

Coventry, Alex, primary, Bull-Otterson, Lara M., additional, Liu, Xiaoming, additional, Clark, Andrew G., additional, Maxwell, Taylor J., additional, Crosby, Jacy, additional, Hixson, James E., additional, Rea, Thomas J., additional, Muzny, Donna M., additional, Lewis, Lora R., additional, Wheeler, David A., additional, Sabo, Aniko, additional, Lusk, Christine, additional, Weiss, Kenneth G., additional, Akbar, Humeira, additional, Cree, Andrew, additional, Hawes, Alicia C., additional, Newsham, Irene, additional, Varghese, Robin T., additional, Villasana, Donna, additional, Gross, Shannon, additional, Joshi, Vandita, additional, Santibanez, Jireh, additional, Morgan, Margaret, additional, Chang, Kyle, additional, IV, Walker Hale, additional, Templeton, Alan R., additional, Boerwinkle, Eric, additional, Gibbs, Richard, additional, and Sing, Charles F., additional

Published
2010
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36. 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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37. 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, Bellé, Robert, additional, Carbonneau, Seth, additional, Cheung, Rocky, additional, Cormier, Patrick, additional, Cosson, Bertrand, additional, Croce, Jenifer, additional, Fernandez-Guerra, Antonio, additional, Genevière, 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, Hallböök, 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, Véronique, additional, Duloquin, Louise, additional, Flytzanis, Constantin, additional, Gache, Christian, additional, Lapraz, François, additional, Lepage, Thierry, additional, Locascio, Annamaria, additional, Martinez, Pedro, additional, Matassi, Giorgio, additional, Matranga, Valeria, additional, Range, Ryan, additional, Rizzo, Francesca, additional, Röttinger, 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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41. Transcranial Motor-Evoked Potentials Combined With Response Recording Through Compound Muscle Action Potential as the Sole Modality of Spinal Cord Monitoring in Spinal Deformity Surgery.

Author

Brian Hsu, Cree, Andrew K., Lagopoulos, Jim, and Cummine, John L.

Subjects
*SPINAL cord, *SPINAL surgery, *SPINE abnormalities, *MUSCLES, *EVOKED potentials (Electrophysiology)
Abstract

The article reports on the sensitivity and specificity of transcranial motor-evoked potentials and compound muscle action potential monitoring as the sole modality in spinal deformity correction surgery. It shows that the monitoring criteria are sufficiently strict to achieve a sensitivity of 1.0 and a specificity of 0.97.

Published
2008
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42. A catalog of reference genomes from the human microbiome.

Author

Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, Rusch DB, Mitreva M, Sodergren E, Chinwalla AT, Feldgarden M, Gevers D, Haas BJ, Madupu R, Ward DV, Birren BW, Gibbs RA, Methe B, Petrosino JF, Strausberg RL, Sutton GG, White OR, Wilson RK, Durkin S, Giglio MG, Gujja S, Howarth C, Kodira CD, Kyrpides N, Mehta T, Muzny DM, Pearson M, Pepin K, Pati A, Qin X, Yandava C, Zeng Q, Zhang L, Berlin AM, Chen L, Hepburn TA, Johnson J, McCorrison J, Miller J, Minx P, Nusbaum C, Russ C, Sykes SM, Tomlinson CM, Young S, Warren WC, Badger J, Crabtree J, Markowitz VM, Orvis J, Cree A, Ferriera S, Fulton LL, Fulton RS, Gillis M, Hemphill LD, Joshi V, Kovar C, Torralba M, Wetterstrand KA, Abouellleil A, Wollam AM, Buhay CJ, Ding Y, Dugan S, FitzGerald MG, Holder M, Hostetler J, Clifton SW, Allen-Vercoe E, Earl AM, Farmer CN, Liolios K, Surette MG, Xu Q, Pohl C, Wilczek-Boney K, and Zhu D

Subjects
Bacteria classification, Bacteria genetics, Bacterial Proteins chemistry, Bacterial Proteins genetics, Biodiversity, Computational Biology, Databases, Genetic, Gastrointestinal Tract microbiology, Genes, Bacterial, Genetic Variation, Genome, Archaeal, Humans, Metagenomics methods, Metagenomics standards, Mouth microbiology, Peptides chemistry, Peptides genetics, Phylogeny, Respiratory System microbiology, Skin microbiology, Urogenital System microbiology, Genome, Bacterial, Metagenome genetics, Sequence Analysis, DNA standards
Abstract

The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.

Published
2010
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43. 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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44. The genome of the model beetle and pest Tribolium castaneum.

Author

Richards S, Gibbs RA, Weinstock GM, Brown SJ, Denell R, Beeman RW, Gibbs R, Beeman RW, Brown SJ, Bucher G, Friedrich M, Grimmelikhuijzen CJ, Klingler M, Lorenzen M, Richards S, Roth S, Schröder R, Tautz D, Zdobnov EM, Muzny D, Gibbs RA, Weinstock GM, Attaway T, Bell S, Buhay CJ, Chandrabose MN, Chavez D, Clerk-Blankenburg KP, Cree A, Dao M, Davis C, Chacko J, Dinh H, Dugan-Rocha S, Fowler G, Garner TT, Garnes J, Gnirke A, Hawes A, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Jackson L, Kovar C, Kowis A, Lee S, Lewis LR, Margolis J, Morgan M, Nazareth LV, Nguyen N, Okwuonu G, Parker D, Richards S, Ruiz SJ, Santibanez J, Savard J, Scherer SE, Schneider B, Sodergren E, Tautz D, Vattahil S, Villasana D, White CS, Wright R, Park Y, Beeman RW, Lord J, Oppert B, Lorenzen M, Brown S, Wang L, Savard J, Tautz D, Richards S, Weinstock G, Gibbs RA, Liu Y, Worley K, Weinstock G, Elsik CG, Reese JT, Elhaik E, Landan G, Graur D, Arensburger P, Atkinson P, Beeman RW, Beidler J, Brown SJ, Demuth JP, Drury DW, Du YZ, Fujiwara H, Lorenzen M, Maselli V, Osanai M, Park Y, Robertson HM, Tu Z, Wang JJ, Wang S, Richards S, Song H, Zhang L, Sodergren E, Werner D, Stanke M, Morgenstern B, Solovyev V, Kosarev P, Brown G, Chen HC, Ermolaeva O, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Maglott D, Pruitt K, Sapojnikov V, Souvorov A, Mackey AJ, Waterhouse RM, Wyder S, Zdobnov EM, Zdobnov EM, Wyder S, Kriventseva EV, Kadowaki T, Bork P, Aranda M, Bao R, Beermann A, Berns N, Bolognesi R, Bonneton F, Bopp D, Brown SJ, Bucher G, Butts T, Chaumot A, Denell RE, Ferrier DE, Friedrich M, Gordon CM, Jindra M, Klingler M, Lan Q, Lattorff HM, Laudet V, von Levetsow C, Liu Z, Lutz R, Lynch JA, da Fonseca RN, Posnien N, Reuter R, Roth S, Savard J, Schinko JB, Schmitt C, Schoppmeier M, Schröder R, Shippy TD, Simonnet F, Marques-Souza H, Tautz D, Tomoyasu Y, Trauner J, Van der Zee M, Vervoort M, Wittkopp N, Wimmer EA, Yang X, Jones AK, Sattelle DB, Ebert PR, Nelson D, Scott JG, Beeman RW, Muthukrishnan S, Kramer KJ, Arakane Y, Beeman RW, Zhu Q, Hogenkamp D, Dixit R, Oppert B, Jiang H, Zou Z, Marshall J, Elpidina E, Vinokurov K, Oppert C, Zou Z, Evans J, Lu Z, Zhao P, Sumathipala N, Altincicek B, Vilcinskas A, Williams M, Hultmark D, Hetru C, Jiang H, Grimmelikhuijzen CJ, Hauser F, Cazzamali G, Williamson M, Park Y, Li B, Tanaka Y, Predel R, Neupert S, Schachtner J, Verleyen P, Raible F, Bork P, Friedrich M, Walden KK, Robertson HM, Angeli S, Forêt S, Bucher G, Schuetz S, Maleszka R, Wimmer EA, Beeman RW, Lorenzen M, Tomoyasu Y, Miller SC, Grossmann D, and Bucher G

Subjects
Animals, Base Composition, Body Patterning genetics, Cytochrome P-450 Enzyme System genetics, DNA Transposable Elements genetics, Growth and Development genetics, Humans, Insecticides pharmacology, Neurotransmitter Agents genetics, Oogenesis genetics, Phylogeny, Proteome genetics, RNA Interference, Receptors, G-Protein-Coupled genetics, Receptors, Odorant genetics, Repetitive Sequences, Nucleic Acid genetics, Taste genetics, Telomere genetics, Tribolium classification, Tribolium embryology, Tribolium physiology, Vision, Ocular genetics, Genes, Insect genetics, Genome, Insect genetics, Tribolium genetics
Abstract

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.

Published
2008
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