3122
IWGSC - Standards and Protocols

The workshop will focus on the assembly and quality control of BAC-based chromosome pseudomolecules and the integration of multiple map and sequence-based resources to produce the bread wheat genome reference sequence.
Date: Tuesday, January 12, 2016
Time: 1:30 PM-6:10 PM
Room: Pacific Salon 3
Organizers:
Jane Rogers and Frederic Choulet
1:30 PM
Introductory Remarks


1:35 PM
W561
Shaping Wheat for the Future: Leveraging the Wheat genome sequence in Crop Efficiency Research and Breeding
John Jacobs, Bayer CropScience NV

PDF file
1:55 PM
W562
Sequencing and Analyses of Chromosome 1B
Frédéric Choulet, INRA GDEC; Hélène Rimbert, INRA GDEC; Ambre-Aurore Josselin, INRA GDEC; Benoît Darrier, INRA GDEC; Pierre Sourdille, INRA GDEC; François Balfourier, INRA GDEC; Valerie Barbe, CEA - Genoscope; Adriana Alberti, CEA - Genoscope; Karine Labadie, CEA - Genoscope; Sophie Mangenot, CEA - Genoscope; Arnaud Couloux, CEA - Genoscope; Patrick Wincker, CEA - Genoscope; Arnaud Bellec, INRA - CNRGV; Hélène Bergès, INRA - CNRGV; Michael Alaux, INRA - URGI; Thomas Letellier, INRA - URGI; Hadi Quesneville, INRA - URGI; Zeev M. Frenkel, Institute of Evolution, University of Haifa; Tzion Fahima, Institute of Evolution, University of Haifa; Abraham B. Korol, Institute of Evolution, University of Haifa; Etienne Paux, INRA GDEC

2:15 PM
W563
Sequencing and Assembling a Pseudomolecule for the Wheat Chromosome 6B
Hiroyuki Kanamori, National Institute of Agrobiological Sciences; Kanako Kurita, National Institute of Agrobiological Sciences; Harumi Sasaki, National Institute of Agrobiological Sciences; Satomi Mori, National Institute of Agrobiological Sciences; Satoshi Katagiri, National Institute of Agrobiological Sciences; Hiroko Fujisawa, National Institute of Agrobiological Sciences; Wataru Karasawa, National Institute of Agrobiological Sciences; Fuminori Kobayashi, National Institute of Agrobiological Sciences; Tsuyoshi Tanaka, National Institute of Agrobiological Sciences; Michihiko Shimomura, Mitsubishi Space Software Co.,Ltd.; Nobukazu Namiki, Mitsubishi Space Software Co.,Ltd.; Hiroshi Ikawa, Mitsubishi Space Software Co.,Ltd.; Takashi Matsumoto, National Institute of Agrobiological Sciences; Yuichi Katayose, National Institute of Agrobiological Sciences; Jianzhong Wu, National Institute of Agrobiological Sciences; Hirokazu Handa, National Institute of Agrobiological Sciences

PDF file
2:35 PM
W564
Never Eat Shredded Wheat – Navigating through Reference and Survey Wheat Assemblies Using Diverse Mate-Pair Libraries
David J. F. Konkin, National Research Council of Canada

PDF file
2:55 PM
W565
Integrating Whole Genome Datasets into a BAC by BAC Approach to Wheat Chromosome Sequencing
Matt Clark, The Genome Analysis Centre

3:15 PM
W566
Application of Single Molecule Sequencing to Facilitate de novo Sequencing of Wheat Chromosome Arm 7DL
Song Weining, Northwest A&F University

3:35 PM
Break


3:55 PM
W567
Construction of Pseudomolecules for the Aegilops tauschii Genome, the Wheat D Genome Progenitor
Tingting Zhu, Department of Plant Sciences, University of California, Davis; Karin R. Deal, Department of Plant Sciences, University of California, Davis; Shuyang Liu, Department of Plant Sciences, University of California; Juan C. Rodriguez, Department of Plant Sciences, University of California; Daniela Puiu, Johns Hopkins University, School of Medicine; Geo Pertea, Johns Hopkins University, School of Medicine; Steven L Salzberg, Johns Hopkins University, School of Medicine; Aleksey Zimin, University of Maryland; Frank M. You, Agriculture and Agri-Food Canada; Jan Dvorak, Department of Plant Sciences, University of California, Davis; Ming-Cheng Luo, Department of Plant Sciences, UC Davis

4:15 PM
W568
Practical Aspects of BioNano Mapping of the Wheat Genome
Hana Simkova, Institute of Experimental Botany; Helena Stankova, Institute of Experimental Botany; Alex Hastie, BioNano Genomics; Saki Chan, BioNano Genomics; Jan Vrana, Institute of Experimental Botany; Zuzana Tulpova, Institute of Experimental Botany; Paul Visendi, University of Queensland; Satomi Hayashi, University of Queensland; Ming-Cheng Luo, Department of Plant Sciences, UC Davis; Jacqueline Batley, University of Western Australia; David Edwards, University of Western Australia; Jaroslav Dolezel, Institute of Experimental Botany

PDF file
4:35 PM
W569
Towards a finished sequence for chromosome 7A: Building a high-quality pseudomolecule
Gabriel Keeble-Gagnere, Murdoch University

PDF file
4:55 PM
W570
Hybrid assembly tools and strategies for a high quality wheat reference
Philippe Rigault, GYDLE

5:15 PM
W571
IWGSC Sequence Repository: Moving Towards Tools to Facilitate Data Integration for the Reference Sequence of Wheat
Michael Alaux, INRA - URGI; Thomas Letellier, INRA - URGI; Françoise Alfama, INRA - URGI; Véronique Jamilloux, INRA - URGI; Jane Rogers, International Wheat Genome Sequencing Consortium; Frederic Choulet, INRA UMR 1095 GDEC; Claire Guerche, INRA - URGI; Mikael Loaec, INRA - URGI; Raphael Flores, INRA - URGI; Célia Michotey, INRA - URGI; Anne-Francoise Adam-Blondon, INRA - URGI; Etienne Paux, INRA GDEC; Kellye Eversole, Eversole Associates; Hadi Quesneville, INRA - URGI

PDF file
5:35 PM
W572
A Wheat Gene Expression Browser Implemented By the expVIP Customisable RNA-Seq Data Analysis and Visualisation Platform
Cristobal Uauy, John Innes Centre; Philippa Borrill, John Innes Centre; Ricardo H. Ramirez-Gonzalez, The Genome Analysis Centre

PDF file
5:55 PM
Discussion


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