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1. The common marmoset genome provides insight into primate biology and evolution

Author

San Juana Ruiz, Daniel Gerlach, Tomas Vinar, Brona Brejova, Saba Sajjadian, Miriam K. Konkel, Muthuswamy Raveendran, Yih Shin Liu, Paul Flicek, Lubomir Tomaska, Donna M. Muzny, Daniel R. Schrider, Megan C. Ranck, Kjersti Aagaard, Huyen Dinh, Jayantha B. Tennakoon, Lucinda Fulton, Lynne V. Nazareth, Brygg Ullmer, George M. Weinstock, Kim D. Delehaunty, Xose S. Puente, Charles E. Vejnar, Shyam Prabhakar, Matthew W. Hahn, J. Scott Moncrieff, Mark A. Batzer, Tina Graves, Catherine C. Fontenot, Carlos López-Otín, Corinna N. Ross, Catrina Fronick, Jeffrey Rogers, Nirmala Arul Rayan, Mario Ventura, Pieter J. De Jong, Elaine R. Mardis, Steve Searle, Christie LKovar, David Haig, Ngoc Nguyen, Shalini N. Jhangiani, Margaret Morgan, Crystal M. Warner, Mimi M. Chandrabose, Keith G. Mansfield, Vandita Joshi, Kathryn Beal, Saverio B. Capuano, Magali Ruffier, Ling Ling Pu, Jerilyn A. Walker, Marvin Diep Dao, John Lopez, Irene Newsham, Yuanqing Wu, Jan Hinnerk Vogel, Arian F.A. Smit, Javier Herrero, Andrew Cree, Tomas Marques-Bonet, Oronzo Capozzi, LaDeana W. Hillier, Robert S. Fulton, Claudio Casola, Mariano Rocchi, Benjamin Soibam, Suzette D. Tardif, Derek E. Wildman, Evgenia V. Kriventseva, Kim C. Worley, Baoli Zhu, Jennifer F. Hughes, Robert Hubley, Geoffrey Okwuonu, Jennifer Hume, Lora Lewis, Ricardo C.H. del Rosario, Devin P. Locke, Lora Perales, David Rio Deiros, David J. Witherspoon, Yi Han, Brian J. Raney, David Rodríguez, Stephen Fitzgerald, Jireh Santibanez, Albert J. Vilella, R. Gerald Fowler, Qing Wang, Belen Lorente-Galdos, Ramatu Ayiesha Gabisi, Víctor Quesada, Weimin Xiao, Nicoletta Archidiacono, Emre Karakor, Helen Skaletsky, R. Alan Harris, Evgeny M. Zdobnov, Richard A. Gibbs, Wesley C. Warren, Patrick Minx, Preethi H. Gunaratne, Rita A. Wright, Doriana Misceo, Jinchuan Xing, Evan E. Eichler, Lynn B. Jorde, Carolin Kosiol, Rick K. Wilson, Sandra L. Lee, University of St Andrews. School of Biology, University of St Andrews. Centre for Biological Diversity, National Human Genome Research Institute (US), National Institutes of Health (US), National Science Foundation (US), Howard Hughes Medical Institute, Louisiana State University, Cullen Foundation, European Research Council, Ministerio de Ciencia e Innovación (España), Instituto Nacional de Bioinformática (España), Gerlach, Daniel, Kriventseva, Evgenia, and Zdobnov, Evgeny

Subjects
endocrine system, animal structures, Evolució molecular, Evolution, QH301 Biology, animal diseases, Molecular Sequence Data, QH426 Genetics, Polymorphism, Single Nucleotide, Genome, Article, Evolution, Molecular, QH301, Phylogenetics, biology.animal, Genetics, Animals, ddc:576.5, Primate, Amino Acid Sequence, Polymorphism, QH426, Phylogeny, New World monkey, biology, Reproduction, Polimorfisme genètic, Callithrix/genetics, Molecular, Marmoset, Callithrix, Single Nucleotide, Sequence Analysis, DNA, biology.organism_classification, Reproduction/genetics, DNA/methods, body regions, MicroRNAs/genetics, MicroRNAs, Evolutionary biology, Female, Sequence Analysis
Abstract

The Marmoset Genome Sequencing and Analysis Consortium.-- Worley, Kim C. et al., We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application. © 2014 Nature America, Inc., The marmoset genome project was funded by the National Human Genome Research Institute (NHGRI), including from grants U54 HG003273 (R.A. Gibbs) and U54 HG003079 (R.K.W.), with additional support from the US National Institutes of Health (NIH), including from grants R01 DK077639 (S.D.T.), R01 GM59290 (L.B.J. and M.A.B.), HG002385 (E.E.E.) and P51-OD011133 (Southwest NPRC), and support from the National Science Foundation (NSF BCS-0751508 to D.E.W.) and the VEGA grant agency: 1/0719/14 (T.V.) and 1/1085/12 (B.B.). C.C.F. and M.C.R. were supported in part by a Howard Hughes Medical Institute grant to Louisiana State University through the Undergraduate Biological Sciences Education program. J.X. was supported by NHGRI grant K99 HG005846. P.H.G. was supported by the Cullen Foundation. T.M.-B. was supported by European Research Council Starting Grant (260372) and MICINN (Spain) grant BFU2011-28549. B.L.-G. was supported by the Spanish National Institute of Bioinformatics (see URLs).

Published
2014
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2. A framework for human microbiome research

Author

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

Subjects
Adult, Male, Adolescent, Statistics as Topic, Population, Computational biology, Biology, Genome, Article, Young Adult, 03 medical and health sciences, Human health, 0302 clinical medicine, RNA, Ribosomal, 16S, Humans, Microbiome, education, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Bacteria, Human microbiome, Reference Standards, Metagenomics, 030220 oncology & carcinogenesis, Earth Microbiome Project, Metagenome, Female, Human Microbiome Project
Abstract

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

Published
2012

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

Author

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

Subjects
Genome evolution, Genomics, Computational biology, Biology, Human accelerated regions, Genome, Article, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, Animals, Humans, Coding region, Disease, Selection, Genetic, Gene, Phylogeny, 030304 developmental biology, Mammals, Genetics, 0303 health sciences, Multidisciplinary, Genome, Human, Molecular Sequence Annotation, Exons, Sequence Analysis, DNA, 3. Good health, Health, RNA, Human genome, Mobile genetic elements, Sequence Alignment, 030217 neurology & neurosurgery
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., National Human Genome Research Institute (U.S.), National Institute of General Medical Sciences (U.S.) (Grant number GM82901), National Science Foundation (U.S.). Postdoctural Fellowship (Award 0905968), National Science Foundation (U.S.). Career (0644282), National Institutes of Health (U.S.) (R01-HG004037), Alfred P. Sloan Foundation., Austrian Science Fund. Erwin Schrodinger Fellowship

Published
2011
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4. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

Author

Sandy Aronson, Leslie Cope, Michael L. Bittner, Daniel C. Koboldt, Alex E. Lash, W. K. Alfred Yung, Margaret Morgan, Devin Absher, Carl F. Schaefer, Roger E. McLendon, Michael D. Prados, Josh Gould, Ju Han, Stacey Gabriel, Scott R. VandenBerg, Ilana Perna, Troy Shelton, Junyuan Wu, Sacha Scott, Steve Scherer, Michael J. T. O’Kelly, Li Ding, Erin Hickey, Elizabeth J. Thomson, Bahram Parvin, Kim D. Delehaunty, Gi Choi Yoon, Mark D. Robinson, Oliver Bogler, Darrell D. Bigner, Michael R. Reich, Jianhua Zhang, Robert S. Fulton, Allan H. Friedman, Tammi L. Vickery, Amita Aggarwal, Subhashree Madhavan, Liuda Ziaugra, Yuan Qi, Vandita Joshi, Eric Van Name, Jane Wilkinson, W. Ruprecht Wiedemeyer, Xiaoqi Shi, Richard A. Gibbs, Lynda Chin, Jessica Chen, Stefano Monti, Erwin G. Van Meir, John Ngai, Amy Hawkins, Elizabeth Lenkiewicz, Brad Ozenberger, Shannon Dorton, Georgia Ren, John N. Weinstein, Gena M. Mastrogianakis, Asif T. Chinwalla, Scott L. Carter, Nicholas D. Socci, Rachel Abbott, Gavin Sherlock, Lucinda Fulton, Hyun Soo Kim, Fei Pan, Magali Cavatore, Gabriele Alexe, Francis S. Collins, Narayanan Sathiamoorthy, Lakshmi Jakkula, Brian H. Dunford-Shore, Jireh Santibanez, Tom Mikkelsen, Huy V. Nguyen, Levi A. Garraway, Christopher A. Miller, Jinghui Zhang, Ken Chen, Timothy Fennell, Robert Sfeir, James A. Robinson, Alexey Stukalov, Richard K. Wilson, Matthew Meyerson, Daniel J. Weisenberger, Mi Yi Joo, Yevgeniy Antipin, Anna Lapuk, Gerald V. Fontenay, Nicolas Stransky, Adam B. Olshen, Elizabeth Purdom, Josh Korn, Huyen Dinh, Sai Balu, Victoria Wang, James G. Herman, Christie Kovar, Kristian Cibulskis, Tisha Chung, Agnes Viale, Paul T. Spellman, Supriya Gupta, Melissa Parkin, Peter J. Park, Maddy Wiechert, John W. Wallis, Peter W. Laird, Nikolaus Schultz, James D. Brooks, David Nassau, Jun Li, John R. Osborne, Anna D. Barker, Peter Fielding, Boris Reva, Karen Vranizan, D. Neil Hayes, Aleksandar Milosavljevic, Lawrence A. Donehower, Won Kong Sek, Daniela S. Gerhard, Otis Hall, Rameen Beroukhim, Audrey Southwick, George M. Weinstock, Chris Markovic, Roel G.W. Verhaak, David Van Den Berg, Joe W. Gray, Yanru Ren, Ethan Cerami, Yiming Zhu, Amrita Ray, Yonghong Xiao, Kristin G. Ardlie, William L. Gerald, Michael S. Lawrence, Gerald R. Fowler, Mark S. Guyer, Isaac S. Kohane, Kornel E. Schuebel, Mitchel S. Berger, Jeffrey J. Olson, Gary W. Swift, Lora Lewis, Sheri Sanders, Norman L. Lehman, Eric S. Lander, Robert Penny, Liliana Villafania, John G. Conboy, Ari B. Kahn, Henry Marr, Heidi S. Feiler, Lynn Nazareth, David J. Dooling, Katherine A. Hoadley, Alicia Hawes, Marc Ladanyi, Aniko Sabo, Wendy Winckler, Vivian Peng, Barbara A. Weir, Daniel J. Brat, Scott Morris, Carolyn C. Compton, Todd R. Golub, Scott Abbott, Michael D. McLellan, Jiqiang Yao, Shalini N. Jhangiani, Michael D. Topal, Michael C. Wendl, Gad Getz, Jun Yao, Derek Y. Chiang, Larry Feng, Steffen Durinck, David A. Wheeler, Yuzhu Tang, Benjamin Gross, Barry S. Taylor, Kenneth Aldape, Craig Pohl, Rick Meyer, Peter J. Good, Ling Lin, Elaine R. Mardis, Robert C. Onofrio, Jane Peterson, Stephen B. Baylin, Li-Xuan Qin, Andrew Cree, Cameron Brennan, Charles M. Perou, William Courtney, Omar Alvi, Donna M. Muzny, Joseph G. Vockley, Jill P. Mesirov, Yan Shi, Alexei Protopopov, Jim Vaught, Craig H. Mermel, Scott Mahan, Laetitia Borsu, Heather Schmidt, Jennifer Baldwin, Tracie L. Miner, Toby Bloom, David E. Larson, Leander Van Neste, Nicholas J. Wang, Kenneth H. Buetow, Raju Kucherlapati, Anthony San Lucas, Martin L. Ferguson, Terence P. Speed, Venkatraman E. Seshan, Debbie Beasley, Carrie Sougnez, Carrie A. Haipek, Richard M. Myers, Chris Sander, Qing Wang Wei, Jon G. Seidman, Rob Nicol, Manuel L. Gonzalez-Garay, Shin Leong, Shannon T. Brady, and University of Groningen

Subjects
Male, Models, Molecular, DNA Repair, Gene Dosage, NEUROFIBROMATOSIS TYPE-1, MISMATCH REPAIR, Phosphatidylinositol 3-Kinases, 0302 clinical medicine, Genes, Tumor Suppressor, DNA Modification Methylases, Proneural Glioblastoma, Aged, 80 and over, Genetics, 0303 health sciences, Neurofibromin 1, Multidisciplinary, Brain Neoplasms, NF1 GENE, Genomics, Middle Aged, TUMORS, ALKYLATING-AGENTS, 3. Good health, Gene Expression Regulation, Neoplastic, 030220 oncology & carcinogenesis, DNA methylation, Female, DNA mismatch repair, Functional genomics, Signal Transduction, Adult, Adolescent, CELL-LINES, Oncogenomics, Biology, Article, 03 medical and health sciences, PIK3CA GENE, Humans, Epigenetics, Gene, Aged, Retrospective Studies, 030304 developmental biology, HIGH-FREQUENCY, Genome, Human, Tumor Suppressor Proteins, SOMATIC MUTATIONS, Genes, erbB-1, DNA Methylation, Protein Structure, Tertiary, MALIGNANT GLIOMAS, DNA Repair Enzymes, Mutation, Glioblastoma
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 primary 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
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5. Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

Author

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

Subjects
Male, Biomedical Research, Pan troglodytes, Macaque, Human accelerated regions, Genome, Evolution, Molecular, Species Specificity, Gene Duplication, biology.animal, Animals, Humans, Primate, Gene Rearrangement, Genetics, Whole genome sequencing, Multidisciplinary, biology, Genetic Diseases, Inborn, Genetic Variation, Sequence Analysis, DNA, Gene rearrangement, biology.organism_classification, Macaca mulatta, Rhesus macaque, Homo sapiens, Evolutionary biology, Multigene Family, Mutation, Female
Abstract

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

Author

Steffen Klasberg, Julie Blommaert, Reed M. Johnson, Ajay Nair, Nehad Saada, Christina Schulte, Terence Murphy, Silvio Erler, Kaat Cappelle, Seth M. Barribeau, Marco Mariotti, Cornelis J. P. Grimmelikhuijzen, Robin Ngo, Marianne Otte, Claire E. Johnson, Fernanda C. Humann, Andrew F. G. Bourke, Séverine D. Buechel, Kathrin Näpflin, Thomas J. Colgan, Taro Fuchikawa, David F. Clarke, Meaghan P. O’Neill, Louis du Plessis, Aarti Venkat, Katharina J. Hoff, Daniela Puiu, Kevin B. Flores, Ivan Meeus, Jireh Santibanez, Jisheng Liu, Olivier Christiaens, Guy Smagghe, Monika Marxer, Na Yu, Ariel D. Chipman, Kim C. Worley, Elizabeth J. Duncan, Matthew E. Hudson, Márcia Maria Gentile Bitondi, Carolina G. Santos, Irene Newsham, Michael Holder, Alvaro G. Hernandez, Vasco Koch, Ling-Ling Pu, Vandita Joshi, Florian Wolschin, Jeffrey D. Lozier, Peter K. Dearden, Mark Blaxter, Andrew G. Cridge, David Collins, Sophie Helbing, Robert M. Waterhouse, Francis M. F. Nunes, Eamonn B. Mallon, Christopher Pham, Frank Hauser, Tanja Gempe, Guy Bloch, Roderic Guigó, Tittu Mathew, Gene E. Robinson, David S. Marco Antonio, Tamas Dalmay, Mark J. F. Brown, Jinzhi Niu, Christine G. Elsik, Regula Schmid-Hempel, Jay D. Evans, Stephanie Dreier, Lars Chittka, Olav Rueppell, Marcus Coyle, Nina Rossié, Sandra L. Lee, Inga Nissen, Eva C. Winnebeck, Flávia Cristina de Paula Freitas, Francisco Câmara, Yuanqing Wu, Geoffrey Okwuonu, Frano Irvine, Eckart Stolle, Christie Kovar, Evgeny M. Zdobnov, F. Bernhard Kraus, Griet Debyser, Robert Mata, Arian Köhler, Andrew K. Jones, LaRonda Jackson, Daniel Guariz Pinheiro, Matthias Van Vaerenbergh, Matthew Beckers, Zilá Luz Paulino Simões, Martin Beye, Tiago Falcon, Megan Leask, Anna K. Bennett, Donna M. Muzny, Monica Munoz-Torres, Ben M. Sadd, Kate L. Ciborowski, Erich Bornberg-Bauer, Stephen Richards, Jürgen Gadau, Richard A. Gibbs, Amy J. Osborne, John G. Oakeshott, Hugh M. Robertson, Michelle P.M. Soares, Seirian Sumner, Klaus Hartfelder, Steven E. Scherer, Matthias Biewer, Jonathan H. Kidner, Joy Jayaseelan, Kerstin P. Blankenburg, Gabrielle A. Lockett, Liezl Francisco, Paul Schmid-Hempel, Dirk C. de Graaf, Didac Santesmasses, Steven L. Salzberg, Robin F. A. Moritz, Tatsuhiko Kadowaki, Björn D. Schmitt, Gro V. Amdam, H. Michael G. Lattorff, Peshtewani K. Aqrawi, Bart Devreese, Martin Hasselmann, Claire Asher, Rebecca Thornton, Luc Swevers, Kimberly K. O. Walden, DeNard Simmons, Lars S. Jermiin, Rossanah Cameron, Jiaxin Qu, James C. Carolan, Bertrand Fouks, Illinois State Univ, ETH, E Carolina Univ, Hebrew Univ Jerusalem, Univ Ghent, Univ Otago, Univ Missouri, Georgetown Univ, Arizona State Univ, Univ Copenhagen, Univ Hohenheim, Univ Alabama, Univ Illinois, Univ Halle Wittenberg, Univ Geneva, Swiss Inst Bioinformat, MIT, MIT &Harvard, Univ Munster, Ctr Genom Regulat CRG, UPF, Ernst Moritz Arndt Univ Greifswald, Univ Calif Berkeley, Natl Lib Med, Norwegian Univ Food Sci, Univ E Anglia, Univ Dusseldorf, Univ Cologne, Universidade de São Paulo (USP), Univ Edinburgh, Royal Holloway Univ London, Maynooth Univ, Univ Bristol, CSIRO, Trin Coll Dublin, Zool Soc London, Swiss Fed Inst Technol, USDA ARS, N Carolina State Univ, Kyoto Univ, Inst Fed Educ Ciencia &Tecnol Sao Paulo, Ohio State Univ, Oxford Brookes Univ, Xian Jiaotong Liverpool Univ, Univ Hosp Halle Saale, German Ctr Integrat Biodivers Res iDiv, Univ Southampton, Univ Leicester, Universidade Federal de São Carlos (UFSCar), Universidade Estadual Paulista (Unesp), Univ N Carolina, Natl Ctr Sci Res Demokritos, Univ Munich, Baylor Coll Med, MD Anderson Canc Ctr, Univ Chicago, Queen Mary Univ London, Guangzhou Univ, Johns Hopkins Univ, and Zdobnov, Evgeny

Subjects
ENTOMOLOGIA, Population, HONEY-BEE, Genomics, HIGH-THROUGHPUT, Bombus impatiens, MULTIPLE SEQUENCE ALIGNMENT, ddc:576.5, education, DNA METHYLATION, Bumblebee, 2. Zero hunger, education.field_of_study, biology, PHYLOGENETIC ANALYSES, Insectes -- Genètica, Research, SEX-DETERMINATION PATHWAY, Biology and Life Sciences, Honey bee, Gene rearrangement, 15. Life on land, biology.organism_classification, Eusociality, DROSOPHILA-MELANOGASTER, Evolutionary biology, Bombus terrestris, MALE COURTSHIP BEHAVIOR, BOMBUS-TERRESTRIS LINNAEUS, BEE APIS-MELLIFERA
Abstract

Made available in DSpace on 2015-10-21T20:31:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-04-24. Added 1 bitstream(s) on 2015-10-22T09:48:01Z : No. of bitstreams: 1 WOS000353676700001.pdf: 2518339 bytes, checksum: d1f8d18bd059b76504f3fcd9aa639a74 (MD5) National Institutes of Health (NIH) Agriculture and Food Research Initiative Competitive grant from the USDA National Institute of Food and Agriculture Research Council of Norway (NFR) PEW Charitable Trust University of East Anglia, UK Israel Science Foundation (ISF) Biotechnology and Biological Sciences Research Council, UK University of East Anglia University of Alabama College of Arts and Sciences Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Marie Curie International Outgoing Fellowship Swiss National Science Foundation New Faculty Initiative Grant (NFIG) from Illinois State University College of Arts and Sciences DFG Instituto Nacional de Bioinformatica (INB) from ISCIII in Spain Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation. Illinois State Univ, Sch Biol Sci, Normal, IL 61790 USA ETH, Inst Integrat Biol, Expt Ecol, CH-8092 Zurich, Switzerland E Carolina Univ, Dept Biol, Greenville, NC 27858 USA Hebrew Univ Jerusalem, Alexander Silberman Inst Life Sci, Dept Ecol Evolut &Behav, Jerusalem, Israel Univ Ghent, Fac Sci, Lab Zoophysiol, B-9000 Ghent, Belgium Univ Otago, Dept Biochem, Labo Evolut &Dev Genet, Dunedin 9054, New Zealand Univ Otago, Dept Biochem, Natl Res Ctr Growth &Dev, Dunedin 9054, New Zealand Univ Missouri, Div Plant Sci, Div Anim Sci, Columbia, MO 65211 USA Univ Missouri, MU Informat Inst, Columbia, MO 65211 USA Georgetown Univ, Dept Biol, Washington, DC 20057 USA Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA Univ Copenhagen, Dept Biol, Ctr Funct &Comparat Insect Gen, Copenhagen, Denmark Univ Hohenheim, Inst Anim Sci, D-70599 Stuttgart, Germany Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA Univ Illinois, Dept Entomol, Urbana, IL 61801 USA Univ Ghent, Fac Biosci Engn, Dept Crop Protect, Lab Agrozool, B-9000 Ghent, Belgium Univ Halle Wittenberg, Inst Biol, Wittenberg, Germany Univ Geneva, Sch Med, Dept Genet Med &Dev, CH-1211 Geneva, Switzerland Swiss Inst Bioinformat, CH-1211 Geneva, Switzerland MIT, Comp Sci &Artificial Intelligence Lab, Cambridge, MA 02139 USA MIT &Harvard, Broad Inst, Cambridge Ctr 7, Cambridge, MA 02142 USA Univ Munster, Inst Evolut &Biodivers, D-48149 Munster, Germany Ctr Genom Regulat CRG, Barcelona 08003, Spain UPF, Barcelona, Spain Ernst Moritz Arndt Univ Greifswald, Inst Math &Comp Sci, D-17487 Greifswald, Germany Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA Natl Lib Med, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA Norwegian Univ Food Sci, Dept Chem Biotechnol &Food Sci, N-1432 As, Norway Univ E Anglia, Sch Comp Sci, Norwich NR4 7TJ, Norfolk, England Univ Dusseldorf, Inst Evolut Genet, D-40225 Dusseldorf, Germany Univ Cologne, Inst Genet, Cologne, Germany Univ Sao Paulo, Dept Biol, Fac Filosofia Ciencias &Letras Ribeirao Preto, BR-14040901 Ribeirao Preto, Brazil Univ Edinburgh, Ashworth Labs, Inst Evolutionary Biol &Edinburgh Gen, Edinburgh EH9 3FL, Midlothian, Scotland Univ E Anglia, Sch Biol Sci, Norwich NR4 7TJ, Norfolk, England Royal Holloway Univ London, Sch Biol Sci, London, England Maynooth Univ, Dept Biol, Co, Kildare, Ireland Univ Bristol, Sch Biol Sci, Bristol BS8 1TQ, Avon, England CSIRO, Land &Water Flagship, Canberra, ACT, Australia Trin Coll Dublin, Sch Nat Sci, Dept Zool, Dublin, Ireland Zool Soc London, Inst Zool, London NW1 4RY, England ETH, Inst Integrat Biol, Theoret Biol, CH-8092 Zurich, Switzerland Swiss Inst Bioinformat, Lausanne, Switzerland Swiss Fed Inst Technol, Dept Biosyst Sci &Engn, Computat Evolut, Basel, Switzerland USDA ARS, Bee Res Lab, Washington, DC 20250 USA Univ Sao Paulo, Dept Genet, Fac Med Ribeirao Preto, BR-14040900 Ribeirao Preto, Brazil N Carolina State Univ, Ctr Res Sci Computat, Raleigh, NC 27695 USA Kyoto Univ, Grad Sch Agr, Lab Insect Ecol, Kyoto, Japan Univ Sao Paulo, Dept Biol Celular &Mol &Bioagentes Patogen, Fac Med Ribeirao Preto, BR-14040900 Ribeirao Preto, Brazil Inst Fed Educ Ciencia &Tecnol Sao Paulo, BR-15991502 Matao, Brazil Ohio State Univ, Dept Entomol, Wooster, OH 44791 USA Oxford Brookes Univ, Fac Hlth &Life Sci, Dept Biol &Med Sci, Oxford OX3 0BP, England Xian Jiaotong Liverpool Univ, Dept Biol Sci, Suzhou, Peoples R China Univ Hosp Halle Saale, Dept Lab Med, Halle, Germany German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany Univ Southampton, Southampton, Hants, England Univ Leicester, Dept Biol, Leicester, Leics, England Univ Fed Sao Carlos, Ctr Ciencias Biol &Saude, Dept Genet &Evolucao, BR-13565905 Sao Carlos, SP, Brazil Univ Estadual Paulista, Fac Ciencias Agr &Vet, Dept Tecnol, BR-14884900 Jaboticabal, Brazil Univ N Carolina, Dept Biol, Greensboro, NC 27403 USA Natl Ctr Sci Res Demokritos, Inst Biosci &Applicat, Athens, Greece Univ Munich, Munich, Germany Baylor Coll Med, Dept Mol &Human Genet, Human Genome Sequencing Ctr, Houston, TX 77030 USA Univ Illinois, Roy J Carver Biotechnol, Urbana, IL 61801 USA Univ Illinois, Dept Crop Sci, Urbana, IL 61801 USA Univ Illinois, Inst Genom Biol, Urbana, IL 61801 USA MD Anderson Canc Ctr, Sch Hlth Profess, Mol Genet Technol Program, Unit 2, Houston, TX 77025 USA Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA Univ Ghent, Dept Biochem &Microbiol, Lab Prot Biochem &Biomol Engn, B-9000 Ghent, Belgium Queen Mary Univ London, Sch Biol &Chem Sci, Dept Biol &Expt Psychol, London E1 4NS, England Guangzhou Univ, Sch Life Sci, Guangzhou, Guangdong, Peoples R China Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Ctr Computat Biol, Baltimore, MD 21205 USA Univ Illinois, Neurosci Program, Dept Entomol, Carl R Woese Inst Genom Biol, Urbana, IL 61801 USA Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, 14884-900, Brazi National Institutes of Health (NIH): DP1 OD006416 National Institutes of Health (NIH): U54 HG003273 Agriculture and Food Research Initiative Competitive grant from the USDA National Institute of Food and Agriculture: 2010-65106-21301 FAPESP: 11/03171-5 Marie Curie International Outgoing Fellowship: PIOF-GA-2011-303312 Swiss National Science Foundation: 31003A-125350 Swiss National Science Foundation: 31003A-143936

Published
2015
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7. Convergent evolution of the genomes of marine mammals

Author

M. Thomas P. Gilbert, Gregg W.C. Thomas, Richard A. Gibbs, Cornelis E van Elk, Jessica Alföldi, Matthew W. Hahn, Annalaura Mancia, Vandita Joshi, Xiang Qin, Tomáš Vinař, Rasmus Nielsen, Jochen B. W. Wolf, Kim C. Worley, Andrew D. Foote, Jiaxin Qu, Christie Kovar, Sandra L. Lee, Brian J. Raney, Ziad Khan, Margaret E. Hunter, Donna M. Muzny, Shannon Dugan, Nagarjun Vijay, Yue Liu, Kerstin Lindblad-Toh, and Jixin Deng

Subjects
Sequence assembly, Genomics, Biology, acquatic environment, Genome, acquatic environment, marine mammals, phenotypic adaptation, Article, Evolution, Molecular, Molecular evolution, Convergent evolution, Genetics, Animals, Humans, 14. Life underwater, Selection, Genetic, marine mammals, Gene, Phylogeny, Mammals, phenotypic adaptation, Ambientale, Phenotypic trait, Adaptation, Physiological, Phenotype, Sister group, Amino Acid Substitution, Evolutionary biology
Abstract

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

Published
2014
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8. Finding the missing honey bee genes: lessons learned from a genome upgrade

Author

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

Subjects
Bees/genetics, TANDEM REPEATS, Gene annotation, Sequence assembly, Genes, Insect, Gene prediction, Repetitive DNA, Abelles, Genome, Open Reading Frames/genetics, PROTEIN FAMILIES, Databases, Genetic, ddc:576.5, 2. Zero hunger, Genetics, Base Composition, Genome project, Peptides/analysis, Bees, APIS-MELLIFERA, Apis mellifera, Research Article, Biotechnology, Genome improvement, OPEN READING FRAMES, Computational biology, Biology, Genome sequencing, Genètica molecular, SOCIAL INSECT, DNA sequencing, DOMAIN DATABASE, Honey Bee Genome Sequencing Consortium, Open Reading Frames, Seqüència d'aminoàcids, Animals, DRAFT GENOME, Whole genome sequencing, GC content, Genome assembly, Sequence Homology, Amino Acid, Sequence Analysis, RNA, fungi, Biology and Life Sciences, Molecular Sequence Annotation, Honey bee, 15. Life on land, DNA-SEQUENCES, Interspersed Repetitive Sequences, TRANSPOSABLE ELEMENTS, CLASSIFICATION-SYSTEM, Peptides, Transcriptome, Interspersed Repetitive Sequences/genetics
Abstract

Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes 5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination. Funding for the project was provided by a grant to RG from the National Human Genome Research Institute, National Institutes of Health (NHGRI, NIH) U54 HG003273. Contributions from members of the CGE lab were supported by Agriculture and Food Research Initiative Competitive grant no. 2010-65205-20407 from the USDA National Institute of Food Agriculture. AKB was supported by a Clare Luce Booth Fellowship at Georgetown University

Published
2014

9. Evaluation of 16S rDNA-based community profiling for human microbiome research

Author

Michael Feldgarden, Shibu Yooseph, Divya Kalra, Theresa A. Hepburn, Navjeet Singh, Richard A. Gibbs, Shawn Leonard, Richard K. Wilson, Elizabeth L. Appelbaum, Niall J. Lennon, Hongyu Gao, Kathie A. Mihindukulasuriya, Bonnie P. Youmans, Lynn K. Carmichael, Yue Shang, Xiang Qin, Ashlee M. Earl, George M. Weinstock, Candace N. Farmer, Scott Anderson, Yu Hui A. Rogers, Erica Sodergren, Otis Hall, Georgia Giannoukos, Joseph F. Petrosino, Brian J. Haas, Todd Z. DeSantis, Kim C. Worley, Michelle O'Laughlin, Craig Pohl, Dawn Ciulla, Matthew C. Ross, Bruce W. Birren, Patrick D. Schloss, Rachel L. Erlich, Lucinda Fulton, Yanjiao Zhou, David J. Dooling, Toby Bloom, Donna M. Muzny, Katarzyna Wilczek-Boney, Leigh Aird, Sarah K. Highlander, Kelvin Li, Elaine R. Mardis, Dirk Gevers, Doyle V. Ward, Vincent Magrini, Keenan Ross, Vandita Joshi, Tulin Ayvaz, John Gill, Christie Kovar, Diana Tabbaa, Susanna Hamilton, Karen E. Nelson, Lora Lewis, Robert S. Fulton, Lisa Hemphill, Jonathan Crabtree, Cesar Arze, Jennifer R. Wortman, Barbara A. Methé, Cristyn Kells, Edward A. Belter, Laura Courtney, and Monika Bihan

Subjects
Ecological Metrics, lcsh:Medicine, Computational biology, Biology, Biochemistry, Microbiology, Microbial Ecology, 03 medical and health sciences, DNA amplification, RNA, Ribosomal, 16S, Humans, Profiling (information science), Genome Sequencing, lcsh:Science, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Bacteria, Ecology, 030306 microbiology, Bacterial Taxonomy, lcsh:R, Human microbiome, Computational Biology, Bayes Theorem, Species Diversity, Bacteriology, DNA, Genomics, Biodiversity, 16S ribosomal RNA, 3. Good health, Nucleic acids, Earth Microbiome Project, Metagenome, lcsh:Q, Metagenomics, Species Richness, Research Article, Human Microbiome Project
Abstract

The Human Microbiome Project will establish a reference data set for analysis of the microbiome of healthy adults by surveying multiple body sites from 300 people and generating data from over 12,000 samples. To characterize these samples, the participating sequencing centers evaluated and adopted 16S rDNA community profiling protocols for ABI 3730 and 454 FLX Titanium sequencing. In the course of establishing protocols, we examined the performance and error characteristics of each technology, and the relationship of sequence error to the utility of 16S rDNA regions for classification- and OTU-based analysis of community structure. The data production protocols used for this work are those used by the participating centers to produce 16S rDNA sequence for the Human Microbiome Project. Thus, these results can be informative for interpreting the large body of clinical 16S rDNA data produced for this project.

Published
2012

10. Structure, function and diversity of the healthy human microbiome

Author

Catherine A. Lozupone, Paul Spicer, Margaret Priest, Todd J. Treangen, Niall J. Lennon, Thomas M. Schmidt, Sandra W. Clifton, Ken Chu, Vandita Joshi, Catherine C. Davis, Omry Koren, Yuanqing Wu, Christie Kovar, Jonathan Friedman, Matthew D. Pearson, Scott T. Kelley, Brandi L. Cantarel, Patrick S. G. Chain, Chad Nusbaum, Jonathan Crabtree, Lu Wang, Bonnie P. Youmans, James A. Katancik, George M. Weinstock, Granger G. Sutton, Lisa Begg, Candace N. Farmer, Victor Felix, Barbara A. Methé, Elena Deych, Martin J. Blaser, Amy L. McGuire, Pamela McInnes, Xiang Qin, James Versalovic, James R. White, Yan Ding, Christian J. Buhay, Jason R. Miller, Susan M. Huse, Wm. Michael Dunne, Vivien Bonazzi, Jeremy Zucker, Ioanna Pagani, Robert C. Edgar, Dana A. Busam, Gina A. Simone, Michael Feldgarden, Vincent Magrini, Richard A. Gibbs, Noam J. Davidovics, Indresh Singh, Lucinda Fulton, Lucia Alvarado, Rob Knight, Emma Allen-Vercoe, Teena Mehta, Patricio S. La Rosa, Carsten Russ, Joshua Orvis, Sahar Abubucker, Jacques Ravel, Richard R. Sharp, Dirk Gevers, Wesley C. Warren, Pamela Sankar, Chad Tomlinson, Donna M. Muzny, Jean E. McEwen, Nihar U. Sheth, Sheila Fisher, Katherine H. Huang, Dennis C. Friedrich, Gary C. Armitage, John Martin, Richard K. Wilson, Katarzyna Wilczek-Boney, Catrina Fronick, Patrick Minx, Rebecca Truty, William D. Shannon, Matthew B. Scholz, Kris A. Wetterstrand, Maria Y. Giovanni, Katherine P. Lemon, Floyd E. Dewhirst, Shaila Chhibba, Anthony A. Fodor, Lan Zhang, Patrick D. Schloss, Lynn M. Schriml, Doyle V. Ward, Diana Tabbaa, Jose C. Clemente, Larry J. Forney, Kimberley D. Delehaunty, Cesar Arze, Sharvari Gujja, Lita M. Proctor, Christopher Smillie, Elizabeth L. Appelbaum, Konstantinos Liolios, Chandri Yandava, David J. Dooling, Emily L. Harris, Katherine S. Pollard, Clinton Howarth, Tatiana A. Vishnivetskaya, Sarah Young, Huaiyang Jiang, Karoline Faust, Janet K. Jansson, Kymberlie Hallsworth-Pepin, Owen White, Thomas J. Sharpton, Yiming Zhu, Yanjiao Zhou, Julia A. Segre, Jason Walker, Heidi H. Kong, Toby Bloom, Mathangi Thiagarajan, Tulin Ayvaz, I. Min A. Chen, Bo Liu, Kim C. Worley, Jennifer R. Wortman, Susan Kinder Haake, Manolito Torralba, Makedonka Mitreva, Kjersti Aagaard, J. Fah Sathirapongsasuti, Carolyn Deal, Jeroen Raes, Olukemi O. Abolude, Yue Liu, Rachel L. Erlich, Gary L. Andersen, Nicola Segata, Christopher Wellington, Todd Wylie, Kristine M. Wylie, Tsegahiwot Belachew, Jonathan H. Badger, Mark A. Watson, Aye Wollam, Zhengyuan Wang, Michelle G. Giglio, Kelvin Li, Diane E. Hoffmann, Cristyn Kells, Daniel D. Sommer, Victor M. Markowitz, Chien Chi Lo, Karen E. Nelson, Brian J. Haas, Ruth M. Farrell, Craig Pohl, Harindra Arachchi, Nicholas B. King, Gregory A. Buck, Konstantinos Mavromatis, Qiandong Zeng, Krishna Palaniappan, Kathie A. Mihindukulasuriya, Dan Knights, Anup Mahurkar, Nathalia Garcia, Mary A. Cutting, Theresa A. Hepburn, Mina Rho, Catherine Jordan, Christina Giblin, Dawn Ciulla, Shital M. Patel, Eric J. Alm, Kevin Riehle, Irene Newsham, Sarah K. Highlander, Jamison McCorrison, Nikos C. Kyrpides, Mircea Podar, Beltran Rodriguez-Mueller, Lora Lewis, Robert S. Fulton, Yuzhen Ye, Joseph L. Campbell, Laurie Zoloth, R. Dwayne Lunsford, Ramana Madupu, A. Scott Durkin, Maria C. Rivera, Sergey Koren, Shibu Yooseph, Ruth E. Ley, Erica Sodergren, Cecil M. Lewis, Heather Huot Creasy, Joseph F. Petrosino, Jacques Izard, Jack D. Sobel, J. Paul Brooks, Jeffrey G. Reid, Antonio Gonzalez, Narmada Shenoy, Elizabeth A. Lobos, Georgia Giannoukos, Matthew C. Ross, Allison D. Griggs, Yu-Hui Rogers, Leslie Foster, Wendy A. Keitel, Lei Chen, Alyxandria M. Schubert, Scott Anderson, Peter J. Mannon, Shane Canon, Hongyu Gao, Mihai Pop, Holli A. Hamilton, Tessa Madden, Michelle Oglaughlin, Karthik Kota, Monika Bihan, Veena Bhonagiri, Michael Holder, Daniel McDonald, Liang Ye, Sandra L. Lee, Rosamond Rhodes, Asif T. Chinwalla, Ashlee M. Earl, Shannon Dugan, Sean Conlan, Johannes B. Goll, Jonathan M. Goldberg, Valentina Di Francesco, Curtis Huttenhower, Brandi Herter, Todd Z. DeSantis, Sean M. Sykes, Michael Fitzgerald, Elaine R. Mardis, Jane Peterson, Bruce W. Birren, Ravi Sanka, Carl C. Baker, Jeffery A. Schloss, Massachusetts Institute of Technology. Computational and Systems Biology Program, Massachusetts Institute of Technology. Department of Biological Engineering, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Alm, Eric J., Friedman, Jonathan, and Smillie, Christopher S.

Subjects
Adult, Male, Adolescent, Ecology (disciplines), Biology, Bioinformatics, 03 medical and health sciences, Young Adult, RNA, Ribosomal, 16S, Humans, Microbiome, Ecosystem, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Bacteria, 030306 microbiology, Gastrointestinal Microbiome, Human microbiome, Biodiversity, Phenotype, Evolutionary biology, Health, Earth Microbiome Project, Metagenome, Enterotype, Female, Oral Microbiome, Metagenomics, Metabolic Networks and Pathways, Human Microbiome Project
Abstract

Author Manuscript date: 2013 February 05., Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

Published
2012

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

Author

Joshua Y Shen, Yoko Kuroki, Lynne V. Nazareth, Shafagh Al Nadaf, Terence P. Speed, Katherine Belov, Kevin R. Nicholas, James Lindsay, Yoshiyuki Sakaki, Anthony T. Papenfuss, Arthur Hsu, Stephen Frankenberg, Hannah V. Siddle, Shalini N. Jhangiani, Fremiet Lara, Jireh Santibanez, Thomas N. Heider, Jixin Deng, Margaret Morgan, Xing-Zhi Henry Song, Rebecca Thornton, Benjamin James Lansdell, Frank W. Nicholas, A. Men, Carmen Troon, Shinji Kondo, William A O'Hara, Christophe Lefevre, Susan M. Forrest, San Juana Ruiz, Geoffrey Okwuonu, Chenwei Wang, Andrew Cree, Yanqiu Hu, Matthew Wakefield, Kyall R. Zenger, Rachel J. O’Neill, Donna M. Muzny, Benjamin G. Cocks, Huyen Dinh, Kaighin A. McColl, Geoff Shaw, Kim C. Worley, Hongshi Yu, Jennifer A. Marshall Graves, Asao Fujiyama, Andrew J Pask, Keng Yih Chew, Janine E. Deakin, Lankesha Yapa, Elizabeth Kuczek, Tanya Levchenko, George M. Weinstock, Kirsty R. Short, Malcolm A. Ferguson-Smith, Yutaka Suzuki, Mehlika Hazar-Rethinam, Chyn Jing, Yuichiro Nishida, Gerald R. Fowler, Paul D. Waters, Lora Lewis, Elizabeth A. Pharo, Timothy A. Hore, Nanette Y. Schneider, Susan Fairley, Danielle Hickford, Zhi-Ping Feng, Annette McGrath, Vandita Joshi, Willem Rens, Jianghui Wang, Javier Herrero, Desmond W. Cooper, Christie Kovar, Kathryn Beal, Daniel Thomas, Yogi Sundaravadanam, Stephen M. J. Searle, David L. A. Wood, Marilyn B. Renfree, Yue-E Liu, Dawn M. Carone, A Mohammadi, Amber E. Stephens, Shoji Tatsumoto, Jessica M Stringer, John Davis, Allison Hall, Sumio Sugano, Peter A Wilson, Margaret L. Delbridge, Atsushi Toyoda, Paul Flicek, Emily S. W. Wong, Lei Chen, Ion Mandiou, Shunsuke Suzuki, Brandon R. Menzies, Richard A. Gibbs, Janette Edson, Sarah E. Williams, Chen-Chen Wu, Ferguson-Smith, Malcolm [0000-0001-9372-1381], and Apollo - University of Cambridge Repository

Subjects
0106 biological sciences, Molecular Sequence Data, wallaby, Sequence assembly, Zoology, Genomics, Genome, 010603 evolutionary biology, 01 natural sciences, DNA sequencing, Mammalian reproduction, symbols.namesake, 03 medical and health sciences, Genomic Imprinting, 0302 clinical medicine, Tammar wallaby, Marsupial, Animals, Macropus, In Situ Hybridization, Fluorescence, 030304 developmental biology, Genetics, Sanger sequencing, Whole genome sequencing, Macropodidae, 0303 health sciences, biology, Research, Reproduction, Australia, Correction, Chromosome Mapping, Sequence Analysis, DNA, biology.organism_classification, Research Highlight, Biological Evolution, Chromosomes, Mammalian, kangaroo, MicroRNAs, Gene Expression Regulation, symbols, Female, Transcriptome, Sequence Alignment, 030217 neurology & neurosurgery
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

12. A catalog of reference genomes from the human microbiome

Author

Dirk Gevers, Doyle V. Ward, Sean M. Sykes, Justin Johnson, Michael Fitzgerald, Jessica B. Hostetler, Sarah Young, Dianhui Zhu, Jason R. Miller, Chinnappa D. Kodira, Aaron M. Berlin, Erica Sodergren, Michael G. Surette, Matthew D. Pearson, Asif T. Chinwalla, Ashlee M. Earl, Michael Feldgarden, Kim C. Worley, Christian J. Buhay, Lisa Hemphill, Manolito Torralba, Xiang Qin, Jonathan H. Badger, Clint Howarth, Marcus Gillis, Candace N. Farmer, Karen E. Nelson, Bruce W. Birren, Richard A. Gibbs, Sandra W. Clifton, Mike Holder, Aye Wollam, Carsten Russ, Wesley C. Warren, Brian J. Haas, Michelle G. Giglio, Qiang Xu, Richard K. Wilson, Patrick Minx, Scott Durkin, Chad Nusbaum, Craig Pohl, Robert S. Fulton, Steve Ferriera, Chandri N. Yandava, Sharvari Gujja, Qiandong Zeng, Ramana Madupu, Victor Markowitz, Joshua Orvis, Andrew Cree, Chad Tomlinson, Donna M. Muzny, Vandita Joshi, Amrita Pati, Christie Kovar, Theresa A. Hepburn, Nikos C. Kyrpides, Kymberlie H. Pepin, Douglas B. Rusch, Granger G. Sutton, Amr Abouellleil, Konstantinos Liolios, Sarah K. Highlander, Yan Ding, Jamison McCorrison, George M. Weinstock, Kris A. Wetterstrand, Emma Allen-Vercoe, Teena Mehta, Lucinda Fulton, Katarzyna Wilczek-Boney, Makedonka Mitreva, Lei Chen, Joseph F. Petrosino, Heather Huot Creasy, Shannon Dugan, Lan Zhang, Owen White, Robert L. Strausberg, Jennifer R. Wortman, Jonathan Crabtree, and Barbara A. Methé

Subjects
Sequence analysis, Respiratory System, Urogenital System, Biology, Genome, Article, Bacterial Proteins, Phylogenetics, Genome, Archaeal, Databases, Genetic, Humans, Microbiome, Gene, Phylogeny, Skin, Genetics, Mouth, Multidisciplinary, Bacteria, Human microbiome, Computational Biology, Genetic Variation, Biodiversity, Sequence Analysis, DNA, Gastrointestinal Tract, Metagenomics, Genes, Bacterial, Metagenome, Peptides, Genome, Bacterial, Reference genome
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

13. The genome sequence of taurine cattle: A window to ruminant biology and evolution

Author

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

Subjects
Male, genome sequence, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, Genome, Genética y Herencia, Segmental duplication, 2. Zero hunger, Genetics, ddc:616, 0303 health sciences, Multidisciplinary, 04 agricultural and veterinary sciences, Bovine genome, Animals, Domestic, Proteins/genetics, Female, CIENCIAS NATURALES Y EXACTAS, Sequence analysis, Evolution, Biotecnología Agropecuaria, Molecular Sequence Data, Tecnología GM, clonación de ganado, selección asistida, diagnósticos, tecnología de producción de biomasa, etc, Biology, Synteny, Article, Ciencias Biológicas, Evolution, Molecular, 03 medical and health sciences, Species Specificity, Animals, Humans, General, Gene, 030304 developmental biology, Whole genome sequencing, ved/biology, Taurine cattle, 0402 animal and dairy science, Genetic Variation, Sequence Analysis, DNA, 040201 dairy & animal science, Bos taurus, Alternative Splicing, MicroRNAs/genetics, CIENCIAS AGRÍCOLAS, cattle, Cattle, genetic
Abstract

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production. Fil: Bovine Genome Sequencing and Analysis Consortium. Bovine Genome Sequencing And Analysis Consortium; Estados Unidos Fil: Amadio, Ariel Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; Argentina

Published
2009
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