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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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2. Curriculum Materials Supporting Problem-Based Teaching

Author

James T. Fey, Karen McLaren, Kimberly Harris, and Robin Marcus

Subjects
Physics and Astronomy (miscellaneous), Investigations in Numbers, Data, and Space, National Science Education Standards, Philosophy of mathematics education, Education, Reform mathematics, Mathematics (miscellaneous), History and Philosophy of Science, Connected Mathematics, ComputingMilieux_COMPUTERSANDEDUCATION, Mathematics education, Core-Plus Mathematics Project, Math wars, Engineering (miscellaneous), Curriculum
Abstract

The vision for school mathematics described by the National Council of Teachers of Mathematics (NCTM) suggests a need for new approaches to the teaching and learning of mathematics, as well as new curriculum materials to support such change. This article discusses implications of the NCTM standards for mathematics curriculum and instruction and provides three examples of lessons from problem-based curricula for various grade levels. These examples illustrate how the teaching of important mathematics through student exploration of interesting problems might unfold, and they highlight the differences between a problem-based approach and more traditional approaches. Considerations for teaching through a problem-based approach are raised, as well as reflections on the potential impact on student learning.

Published
2001

3. The zebrafish reference genome sequence and its relationship to the human genome

Author

Kerstin Howe, Matthew D. Clark, Carlos F. Torroja, James Torrance, Camille Berthelot, Matthieu Muffato, John E. Collins, Sean Humphray, Karen McLaren, Lucy Matthews, Stuart McLaren, Ian Sealy, Mario Caccamo, Carol Churcher, Carol Scott, Jeffrey C. Barrett, Romke Koch, Gerd-Jörg Rauch, Simon White, William Chow, Britt Kilian, Leonor T. Quintais, José A. Guerra-Assunção, Yi Zhou, Yong Gu, Jennifer Yen, Jan-Hinnerk Vogel, Tina Eyre, Seth Redmond, Ruby Banerjee, Jianxiang Chi, Beiyuan Fu, Elizabeth Langley, Sean F. Maguire, Gavin K. Laird, David Lloyd, Emma Kenyon, Sarah Donaldson, Harminder Sehra, Jeff Almeida-King, Jane Loveland, Stephen Trevanion, Matt Jones, Mike Quail, Dave Willey, Adrienne Hunt, John Burton, Sarah Sims, Kirsten McLay, Bob Plumb, Joy Davis, Chris Clee, Karen Oliver, Richard Clark, Clare Riddle, David Elliott, Glen Threadgold, Glenn Harden, Darren Ware, Sharmin Begum, Beverley Mortimore, Giselle Kerry, Paul Heath, Benjamin Phillimore, Alan Tracey, Nicole Corby, Matthew Dunn, Christopher Johnson, Jonathan Wood, Susan Clark, Sarah Pelan, Guy Griffiths, Michelle Smith, Rebecca Glithero, Philip Howden, Nicholas Barker, Christine Lloyd, Christopher Stevens, Joanna Harley, Karen Holt, Georgios Panagiotidis, Jamieson Lovell, Helen Beasley, Carl Henderson, Daria Gordon, Katherine Auger, Deborah Wright, Joanna Collins, Claire Raisen, Lauren Dyer, Kenric Leung, Lauren Robertson, Kirsty Ambridge, Daniel Leongamornlert, Sarah McGuire, Ruth Gilderthorp, Coline Griffiths, Deepa Manthravadi, Sarah Nichol, Gary Barker, Siobhan Whitehead, Michael Kay, Jacqueline Brown, Clare Murnane, Emma Gray, Matthew Humphries, Neil Sycamore, Darren Barker, David Saunders, Justene Wallis, Anne Babbage, Sian Hammond, Maryam Mashreghi-Mohammadi, Lucy Barr, Sancha Martin, Paul Wray, Andrew Ellington, Nicholas Matthews, Matthew Ellwood, Rebecca Woodmansey, Graham Clark, James D. Cooper, Anthony Tromans, Darren Grafham, Carl Skuce, Richard Pandian, Robert Andrews, Elliot Harrison, Andrew Kimberley, Jane Garnett, Nigel Fosker, Rebekah Hall, Patrick Garner, Daniel Kelly, Christine Bird, Sophie Palmer, Ines Gehring, Andrea Berger, Christopher M. Dooley, Zübeyde Ersan-Ürün, Cigdem Eser, Horst Geiger, Maria Geisler, Lena Karotki, Anette Kirn, Judith Konantz, Martina Konantz, Martina Oberländer, Silke Rudolph-Geiger, Mathias Teucke, Christa Lanz, Günter Raddatz, Kazutoyo Osoegawa, Baoli Zhu, Amanda Rapp, Sara Widaa, Cordelia Langford, Fengtang Yang, Stephan C. Schuster, Nigel P. Carter, Jennifer Harrow, Zemin Ning, Javier Herrero, Steve M. J. Searle, Anton Enright, Robert Geisler, Ronald H. A. Plasterk, Charles Lee, Monte Westerfield, Pieter J. de Jong, Leonard I. Zon, John H. Postlethwait, Christiane Nüsslein-Volhard, Tim J. P. Hubbard, Hugues Roest Crollius, Jane Rogers, Derek L. Stemple, and Hubrecht Institute for Developmental Biology and Stem Cell Research

Subjects
Genetics, 0303 health sciences, Genome evolution, Multidisciplinary, Gene prediction, Pseudogene, Genome project, Biology, biology.organism_classification, Genome, Article, 03 medical and health sciences, 0302 clinical medicine, Gene density, Zebrafish, 030217 neurology & neurosurgery, 030304 developmental biology, Reference genome
Abstract

Zebrafish have become a popular organism for the study of vertebrate gene function1,2. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease3–5. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes6, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.

Published
2013

4. 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

5. 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

6. Erratum: Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

Author

Alan Tracey, Lucy Barr, Karen Holt, Stephen J. Trevanion, Bob Plumb, Daniel Leongamornlert, Paul Wray, Carol Churcher, J. C. Davis, Ruth Gilderthorp, Christine Lloyd, Adrienne Hunt, Michelle Smith, Britt Kilian, Martina Konantz, Jeff Almeida-King, Richard M. Clark, Nick Barker, Kirsty Ambridge, Susan J. Clark, Karen Oliver, Glen Threadgold, Yong Gu, Jane E. Loveland, David Lloyd, Guy Griffiths, Ronald H.A. Plasterk, Karen McLaren, Sarah Pelan, Sarah Nichol, Kenric Leung, Rebecca Woodmansey, Sharmin Begum, Cigdem Eser, Sophie Palmer, Jacqueline Brown, Ian M Sealy, James Torrance, J Lovell, John E. Collins, Sara Widaa, A M Kimberley, A Tromans, Richard Pandian, Judith Konantz, Maria Geisler, Carlos Torroja, N Sycamore, Sancha Martin, Darren Barker, Amanda Rapp, Monte Westerfield, Silke Rudolph-Geiger, Zemin Ning, José Afonso Guerra-Assunção, Clare Riddle, Rebecca Glithero, Daniel P. Kelly, Nicholas Matthews, Pieter J. de Jong, Nigel P. Carter, Camille Berthelot, Fengtang Yang, A K Babbage, Graham Clark, Andrea Berger, Robert Andrews, C Griffiths, Jennifer Harrow, Gerd Jörg Rauch, Steve Searle, J. M. Wallis, Christa Lanz, Ruby Banerjee, William Chow, Jan Hinnerk Vogel, Matthieu Muffato, David Elliott, Mathias Teucke, Derek L. Stemple, Debbie E. Wright, Deepa Manthravadi, Gavin K. Laird, Sarah Sims, M Mashreghi-Mohammadi, David S. Saunders, Lena Karotki, P Garner, Paul Heath, Jane Rogers, Ines Gehring, J Garnett, Charles Lee, Philip Howden, John H. Postlethwait, Robert Geisler, Sarah Donaldson, Elizabeth Langley, Claire Raisen, Katherine Auger, Javier Herrero, Beiyuan Fu, Carol Scott, Zübeyde Ersan-Ürün, Mario Caccamo, Sean Humphray, Gary L A Barker, S. Whitehead, Darren Ware, Baoli Zhu, Jianxiang Chi, Jonathan Wood, Nigel Fosker, Sarah McGuire, Stephan C. Schuster, Chris Clee, Martina Oberländer, Daria Gordon, Clare Murnane, Romke Koch, Emma Gray, Beverley J. Mortimore, Harminder Sehra, Joanna Collins, Hugues Roest Crollius, Kirsten McLay, Kerstin Howe, Lauren Dyer, Christopher Stevens, Andrew D. Ellington, Kazutoyo Osoegawa, Stuart McLaren, Christopher N. Johnson, Giselle Kerry, Helen Beasley, Georgios Panagiotidis, Christiane Nüsslein Volhard, Tina Eyre, Horst Geiger, Jennifer Yen, Matthew Ellwood, Christine P. Bird, N Corby, Matthew Dunn, Darren Grafham, Günter Raddatz, Matthew Humphries, Anette Kirn, Yi Zhou, James D. Cooper, John Burton, Simon D. M. White, Anton J. Enright, Dave Willey, Tim Hubbard, Rebekah Hall, Michael Kay, Matthew D. Clark, Matthew Jones, Glenn Harden, C. D. Skuce, Lauren Robertson, Leonard I. Zon, Lucy Matthews, Jeffrey C. Barrett, Michael A. Quail, Emma J. Kenyon, Leonor T. Quintais, Benjamin Phillimore, S Hammond, Carl Henderson, Joanna Harley, Elliot Harrison, Cordelia Langford, Christopher M. Dooley, and Sean Maguire

Subjects
Max planck institute, Comparative genomics, Multidisciplinary, Reference genome sequence, biology, Evolutionary biology, Philosophy, Human genome, Bioinformatics, biology.organism_classification, Zebrafish
Abstract

Nature 496, 498–503 (2013); doi:10.1038/nature12111 In this Letter, five authors were inadvertently omitted: Sharmin Begum and Christine Lloyd from the Wellcome Trust Sanger Institute, and Christa Lanz, Gunter Raddatz and Stephan C. Schuster from the Max Planck Institute for Developmental Biology. David Elliot was incorrectly listed as David Eliot, Beverley Mortimore was incorrectly listed as Beverly Mortimer, and James D.

Published
2013

7. Dynamic instability of the Major Urinary Protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice

Author

Jonathan M. Mudge, Christine Nicholson, Jane L. Hurst, Robert J. Beynon, Jennifer Harrow, Stuart D. Armstrong, Laurens G. Wilming, Duncan H. L. Robertson, and Karen McLaren

Subjects
Male, Pseudogene, Mice, Inbred Strains, Biology, Mass Spectrometry, Evolution, Molecular, Mice, 03 medical and health sciences, 0302 clinical medicine, Species Specificity, Gene cluster, Animals, Gene family, Gene, 030304 developmental biology, Genetics, 0303 health sciences, Major urinary proteins, Phylogenetic tree, Research, Proteins, Genome project, Mice, Inbred C57BL, Molecular Weight, Female, 030217 neurology & neurosurgery, Functional divergence
Abstract

Targeted sequencing, manual genome annotation, phylogenetic analysis and mass spectrometry were used to characterise major urinary proteins (MUPs) and the Mup clusters of two strains of inbred mice., Background The major urinary proteins (MUPs) of Mus musculus domesticus are deposited in urine in large quantities, where they bind and release pheromones and also provide an individual 'recognition signal' via their phenotypic polymorphism. Whilst important information about MUP functionality has been gained in recent years, the gene cluster is poorly studied in terms of structure, genic polymorphism and evolution. Results We combine targeted sequencing, manual genome annotation and phylogenetic analysis to compare the Mup clusters of C57BL/6J and 129 strains of mice. We describe organizational heterogeneity within both clusters: a central array of cassettes containing Mup genes highly similar at the protein level, flanked by regions containing Mup genes displaying significantly elevated divergence. Observed genomic rearrangements in all regions have likely been mediated by endogenous retroviral elements. Mup loci with coding sequences that differ between the strains are identified - including a gene/pseudogene pair - suggesting that these inbred lineages exhibit variation that exists in wild populations. We have characterized the distinct MUP profiles in the urine of both strains by mass spectrometry. The total MUP phenotype data is reconciled with our genomic sequence data, matching all proteins identified in urine to annotated genes. Conclusion Our observations indicate that the MUP phenotypic polymorphism observed in wild populations results from a combination of Mup gene turnover coupled with currently unidentified mechanisms regulating gene expression patterns. We propose that the structural heterogeneity described within the cluster reflects functional divergence within the Mup gene family.

Published
2008

8. Finishing the finished human chromosome 22 sequence

Author

Zemin Ning, Karen Oliver, Fengtang Yang, O. T. McCann, David Beare, David Willey, Susan M. Gribble, Charlotte G. Cole, John E. Collins, Ian Dunham, Karen McLaren, and Jane Rogers

Subjects
Genetics, Chromosomes, Artificial, Bacterial, 0303 health sciences, Bacterial artificial chromosome, Base Sequence, Euchromatin, Genome, Human, Sequence analysis, Chromosomes, Human, Pair 22, Research, Chromosome Mapping, Sequence Analysis, DNA, Biology, Genome, Human genetics, 03 medical and health sciences, 0302 clinical medicine, Humans, Human genome, Chromosome 22, 030217 neurology & neurosurgery, 030304 developmental biology, Sequence (medicine)
Abstract

A combination of approaches was used to close 8 of the 11 gaps in the original sequence of human chromosome 22, and to generate a total 1.018 Mb of new sequence., Background Although the human genome sequence was declared complete in 2004, the sequence was interrupted by 341 gaps of which 308 lay in an estimated approximately 28 Mb of euchromatin. While these gaps constitute only approximately 1% of the sequence, knowledge of the full complement of human genes and regulatory elements is incomplete without their sequences. Results We have used a combination of conventional chromosome walking (aided by the availability of end sequences) in fosmid and bacterial artificial chromosome (BAC) libraries, whole chromosome shotgun sequencing, comparative genome analysis and long PCR to finish 8 of the 11 gaps in the initial chromosome 22 sequence. In addition, we have patched four regions of the initial sequence where the original clones were found to be deleted, or contained a deletion allele of a known gene, with a further 126 kb of new sequence. Over 1.018 Mb of new sequence has been generated to extend into and close the gaps, and we have annotated 16 new or extended gene structures and one pseudogene. Conclusion Thus, we have made significant progress to completing the sequence of the euchromatic regions of human chromosome 22 using a combination of detailed approaches. Our experience suggests that substantial work remains to close the outstanding gaps in the human genome sequence.

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