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1. A Snapshot of the Emerging Tomato Genome Sequence

Author

Lukas A. Mueller, René Klein Lankhorst, Steven D. Tanksley, James J. Giovannoni, Ruth White, Julia Vrebalov, Zhangjun Fei, Joyce van Eck, Robert Buels, Adri A. Mills, Naama Menda, Isaak Y. Tecle, Aureliano Bombarely, Stephen Stack, Suzanne M. Royer, Song-Bin Chang, Lindsay A. Shearer, Byung Dong Kim, Sung-Hwan Jo, Cheol-Goo Hur, Doil Choi, Chang-Bao Li, Jiuhai Zhao, Hongling Jiang, Yu Geng, Yuanyuan Dai, Huajie Fan, Jinfeng Chen, Fei Lu, Jinfeng Shi, Shouhong Sun, Jianjun Chen, Xiaohua Yang, Chen Lu, Mingsheng Chen, Zhukuan Cheng, Chuanyou Li, Hongqing Ling, Yongbiao Xue, Ying Wang, Graham B. Seymour, Gerard J. Bishop, Glenn Bryan, Jane Rogers, Sarah Sims, Sarah Butcher, Daniel Buchan, James Abbott, Helen Beasley, Christine Nicholson, Clare Riddle, Sean Humphray, Karen McLaren, Saloni Mathur, Shailendra Vyas, Amolkumar U. Solanke, Rahul Kumar, Vikrant Gupta, Arun K. Sharma, Paramjit Khurana, Jitendra P. Khurana, Akhilesh Tyagi, Sarita, Parul Chowdhury, Smriti Shridhar, Debasis Chattopadhyay, Awadhesh Pandit, Pradeep Singh, Ajay Kumar, Rekha Dixit, Archana Singh, Sumera Praveen, Vivek Dalal, Mahavir Yadav, Irfan Ahmad Ghazi, Kishor Gaikwad, Tilak Raj Sharma, Trilochan Mohapatra, Nagendra Kumar Singh, Dóra Szinay, Hans de Jong, Sander Peters, Marjo van Staveren, Erwin Datema, Mark W.E.J. Fiers, Roeland C.H.J. van Ham, P. Lindhout, Murielle Philippot, Pierre Frasse, Farid Regad, Mohamed Zouine, Mondher Bouzayen, Erika Asamizu, Shusei Sato, Hiroyuki Fukuoka, Satoshi Tabata, Daisuke Shibata, Miguel A. Botella, M. Perez-Alonso, V. Fernandez-Pedrosa, Sonia Osorio, Amparo Mico, Antonio Granell, Zhonghua Zhang, Jun He, Sanwen Huang, Yongchen Du, Dongyu Qu, Longfei Liu, Dongyuan Liu, Jun Wang, Zhibiao Ye, Wencai Yang, Guoping Wang, Alessandro Vezzi, Sara Todesco, Giorgio Valle, Giulia Falcone, Marco Pietrella, Giovanni Giuliano, Silvana Grandillo, Alessandra Traini, Nunzio D'Agostino, Maria Luisa Chiusano, Mara Ercolano, Amalia Barone, Luigi Frusciante, Heiko Schoof, Anika Jöcker, Rémy Bruggmann, Manuel Spannagl, Klaus X.F. Mayer, Roderic Guigó, Francisco Camara, Stephane Rombauts, Jeffrey A. Fawcett, Yves Van de Peer, Sandra Knapp, Dani Zamir, and Willem Stiekema

Subjects
Plant culture, SB1-1110, Genetics, QH426-470
Abstract

The genome of tomato ( L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato ( L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.

Published
2009
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4. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

Author

Claude Scarpelli, Thomas Schiex, Ghislaine Magdelenat, Michael K. Udvardi, Baifang Qin, Xinbin Dai, Jeff J. Doyle, Patrick X. Zhao, Hélène Bergès, Vagner A. Benedito, Arvind K. Bharti, Chrystel Gibelin, Dong-Hoon Jeong, Stéphane De Mita, Stephane Rombauts, Mingyi Wang, Nathalie Choisne, Simone L. Macmil, Patrick Wincker, Senjuti Sinharoy, Sylvie Samain, Christopher D. Town, Susan R. Singer, Heidrun Gundlach, Anne Berger, Jane Rogers, Kathrin Klee, Sarah Sims, Nevin D. Young, Stéphanie Fouteau, Claire Riddle, Iryna Sanders, John Gish, Limei Yang, René Geurts, Gregory D. May, Shiguo Zhou, Shweta Deshpande, David C. Schwartz, Anika Jöcker, Christine Nicholson, Ton Bisseling, Klaus F. X. Mayer, Antoine Zuber, Roxanne Denny, Chunting Lang, Carolien Franken, Douglas R. Cook, Ruihua Shi, Frédéric Debellé, Valérie Barbe, Giles E. D. Oldroyd, Foo Cheung, Lucy Matthews, Blake C. Meyers, Jeremy D. Murray, Dong-Jin Kim, Joann Mudge, Agnès Viollet, Heiko Schoof, Graham B. Wiley, Benjamin D. Rosen, Jean Dénarié, Florent Prion, Keqin Wang, Arnaud Bellec, Béatrice Segurens, Jeong Hwan Mun, Ernest F. Retzel, Sean Humphray, Andrew Farmer, D. Janine Sherrier, Lieven Sterck, Richard A. Dixon, Steven B. Cannon, Steve Kenton, Philippe Bardou, Alvaro J. González, Haibao Tang, Julie Poulain, Arnaud Couloux, Majesta O'Bleness, Pamela J. Green, Manuel Spannagl, Shelby L. Bidwell, Jixian Zhai, Asis Hallab, Anne Marie Dudez, Michael Bechner, Marina Naoumkina, James D. White, Francis Quetier, Marijke Hartog, Erin L. Monaghan, Charles Paule, Chunmei Qu, Andrew J. Severin, Céline Noirot, Fu Ying, Shaoping Lin, Ziyun Yao, Vivek Krishnakumar, Steven A. Goldstein, Axin Hua, Erika Sallet, Bing Bing Wang, Peng Zhou, Hongshing Lai, Yanbo Xing, Nicolas Samson, Jamison McCorrison, Doug White, Yi Jing, Olivier Saurat, Liping Zhou, Kevin A. T. Silverstein, Jean Weissenbach, Bruce A. Roe, Sebastian Proost, Yves Van de Peer, Xiaohong Wang, Jens Warfsmann, Jérôme Gouzy, Fares Z. Najar, University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Department of Disease and Stress Biology, John Innes Centre [Norwich], Laboratory of Molecular Biology, Department of Plant Science, Wageningen University and Research [Wageningen] (WUR), Corn Insects and Crop Genetics Research Unit, USDA-ARS : Agricultural Research Service, Department of Agronomy, Purdue University [West Lafayette], Plant Biology Division, The Samuel Roberts Noble Foundation, West Virginia University, German Research Center for Environmental Health - Helmholtz Center München (GmbH), Centre National de la Recherche Scientifique (CNRS), Rheinische Friedrich-Wilhelms-Universität Bonn, Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Department plant pathology, Pennsylvania State University (Penn State), Penn State System-Penn State System, University of Delaware [Newark], J. Craig Venter Institute [La Jolla, USA] (JCVI), Interactions Arbres-Microorganismes (IAM), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, National center for genome resources (NCGR), BBSRC John Innes Centre, Partenaires INRAE, Bayer Cropscience, Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), College of Science [Swansea], Swansea University, University of Oklahoma (OU), Department of Plant Biology, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Max Planck Institute for Plant Breeding Research (MPIPZ), Wageningen University and Research Centre (WUR), Wellcome Trust, International Institute of Tropical Agriculture, Department of Plant Pathology, University of Kentucky, Rural Development Administration, Unité de Biométrie et Intelligence Artificielle (UBIA), Carleton College, Funding support to N.D.Y., C. D. T. and B. A. R. from The Noble Foundation and NSF-PGRP 0321460, 0604966, to N.D.Y., J.M. and G. D. M. from NSF-PGRP 0820005, to C. D. T. from NSF-PGRP 0821966, to F. D., G.E.D.O., R. G., K. F. X. M., T. B., J. Denarie, F. Q. and J. R. from FP6 EU project GLIP/Grain Legumes FOOD-CT-2004-506223, to G.E.D.O. and J.R. from BBSRC BBS/B/11524, to F. D. and F. Q. from ANR project SEQMEDIC 2006-01122, to R. G. from the Dutch Science Organization VIDI 864.06.007, ERA-PG FP-06.038A, to Y.V.d.P. from the Belgian Federal Science Policy Office IUAP P6/25, Fund for Scientific Research Flanders, Institute for the Promotion of Innovation by Science and Technology in Flanders and Ghent University (MRP N2N), to D. R. C. from NSF IOS-0531408, IOS-0605251, to D.J.S., B. C. M. and P.J.G. from USDA CSREES 2006-03567, and to J. Gouzy from 'Laboratoire d'Excellence' (LABEX) TULIP (ANR-10-LABX-41). We also acknowledge technical support from the University of Minnesota Supercomputer Institute and thank Y.W. Nam for a BamHI BAC library used by Genoscope, S. Park and M. Accerbi for RNA isolation, T. Paape for statistical consulting, and M. Harrison for supplying myc infected and control root tissues used to make small RNA libraries.

Subjects
0106 biological sciences, multidisciplinary science, 01 natural sciences, Genome, genomic, flavonoid biosynthesis, Vitis, genes, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Medicago, biology, truncatula, food and beverages, Biological Evolution, Medicago truncatula, plant science, duplications, Rhizobium, Laboratory of Molecular Biology, Genome, Plant, signal-transduction, science and technology, Lotus japonicus, Molecular Sequence Data, Genomics, Synteny, tetraploidy, Article, 03 medical and health sciences, Nitrogen Fixation, Botany, evolution, expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Laboratorium voor Moleculaire Biologie, Medicago sativa, Symbiosis, 030304 developmental biology, fungi, Fabaceae, sequence, biology.organism_classification, arabidopsis, leguminosae, Soybeans, genetic, EPS, 010606 plant biology & botany
Abstract

Chantier qualité GA; International audience; Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.

Published
2011

5. The ORFeome Collaboration: a genome-scale human ORF-clone resource

Author

Anja van Brabant Smith, Ruth Wellenreuther, Shuwei Yang, Sun Lu, Gary F. Temple, Yoshihide Hayashizaki, Jin Park, J. Wade Harper, Yanhui Hu, Oliver Heil, Tong Hao, Jun Kawai, Blake A. Simmons, Kourosh Salehi-Ashtiani, Christoph Koenig, Ian Dunham, Catherine Seiler, Steffen Hennig, Anika Jöcker, Piero Carninci, Cristen Lambert, Troy Moore, Anita Lebeau, David E. Hill, Melanie Busse, Tom Weaver, Preston Hunter, Wonhee Jang, Matthias Harbers, Marc Vidal, Graeme Bethel, Mark Diekhans, Osamu Ohara, Bernhard Korn, Joshua La Baer, Lukas Wagner, Alexandra Amiet, Daniela S. Gerhard, Andreas Rolfs, Johannes Maurer, Christa Pennacchio, Jason Steel, Stefan Wiemann, and Agnes Hotz-Wagenblatt

Subjects
0301 basic medicine, Internet, Resource (biology), Proteome, Genome, Human, Clone (cell biology), Genome scale, Cell Biology, Computational biology, Biology, Biochemistry, Clone Cells, Open Reading Frames, User-Computer Interface, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, 030220 oncology & carcinogenesis, Databases, Genetic, Database Management Systems, Humans, Cloning, Molecular, ORFeome, Molecular Biology, Biotechnology
Published
2016

6. Microspot immunoassay-based analysis of plasma protein profiles for biomarker discovery strategies

Author

Johanna, Sonntag, Heiko, Mannsperger, Anika, Jöcker, and Ulrike, Korf

Subjects
Immunoassay, Protein Array Analysis, Humans, Blood Proteins, Precision Medicine, Antibodies, Biomarkers
Abstract

To expedite the development of personalized medicine, new and reliable biomarkers are required to facilitate early diagnosis, to determine prognosis, predict response or resistance to different therapies, and to monitor disease progression or recurrence. Human body fluids, such as blood, present a promising resource for biomarker discovery, in every sense. Microspot immunoassays allow the simultaneous quantification of multiple analytes from a minute amount of samples in a single measurement. The experimental design of microspot immunoassays is based on antibody pairs recognizing different epitopes of the analyte. The first antibody is used to capture the analyte from the complex sample, and the second antibody is used for detection. As with traditional enzyme-linked immunosorbent assays, highly reliable and reproducible results are obtained.

Published
2011

7. Quantitative analysis of phosphoproteins using microspot immunoassays

Author

Frauke, Henjes, Frank, Götschel, Anika, Jöcker, and Ulrike, Korf

Subjects
Immunoassay, Proteomics, Protein Array Analysis, Phosphorylation, Phosphoproteins, Antibodies, Signal Transduction
Abstract

Protein microarrays are an ideal technology platform which allow for a robust and standardized profiling of the cellular proteome. Many cellular functions are not simply controlled by the presence of certain proteins, especially the propagation of external stimuli, which depend on transient post-translational modifications that determine whether a protein is in its active or inactive state. Thus, complex biological processes require the availability of a sound set of quantitative and time-resolved measurements to be understood. For this reason, new assay platforms which allow for the investigation of several proteins in parallel are necessary. The current best understood mode of cellular regulation occurs via phosphorylation and dephosphorylation processes, which are mediated via a large panel of kinases and phosphatases. The microspot immunoassay technique described here allows for an exact determination of several different phosphorylated proteins in parallel, as well as from small sample amounts, and is therefore an appropriate system to deepen the understanding of the complex regulatory networks implicated in health and disease.

Published
2011

8. Quantitative Analysis of Phosphoproteins Using Microspot Immunoassays

Author

Frank Götschel, Ulrike Korf, Anika Jöcker, and Frauke Henjes

Subjects
Dephosphorylation, Chemistry, Kinase, Proteome, Phosphatase, Cellular Regulation, Cellular functions, Protein microarray, Phosphorylation, Computational biology
Abstract

Protein microarrays are an ideal technology platform which allow for a robust and standardized profiling of the cellular proteome. Many cellular functions are not simply controlled by the presence of certain proteins, especially the propagation of external stimuli, which depend on transient post-translational modifications that determine whether a protein is in its active or inactive state. Thus, complex biological processes require the availability of a sound set of quantitative and time-resolved measurements to be understood. For this reason, new assay platforms which allow for the investigation of several proteins in parallel are necessary. The current best understood mode of cellular regulation occurs via phosphorylation and dephosphorylation processes, which are mediated via a large panel of kinases and phosphatases. The microspot immunoassay technique described here allows for an exact determination of several different phosphorylated proteins in parallel, as well as from small sample amounts, and is therefore an appropriate system to deepen the understanding of the complex regulatory networks implicated in health and disease.

Published
2011

10. QuantProReloaded: quantitative analysis of microspot immunoassays

Author

Frauke Henjes, Anika Jöcker, Achim Tresch, Frank Götschel, Ulrike Korf, Johanna Sonntag, Stefan Wiemann, and Tim Beißbarth

Subjects
0106 biological sciences, Statistics and Probability, Cell lysates, Proteomics, Proteome, Computer science, Protein Array Analysis, Computational biology, computer.software_genre, 01 natural sciences, Biochemistry, 03 medical and health sciences, User-Computer Interface, 010608 biotechnology, medicine, Molecular Biology, 030304 developmental biology, Immunoassay, 0303 health sciences, medicine.diagnostic_test, 3. Good health, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Quantitative analysis (finance), Data analysis, Protein microarray, Data mining, computer, Quantitative analysis (chemistry), Software
Abstract

Summary: Protein microarrays are well-established as sensitive tools for proteomics. Particularly, the microspot immunoassay (MIA) platform enables a quantitative analysis of (phospho-) proteins in complex solutions (e.g. cell lysates or blood plasma) and with low consumption of samples and reagents. Despite numerous biological and clinical applications of MIAs there is currently no user-friendly open source data analysis software available with versatile options for data analysis and data visualization. Here, we introduce the open source software QuantProReloaded that is specifically designed for the analysis of data from MIA experiments. Availability and implementation: QuantProReloaded is written in R and Java and is open for download under the BSB license at http://code.google.com/p/quantproreloaded/ Contact: a.joecker@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online.

Published
2010

11. A Snapshot of the Emerging Tomato Genome Sequence

Author

Mueller, LUKAS A., RENÉ KLEIN LANKHORST, Tanksley, STEVEN D., Giovannoni, JAMES J., Ruth, White, Julia, Vrebalov, Zhangjun, Fei, JOYCE VAN ECK, Robert, Buels, Mills, ADRI A., Naama, Menda, Tecle, ISAAK Y., Aureliano, Bombarely, Stephen, Stack, Royer, SUZANNE M., SONG BIN CHANG, Shearer, LINDSAY A., BYUNG DONG KIM, SUNG HWAN JO, CHEOL GOO HUR, Doil, Choi, CHANG BAO LI, Jiuhai, Zhao, Hongling, Jiang, Geng, Yu, Yuanyuan, Dai, Huajie, Fan, Jinfeng, Chen, Fei, Lu, Jinfeng, Shi, Shouhong, Sun, Jianjun, Chen, Xiaohua, Yang, Chen, Lu, Mingsheng, Chen, Zhukuan, Cheng, Chuanyou, Li, Hongqing, Ling, Yongbiao, Xue, Ying, Wang, Seymour, GRAHAM B., Bishop, GERARD J., Glenn, Bryan, Jane, Rogers, Sarah, Sims, Sarah, Butcher, Daniel, Buchan, James, Abbott, Helen, Beasley, Christine, Nicholson, Clare, Riddle, Sean, Humphray, Karen, Mclaren, Saloni, Mathur, Shailendra, Vyas, Solanke, AMOLKUMAR U., Rahul, Kumar, Vikrant, Gupta, Sharma, ARUN K., Paramjit, Khurana, Khurana, JITENDRA P., Akhilesh, Tyagi, Sarita, Parul, Chowdhury, Smriti, Shridhar, Debasis, Chattopadhyay, Awadhesh, Pandit, Pradeep, Singh, Ajay, Kumar, Rekha, Dixit, Archana, Singh, Sumera, Praveen, Vivek, Dalal, Mahavir, Yadav, IRFAN AHMAD GHAZI, Kishor, Gaikwad, TILAK RAJ SHARMA, Trilochan, Mohapatra, NAGENDRA KUMAR SINGH, Dóra, Szinay, HANS DE JONG, Sander, Peters, MARJO VAN STAVEREN, Erwin, Datema, Fiers, MARK W. E. J., VAN HAM, ROELAND C. H. J., Lindhout, P., Murielle, Philippot, Pierre, Frasse, Farid, Regad, Mohamed, Zouine, Mondher, Bouzayen, Erika, Asamizu, Shusei, Sato, Hiroyuki, Fukuoka, Satoshi, Tabata, Daisuke, Shibata, Botella, MIGUEL A., PEREZ ALONSO, M., FERNANDEZ PEDROSA, V., Sonia, Osorio, Amparo, Mico, Antonio, Granell, Zhonghua, Zhang, Jun, He, Sanwen, Huang, Yongchen, Du, Dongyu, Qu, Longfei, Liu, Dongyuan, Liu, Jun, Wang, Zhibiao, Ye, Wencai, Yang, Guoping, Wang, Vezzi, Alessandro, Sara, Todesco, Valle, Giorgio, Giulia, Falcone, Marco, Pietrella, Giovanni, Giuliano, Silvana, Grandillo, Alessandra, Traini, Nunzio, D'Agostino, MARIA LUISA CHIUSANO, Mara, Ercolano, Amalia, Barone, Luigi, Frusciante, Heiko, Schoof, Anika, Jöcker, Rémy, Bruggmann, Manuel, Spannagl, Mayer, KLAUS X. F., Roderic, Guigó, Francisco, Camara, Stephane, Rombauts, Fawcett, JEFFREY A., YVES VAN DE PEER, Sandra, Knapp, and DANI ZAMIR AND WILLEM STIEKEMA

Published
2009

12. A snapshot of the emerging tomato genome sequence

Author

Sandra Knapp, Ying Wang, Antonio Granell, Dongyu Qu, Erika Asamizu, Pierre Frasse, Hongling Jiang, Mohamed Zouine, Pradeep Kumar Singh, Vivek Dalal, Luigi Frusciante, Robert M. Buels, Hans de Jong, Dongyuan Liu, James J. Giovannoni, Sander Peters, Sarita, Satoshi Tabata, Isaak Y. Tecle, Mara Ercolano, Jun Wang, Longfei Liu, Rekha Dixit, Heiko Schoof, Yongbiao Xue, Kishor Gaikwad, Julia Vrebalov, Alessandra Traini, Nunzio D’Agostino, Ruth White, Zhibiao Ye, Amparo Mico, Cheol-Goo Hur, Jitendra P. Khurana, Roderic Guigó, Arun Sharma, Paramjit Khurana, Jiuhai Zhao, Hiroyuki Fukuoka, Byung-Dong Kim, Smriti Shridhar, René Klein Lankhorst, Yuanyuan Dai, Dani Zamir, Sumera Praveen, Helen Beasley, Manuel Spannagl, Erwin Datema, Klaus X.F. Mayer, Yves Van de Peer, Akhilesh K. Tyagi, Aureliano Bombarely, P. Lindhout, Mark Fiers, Silvana Grandillo, Jane Rogers, Zhangjun Fei, Changbao Li, Giorgio Valle, Karen McLaren, Alok Singh, Sung-Hwan Jo, Sarah Butcher, Willem J. Stiekema, Murielle Philippot, Huajie Fan, Glenn J. Bryan, Fei Lu, Doil Choi, Jun He, Daniel W. A. Buchan, Stephane Rombauts, Jinfeng Chen, Yongchen Du, Xiao-Hua Yang, Shailendra Vyas, Daisuke Shibata, Maria Luisa Chiusano, Rajesh Kumar, Song Bin Chang, Marjo J. van Staveren, Gerard J. Bishop, Victoria Fernandez-Pedrosa, Hong-Qing Ling, Graham B. Seymour, Lukas A. Mueller, Mondher Bouzayen, Stephen M. Stack, Rémy Bruggmann, Ajay Kumar, Zhonghua Zhang, Christine Nicholson, Guoping Wang, Saloni Mathur, Sean Humphray, Vikrant Gupta, Jinfeng Shi, Roeland C. H. J. van Ham, Debasis Chattopadhyay, Amolkumar U. Solanke, Mingsheng Chen, Shusei Sato, Sanwen Huang, Sonia Osorio, Chen Lu, Zhukuan Cheng, Tilak Raj Sharma, Dóra Szinay, James Abbott, Awadhesh Pandit, Yu Geng, Mahavir Yadav, Sara Todesco, Manuel Pérez-Alonso, Giovanni Giuliano, Amalia Barone, Trilochan Mohapatra, Irfan Ahmad Ghazi, Wencai Yang, Francisco Camara, Giulia Falcone, Anika Jöcker, Clare Riddle, Alessandro Vezzi, Jianjun Chen, Shouhong Sun, Marco Pietrella, Joyce Van Eck, Lindsay A. Shearer, Adri A. Mills, Steven D. Tanksley, Miguel A. Botella, Chuanyou Li, Sarah Sims, Farid Regad, Jeffrey A. Fawcett, Parul Chowdhury, Naama Menda, Suzanne M. Royer, Nagendra K. Singh, Mueller, L. A., Lankhorst, R. K., Tanksley, S. D., Giovannoni, J. J., White, R., Vrebalov, J., Fei, Z., van Eck, J., Buels, R., Mills, A. A., Menda, N., Tecle, I. Y., Bombarely, A., Stack, S., Royer, S. M., Chang, S. B., Shearer, L. A., Kim, B. D., Jo, S. H., Hur, C. G., Choi, D., Li, C. B., Zhao, J., Jiang, H., Geng, Y., Dai, Y., Fan, H., Chen, J., Lu, F., Shi, J., Sun, S., Yang, X., Lu, C., Chen, M., Cheng, Z., Li, C., Ling, H., Xue, Y., Wang, Y., Seymour, G. B., Bishop, G. J., Bryan, G., Rogers, J., Sims, S., Butcher, S., Buchan, D., Abbott, J., Beasley, H., Nicholson, C., Riddle, C., Humphray, S., Mclaren, K., Mathur, S., Vyas, S., Solanke, A. U., Kumar, R., Gupta, V., Sharma, A. K., Khurana, P., Khurana, J. P., Tyagi, A., Sarita, Chowdhury, P., Shridhar, S., Chattopadhyay, D., Pandit, A., Singh, P., Kumar, A., Dixit, R., Singh, A., Praveen, S., Dalal, V., Yadav, M., Ghazi, I. A., Gaikwad, K., Sharma, T. R., Mohapatra, T., Singh, N. K., Szinay, D., de Jong, H., Peters, S., van Staveren, M., Datema, E., Fiers, M. W. E. J., van Ham, R. C. H. J., Lindhout, P., Philippot, M., Frasse, P., Regad, F., Zouine, M., Bouzayen, M., Asamizu, E., Sato, S., Fukuoka, H., Tabata, S., Shibata, D., Botella, M. A., Perez Alonso, M., Fernandez Pedrosa, V., Osorio, S., Mico, A., Granell, A., Zhang, Z., He, J., Huang, S., Du, Y., Qu, D., Liu, L., Liu, D., Wang, J., Ye, Z., Yang, W., Wang, G., Vezzi, A., Todesco, S., Valle, G., Falcone, G., Pietrella, M., Giuliano, G., Grandillo, S., Traini, A., D'Agostino, Nunzio, Chiusano, MARIA LUISA, Ercolano, MARIA RAFFAELLA, Barone, Amalia, Frusciante, Luigi, Schoof, H., Jöcker, A., Bruggmann, R., Spannagl, M., Mayer, K. X. F., Guigó, R., Camara, F., Rombauts, S., Fawcett, J. A., Van de Peer, Y., Knapp, S., Zamir, D., and Stiekema, W.

Subjects
0106 biological sciences, lcsh:QH426-470, Bioinformatics, Genomics, Plant Science, Computational biology, lcsh:Plant culture, Biology, Laboratorium voor Erfelijkheidsleer, ENCODE, 01 natural sciences, Genome, 03 medical and health sciences, Laboratorium voor Plantenveredeling, Bioinformatica, Genetics, Life Science, lcsh:SB1-1110, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Bacterial artificial chromosome, EPS-4, fungi, food and beverages, Biology and Life Sciences, Genome project, PRI Bioscience, lcsh:Genetics, Plant Breeding, GenBank, Laboratory of Genetics, Agronomy and Crop Science, 010606 plant biology & botany, Reference genome
Abstract

The genome of tomato (Solanum lycopersicum L.) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States) as part of the larger “International Solanaceae Genome Project (SOL): Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC) approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN). Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato (Solanum tuberosum L.) sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.

Published
2009

13. Protein function prediction and annotation in an integrated environment powered by web services (AFAWE)

Author

Andreas Groscurth, Anika Jöcker, Heiko Schoof, and Fabian Hoffmann

Subjects
Statistics and Probability, Computer science, media_common.quotation_subject, Interface (computing), computer.software_genre, Biochemistry, User-Computer Interface, Annotation, Medicago truncatula, Animals, Humans, Protein function prediction, Databases, Protein, Function (engineering), Molecular Biology, Gene, media_common, Internet, Computational Biology, Proteins, Pipeline (software), Computer Science Applications, Computational Mathematics, Task (computing), Computational Theory and Mathematics, Data mining, Web service, computer, Software
Abstract

Summary: Many sequenced genes are mainly annotated through automatic transfer of annotation from similar sequences. Manual comparison of results or intermediate results from different tools can help avoid wrong annotations and give hints to the function of a gene even if none of the automated tools could return any result. AFAWE simplifies the task of manual functional annotation by running different tools and workflows for automatic function prediction and displaying the results in a way that facilitates comparison. Because all programs are executed as web services, AFAWE is easily extensible and can directly query primary databases, thereby always using the most up-to-date data sources. Visual filters help to distinguish trustworthy results from non-significant results. Furthermore, an interface to add detailed manual annotation to each gene is provided, which can be displayed to other users. Availability: AFAWE is available at http://bioinfo.mpiz-koeln.mpg.de/afawe/ Contact: afawe-admin@mpiz-koeln.mpg.de Supplementary information: SIFTER pipeline (S1), AFAWE tutorial (S2).

Published
2008

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