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1. Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions

Author

Westermann, Alexander J., Forstner, Konrad U., Amman, Fabian, Barquist, Lars, Chao, Yanjie, Schulte, Leon N., Muller, Lydia, Reinhardt, Richard, Stadler, Peter F., and Vogel, Jorg

Subjects
Virulence (Microbiology) -- Analysis -- Health aspects, Gene expression -- Analysis, RNA sequencing -- Analysis, Antisense RNA -- Analysis -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK-STAT signalling, and we identify infectionspecific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes., Regulatory RNAs crucially contribute to post-transcriptional control of gene expression in a wide array of organisms, including pathogenic bacteria (1-3). The facultative intracellular pathogen Salmonella enterica serovar Typhimurium (hereafter referred [...]

Published
2016
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2. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Author

Dohm, Juliane C., Minoche, Andre E., Holtgrawe, Daniela, Capella-Gutierrez, Salvador, Zakrzewski, Falk, Tafer, Hakim, Rupp, Oliver, Sorensen, Thomas Rosleff, Stracke, Ralf, Reinhardt, Richard, Goesmann, Alexander, Kraft, Thomas, Schulz, Britta, Stadler, Peter F., Schmidt, Thomas, Gabaldon, Toni, Lehrach, Hans, Weisshaar, Bernd, and Himmelbauer, Heinz

Subjects
Plant genetics -- Research, Sugar beet -- Physiological aspects -- Genetic aspects, Plant breeding -- Research, Botanical research, Plant physiology -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n = 18 chromosomes, has an estimated genome size of 714-758 megabases (1) and shares an ancient genome triplication with other eudicot plants (2). Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet (3). Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated (4) to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology., During the last 200 years of sugar beet breeding, the sugar content has increased from 8% to 18% in today's cultivars. Breeding has also actively selected for traits like resistance [...]

Published
2014
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3. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

Author

Bulgarelli, Davide, Rott, Matthias, Schlaeppi, Klaus, van Themaat, Emiel Ver Loren, Ahmadinejad, Nahal, Assenza, Federica, Rauf, Philipp, Huettel, Bruno, Reinhardt, Richard, Schmelzer, Elmon, Peplies, Joerg, Gloeckner, Frank Oliver, Amann, Rudolf, Eickhorst, Thilo, and Schulze-Lefert, Paul

Subjects
Microbiota (Symbiotic organisms) -- Comparative analysis -- Research -- Physiological aspects, Arabidopsis thaliana -- Physiological aspects -- Comparative analysis -- Research, Microbial colonies -- Comparative analysis -- Physiological aspects -- Research, Host-bacteria relationships -- Research -- Physiological aspects -- Comparative analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth (1). Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development (2), with implications ranging from enhanced crop productivity (3) to phytoremediation (4). Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication (5). Several studies attempted to describe the structure of bacterial root endophytes (6); however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells., We have grown Arabidopsis ecotypes Shakdara (Sha) and Landsberg erecta (Ler) in natural soils of contrasting geochemistry, designated Cologne (clay- and silt-rich) or Golm (sand-rich) soil, under controlled environmental conditions [...]

Published
2013

4. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

Author

Bulgarelli, Davide, Rott, Matthias, Schlaeppi, Klaus, van Themaat, Emiel Ver Loren, Ahmadinejad, Nahal, Assenza, Federica, Rauf, Philipp, Huettel, Bruno, Reinhardt, Richard, Schmelzer, Elmon, Peplies, Joerg, Gloeckner, Frank Oliver, Amann, Rudolf, Eickhorst, Thilo, and Schulze-Lefert, Paul

Subjects
Arabidopsis -- Physiological aspects -- Diseases and pests, Microbial colonies -- Physiological aspects -- Health aspects, Host-parasite relationships -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth (1). Notably, soil bacteria are able to multiply inside roots [...]

Published
2012

5. The primary transcriptome of the major human pathogen Helicobacter pylori

Author

Sharma, Cynthia M., Hoffmann, Steve, Darfeuille, Fabien, Reignier, Jeremy, Findeiss, Sven, Sittka, Alexandra, Chabas, Sandrine, Reiche, Kristin, Hackermuller, Jorg, Reinhardt, Richard, and Vogel, Peter F. Stadler Jorg

Subjects
Gene expression -- Analysis, Helicobacter pylori -- Analysis -- Genetic aspects -- Physiological aspects, Genetic transcription -- Analysis, Antisense RNA -- Analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of ~60 small RNAs including the e-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species., About 50% of all humans are infected with Helicobacter pylori, a microaerophilic, Gram-negative e-proteobacterium that thrives in the acidic environment of the stomach, and is associated with severe inflammation' peptic [...]

Published
2010
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6. Ktu/PF13 is required for cytoplasmic pre-assembly of axonemal dyneins

Author

Omran, Heymut, Kobayashi, Daisuke, Olbrich, Heike, Tsukahara, Tatsuya, Loges, Niki T., Hagiwara, Haruo, Zhang, Qi, Leblond, Gerard, O'Toole, Eileen, Hara, Chikako, Mizuno, Hideaki, Kawano, Hiroyuki, Fliegauf, Manfred, Yagi, Toshiki, Koshida, Sumito, Miyawaki, Atsushi, Zentgraf, Hanswalter, Seithe, Horst, Reinhardt, Richard, Watanabe, Yoshinori, Kamiya, Ritsu, Mitchell, David R., and Takeda, Hiroyuki

Subjects
Flagella (Microbiology) -- Physiological aspects -- Genetic aspects, Gene expression -- Physiological aspects -- Genetic aspects, Cilia and ciliary motion -- Physiological aspects -- Genetic aspects, Dynein -- Physiological aspects -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Physiological aspects, Genetic aspects
Abstract

Cilia and flagella are highly conserved organelles that have diverse roles in cell motility and sensing extracellular signals. Motility defects in cilia and flagella often result in primary ciliary dyskinesia. [...]

Published
2008

7. 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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8. 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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9. Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica

Author

Seo, Hee-Chan, Edvardsen, Rolf Brudvik, Maeland, Anne Dorthea, Bjordal, Marianne, Jensen, Marit Flo, Hansen, Anette, Flaat, Mette, Weissenbach, Jean, Lehrach, Hans, Wincker, Patrick, Reinhardt, Richard, and Chourrout, Daniel

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

Author(s): Hee-Chan Seo [1]; Rolf Brudvik Edvardsen [1]; Anne Dorthea Maeland [1]; Marianne Bjordal [1]; Marit Flo Jensen [1]; Anette Hansen [1]; Mette Flaat [1]; Jean Weissenbach [3]; Hans Lehrach [...]

Published
2004
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10. A conspicuous nickel protein in microbial mats that oxidize methane anaerobically

Author

Kruger, Martin, Meyerdierks, Anke, Glockner, Frank Oliver, Amann, Rudolf, Widdel, Friedrich, Kube, Michael, Reinhardt, Richard, Kahnt, Jorg, Bocher, Reinhard, Thauer, Rudolf K., and Shima, Seigo

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

Author(s): Martin Krüger [1]; Anke Meyerdierks [1]; Frank Oliver Glöckner [1]; Rudolf Amann [1]; Friedrich Widdel (corresponding author) [1]; Michael Kube [2]; Richard Reinhardt [2]; Jörg Kahnt [3]; Reinhard Böcher [...]

Published
2003
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11. Initial sequencing and analysis of the human genome

Author

Lander, Eric S., Linton, Lauren M., Birren, Bruce, Nusbaum, Chad, Zody, Michael C., Baldwin, Jennifer, Devon, Keri, Dewar, Ken, Doyle, Michael, FitzHugh, William, Funke, Roel, Gage, Diane, Harris, Katrina, Heaford, Andrew, Howland, John, Kann, Lisa, Lehoczky, Jessica, LeVine, Rosie, McEwan, Paul, McKernan, Kevin, Meldrim, James, Mesirov, Jill P., Miranda, Cher, Morris, William, Naylor, Jerome, Raymond, Christina, Rosetti, Mark, Santos, Ralph, Sheridan, Andrew, Sougnez, Carrie, Stange-Thomann, Nicole, Stojanovic, Nikola, Subramanian, Aravind, Wyman, Dudley, Rogers, Jane, Sulston, John, Ainscough, Rachael, Beck, Stephan, Bentley, David, Burton, John, Clee, Christopher, Carter, Nigel, Coulson, Alan, Deadman, Rebecca, Deloukas, Panos, Dunham, Andrew, Dunham, Ian, Durbin, Richard, French, Lisa, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Humphray, Sean, Hunt, Adrienne, Jones, Matthew, Lloyd, Christine, McMurray, Amanda, Matthews, Lucy, Mercer, Simon, Milne, Sarah, Mullikin, James C., Mungall, Andrew, Plumb, Robert, Ross, Mark, Shownkeen, Ratna, Sims, Sarah, Waterston, Robert H., Wilson, Richard K., Hillier, LaDeana W., McPherson, John D., Marra, Marco A., Mardis, Elaine R., Fulton, Lucinda A., Chinwalla, Asif T., Pepin, Kymberlie H., Gish, Warren R., Chissoe, Stephanie L., Wendl, Michael C., Delehaunty, Kim D., Miner, Tracie L., Delehaunty, Andrew, Kramer, Jason B., Cook, Lisa L., Fulton, Robert S., Johnson, Douglas L., Minx, Patrick J., Clifton, Sandra W., Hawkins, Trevor, Branscomb, Elbert, Predki, Paul, Richardson, Paul, Wenning, Sarah, Slezak, Tom, Doggett, Norman, Cheng, Jan-Fang, Olsen, Anne, Lucas, Susan, Elkin, Christopher, Uberbacher, Edward, Frazier, Marvin, Gibbs, Richard A., Muzny, Donna M., Scherer, Steven E., Bouck, John B., Sodergren, Erica J., Worley, Kim C., Rives, Catherine M., Gorrell, James H., Metzker, Michael L., Naylor, Susan L., Kucherlapati, Raju S., Nelson, David L., Weinstock, George M., Sakaki, Yoshiyuki, Fujiyama, Asao, Hattori, Masahira, Yada, Tetsushi, Toyoda, Atsushi, Itoh, Takehiko, Kawagoe, Chiharu, Watanabe, Hidemi, Totoki, Yasushi, Taylor, Todd, Weissenbach, Jean, Heilig, Roland, Saurin, William, Artiguenave, Francois, Brottier, Philippe, Bruls, Thomas, Pelletier, Eric, Robert, Catherine, Wincker, Patrick, Rosenthal, Andre, Platzer, Matthias, Nyakatura, Gerald, Taudien, Stefan, Rump, Andreas, Smith, Douglas R., Doucette-Stamm, Lynn, Rubenfield, Marc, Weinstock, Keith, Lee, Hong Mei, Dubois, JoAnn, Yang, Huanming, Yu, Jun, Wang, Jian, Huang, Guyang, Gu, Jun, Hood, Leroy, Rowen, Lee, Madan, Anup, Qin, Shizen, Davis, Ronald W., Federspiel, Nancy A., Abola, A. Pia, Proctor, Michael J., Roe, Bruce A., Chen, Feng, Pan, Huaqin, Ramser, Juliane, Lehrach, Hans, Reinhardt, Richard, McCombie, W. Richard, de la Bastide, Melissa, Dedhia, Neilay, Blocker, Helmut, Hornischer, Klaus, Nordsiek, Gabriele, Agarwala, Richa, Aravind, L., Bailey, Jeffrey A., Bateman, Alex, Batzoglou, Serafim, Birney, Ewan, Bork, Peer, Brown, Daniel G., Burge, Christopher B., Cerutti, Lorenzo, Chen, Hsiu-Chuan, Church, Deanna, Clamp, Michele, Copley, Richard R., Doerks, Tobias, Eddy, Sean R., Eichler, Evan E., Furey, Terrence S., Galagan, James, Gilbert, James G. R., Harmon, Cyrus, Hayashizaki, Yoshihide, Haussler, David, Hermjakob, Henning, Hokamp, Karsten, Jang, Wonhee, Johnson, L. Steven, Jones, Thomas A., Kasif, Simon, Kaspryzk, Arek, Kennedy, Scot, Kent, W. James, Kitts, Paul, Koonin, Eugene V., Korf, Ian, Kulp, David, Lancet, Doron, Lowe, Todd M., McLysaght, Aoife, Mikkelsen, Tarjei, Moran, John V., Mulder, Nicola, Pollara, Victor J., Ponting, Chris P., Schuler, Greg, Schultz, Jorg, Slater, Guy, Smit, Arian F. A., Stupka, Elia, Szustakowki, Joseph, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Wallis, John, Wheeler, Raymond, Williams, Alan, Wolf, Yuri I., Wolfe, Kenneth H., Yang, Shiaw-Pyng, Yeh, Ru-Fang, Collins, Francis, Guyer, Mark S., Peterson, Jane, Felsenfeld, Adam, Wetterstrand, Kris A., Myers, Richard M., Schmutz, Jeremy, Dickson, Mark, Grimwood, Jane, Cox, David R., Olson, Maynard V., Kaul, Rajinder, Raymond, Christopher, Shimizu, Nobuyoshi, Kawasaki, Kazuhiko, Minoshima, Shinsei, Evans, Glen A., Athanasiou, Maria, Schultz, Roger, Patrinos, Aristides, and Morgan, Michael J.

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

Author(s): International Human Genome Sequencing Consortium; Whitehead Institute for Biomedical Research, Center for Genome Research:; Eric S. Lander [1]; Lauren M. Linton [1]; Bruce Birren [1]; Chad Nusbaum [1]; Michael [...]

Published
2001
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12. A physical map of the human genome

Author

McPherson, John D., Marra, Marco, Hillier, LaDeana, Waterston, Robert H., Chinwalla, Asif, Wallis, John, Sekhon, Mandeep, Wylie, Kristine, Mardis, Elaine R., Wilson, Richard K., Fulton, Robert, Kucaba, Tamara A., Wagner-McPherson, Caryn, Barbazuk, William B., Gregory, Simon G., Humphray, Sean J., French, Lisa, Evans, Richard S., Bethel, Graeme, Whittaker, Adam, Holden, Jane L., McCann, Owen T., Dunham, Andrew, Soderlund, Carol, Scott, Carol E., Bentley, David R., Schuler, Gregory, Chen, Hsiu-Chuan, Jang, Wonhee, Green, Eric D., Idol, Jacquelyn R., Maduro, Valerie V. Braden, Montgomery, Kate T., Lee, Eunice, Miller, Ashley, Emerling, Suzanne, Kucherlapati, Raju, Gibbs, Richard, Scherer, Steve, Gorrell, J. Harley, Sodergren, Erica, Clerc-Blankenburg, Kerstin, Tabor, Paul, Naylor, Susan, Garcia, Dawn, de Jong, Pieter J., Catanese, Joseph J., Nowak, Norma, Osoegawa, Kazutoyo, Qin, Shizhen, Rowen, Lee, Madan, Anuradha, Dors, Monica, Hood, Leroy, Trask, Barbara, Friedman, Cynthia, Massa, Hillary, Cheung, Vivian G., Kirsch, Ilan R., Reid, Thomas, Yonescu, Raluca, Weissenbach, Jean, Bruls, Thomas, Heilig, Roland, Branscomb, Elbert, Olsen, Anne, Doggett, Norman, Cheng, Jan-Fang, Hawkins, Trevor, Myers, Richard M., Shang, Jin, Ramirez, Lucia, Schmutz, Jeremy, Velasquez, Olivia, Dixon, Kami, Stone, Nancy E., Cox, David R., Haussler, David, Kent, W. James, Furey, Terrence, Rogic, Sanja, Kennedy, Scot, Jones, Steven, Rosenthal, Andre, Wen, Gaiping, Schilhabel, Markus, Gloeckner, Gernot, Nyakatura, Gerald, Siebert, Reiner, Schlegelberger, Brigitte, Korenberg, Julie, Chen, Xiao-Ning, Fujiyama, Asao, Hattori, Masahira, Toyoda, Atsushi, Yada, Tetsushi, Park, Hong-Seok, Sakaki, Yoshiyuki, Shimizu, Nobuyoshi, Asakawa, Shuichi, Kawasaki, Kazuhiko, Sasaki, Takashi, Shintani, Ai, Shimizu, Atsushi, Shibuya, Kazunori, Kudoh, Jun, Minoshima, Shinsei, Ramser, Juliane, Seranski, Peter, Hoff, Celine, Poustka, Annemarie, Reinhardt, Richard, and Lehrach, Hans

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

Author(s): The International Human Genome Mapping Consortium ; Washington University School of Medicine, Genome Sequencing Center: ; John D. McPherson (corresponding author) [1]; Marco Marra [1]; LaDeana Hillier [1]; Robert [...]

Published
2001
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13. The genome sequence of Atlantic cod reveals a unique immune system

Author

Star, Bastiaan, Nederbragt, Alexander J., Jentoft, Sissel, Grimholt, Unni, Malmstrøm, Martin, Gregers, Tone F., Rounge, Trine B., Paulsen, Jonas, Solbakken, Monica H., Sharma, Animesh, Wetten, Ola F., Lanzén, Anders, Winer, Roger, Knight, James, Vogel, Jan-Hinnerk, Aken, Bronwen, Andersen, Øivind, Lagesen, Karin, Tooming-Klunderud, Ave, Edvardsen, Rolf B., Tina, Kirubakaran G., Espelund, Mari, Nepal, Chirag, Previti, Christopher, Karlsen, Bård Ove, Moum, Truls, Skage, Morten, Berg, Paul R., Gjøen, Tor, Kuhl, Heiner, Thorsen, Jim, Malde, Ketil, Reinhardt, Richard, Du, Lei, Johansen, Steinar D., Searle, Steve, Lien, Sigbjørn, Nilsen, Frank, Jonassen, Inge, Omholt, Stig W., Stenseth, Nils Chr., and Jakobsen, Kjetill S.

Published
2011
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14. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Author

Dohm, Juliane C., primary, Minoche, André E., additional, Holtgräwe, Daniela, additional, Capella-Gutiérrez, Salvador, additional, Zakrzewski, Falk, additional, Tafer, Hakim, additional, Rupp, Oliver, additional, Sörensen, Thomas Rosleff, additional, Stracke, Ralf, additional, Reinhardt, Richard, additional, Goesmann, Alexander, additional, Kraft, Thomas, additional, Schulz, Britta, additional, Stadler, Peter F., additional, Schmidt, Thomas, additional, Gabaldón, Toni, additional, Lehrach, Hans, additional, Weisshaar, Bernd, additional, and Himmelbauer, Heinz, additional

Published
2013
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15. Erratum: Genome analysis of the platypus reveals unique signatures of evolution

Author

Warren, Wesley C., primary, Hillier, LaDeana W., additional, Marshall Graves, Jennifer A., additional, Birney, Ewan, additional, Ponting, Chris P., additional, Grützner, Frank, additional, Belov, Katherine, additional, Miller, Webb, additional, Clarke, Laura, additional, Chinwalla, Asif T., additional, Yang, Shiaw-Pyng, additional, Heger, Andreas, additional, Locke, Devin P., additional, Miethke, Pat, additional, Waters, Paul D., additional, Veyrunes, Frédéric, additional, Fulton, Lucinda, additional, Fulton, Bob, additional, Graves, Tina, additional, Wallis, John, additional, Puente, Xose S., additional, López-Otín, Carlos, additional, Ordóñez, Gonzalo R., additional, Eichler, Evan E., additional, Chen, Lin, additional, Cheng, Ze, additional, Deakin, Janine E., additional, Alsop, Amber, additional, Thompson, Katherine, additional, Kirby, Patrick, additional, Papenfuss, Anthony T., additional, Wakefield, Matthew J., additional, Olender, Tsviya, additional, Lancet, Doron, additional, Huttley, Gavin A., additional, Smit, Arian F. A., additional, Pask, Andrew, additional, Temple-Smith, Peter, additional, Batzer, Mark A., additional, Walker, Jerilyn A., additional, Konkel, Miriam K., additional, Harris, Robert S., additional, Whittington, Camilla M., additional, Wong, Emily S. W., additional, Gemmell, Neil J., additional, Buschiazzo, Emmanuel, additional, Vargas Jentzsch, Iris M., additional, Merkel, Angelika, additional, Schmitz, Juergen, additional, Zemann, Anja, additional, Churakov, Gennady, additional, Kriegs, Jan Ole, additional, Brosius, Juergen, additional, Murchison, Elizabeth P., additional, Sachidanandam, Ravi, additional, Smith, Carly, additional, Hannon, Gregory J., additional, Tsend-Ayush, Enkhjargal, additional, McMillan, Daniel, additional, Attenborough, Rosalind, additional, Rens, Willem, additional, Ferguson-Smith, Malcolm, additional, Lefèvre, Christophe M., additional, Sharp, Julie A., additional, Nicholas, Kevin R., additional, Ray, David A., additional, Kube, Michael, additional, Reinhardt, Richard, additional, Pringle, Thomas H., additional, Taylor, James, additional, Jones, Russell C., additional, Nixon, Brett, additional, Dacheux, Jean-Louis, additional, Niwa, Hitoshi, additional, Sekita, Yoko, additional, Huang, Xiaoqiu, additional, Stark, Alexander, additional, Kheradpour, Pouya, additional, Kellis, Manolis, additional, Flicek, Paul, additional, Chen, Yuan, additional, Webber, Caleb, additional, Hardison, Ross, additional, Nelson, Joanne, additional, Hallsworth-Pepin, Kym, additional, Delehaunty, Kim, additional, Markovic, Chris, additional, Minx, Pat, additional, Feng, Yucheng, additional, Kremitzki, Colin, additional, Mitreva, Makedonka, additional, Glasscock, Jarret, additional, Wylie, Todd, additional, Wohldmann, Patricia, additional, Thiru, Prathapan, additional, Nhan, Michael N., additional, Pohl, Craig S., additional, Smith, Scott M., additional, Hou, Shunfeng, additional, Nefedov, Mikhail, additional, de Jong, Pieter J., additional, Renfree, Marilyn B., additional, Mardis, Elaine R., additional, and Wilson, Richard K., additional

Published
2008
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16. Hox cluster disintegration with persistent anteroposterior order of expression in Oikopleura dioica.

Author

Hee-Chan Seo, Edvardsen, Rolf Brudvik, Maeland, Anne Dorthea, Bjordal, Marianne, Jensen, Marit Flo, Hansen, Anette, Flaat, Mette, Weissenbach, Jean, Lehrach, Hans, Wincker, Patrick, Reinhardt, Richard, and Chourrout, Daniel

Subjects
EMBRYOS, CHORDATA, PHYLOGENY, GENE expression, TISSUES
Abstract

Tunicate embryos and larvae have small cell numbers and simple anatomical features in comparison with other chordates, including vertebrates. Although they branch near the base of chordate phylogenetic trees1, their degree of divergence from the common chordate ancestor remains difficult to evaluate. Here we show that the tunicate Oikopleura dioica has a complement of nine Hox genes in which all central genes are lacking but a full vertebrate-like set of posterior genes is present. In contrast to all bilaterians studied so far, Hox genes are not clustered in the Oikopleura genome. Their expression occurs mostly in the tail, with some tissue preference, and a strong partition of expression domains in the nerve cord, in the notochord and in the muscle. In each tissue of the tail, the anteroposterior order of Hox gene expression evokes spatial collinearity, with several alterations. We propose a relationship between the Hox cluster breakdown, the separation of Hox expression domains, and a transition to a determinative mode of development. [ABSTRACT FROM AUTHOR]

Published
2004
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17. Genome analysis of the platypus reveals unique signatures of evolution.

Author

Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, and Wilson RK

Subjects
Animals, Base Composition, Dentition, Female, Genomic Imprinting genetics, Humans, Immunity genetics, Male, Mammals genetics, MicroRNAs genetics, Milk Proteins genetics, Phylogeny, Platypus immunology, Platypus physiology, Receptors, Odorant genetics, Repetitive Sequences, Nucleic Acid genetics, Reptiles genetics, Sequence Analysis, DNA, Spermatozoa metabolism, Venoms genetics, Zona Pellucida metabolism, Evolution, Molecular, Genome genetics, Platypus genetics
Abstract

We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.

Published
2008
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