Development of genome sequencing infrastructure and progress toward sequencing of chromosomes 1, 10 and 11 Steve Tanksley, Cornell U Steve Stack, Colorado.

Slides:

Advertisements

Similar presentations

Sequencing the Maize Genome Maize Genome Sequencing Consortium

Advertisements

Maize Genetics, Genomics, Bioinformatics workshop

Chr9 A ntonio Granell IBMCP-Valencia Spain Tomato Sequencing, Madison July 2006.

The Role of Fluorescence in situ hybridization (FISH) in Sequencing the Tomato Genome.

The International Tomato Sequencing Project: The first Cornerstone of the SOL Project Lukas Mueller on behalf of International SOL Tomato Sequencing Project.

US Tomato sequencing project update January 14, 2007.

PAA / Solanaceae July 23-27, Madison, Wisconsin, USA Sequencing the gene-rich space of tomato chromosome 7 Current status of the French effort.

Sequencing Status of the Chromosome 8 and New Marker Development toward a Genetic Map Construction between Micro-Tom and Ailsa Craig SOL Genomics Workshop.

Physical Mapping I CIS 667 February 26, Physical Mapping A physical map of a piece of DNA tells us the location of certain markers  A marker is.

1 Sequencing Workshop Koln, October 15, 2008 Toni Granell My apologies for not being here Thanks Joyce Chr9 sequencing update Spain.

Sequencing Tomato Chr9 Tomato Sequencing Meeting PAG XV 2007 San Diego, 14 January 2007 Antonio Granell IBMCP, Valencia.

Expanding the Tool Kit for BAC Extension Summary of completion criteria developed for NSF Tomato Sequencing Workshop January 14, 2007.

International Tomato Finishing Workshop Wellcome Trust Sanger Institute April 2007 Wellcome Trust Medical Photographic Library.

Use of FISH in sequencing tomato chromosome 6 René Klein Lankhorst Hans de Jong Korea meeting 2007.

Tomato Chromosome 8 sequencing at Kazusa DNA Research Institute Erika Asamizu.

Genome sequencing. Vocabulary Bac: Bacterial Artificial Chromosome: cloning vector for yeast Pac, cosmid, fosmid, plasmid: cloning vectors for E. coli.

EU-SOL 2008 November 13-16, Toulouse, FRANCE CHROMOSOME 7 SEQUENCING Current status and perspective TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497.

SOL Genomics Network Formed in 2003 to answer two questions: – How can a common set of genes give rise to such a wide range of morphologically and ecologically.

Plant and Animal Genome Conference January 11, 2009.

Chromosome 8 Sequencing: Current Status and Future Prospects toward Finishing Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata.

What is SGN? S GN is a rapidly evolving comparative resource for the plants of the Solanaceae family, which includes important crop and model plants such.

Solanum lycopersicum Chromosome 4 Sequencing Update SOL Germany– October 2008 Wellcome Trust Medical Photographic Library.

The New Zealand Institute for Plant & Food Research Limited Potato Genome Sequencing Consortium, notes from the edge Dr Susan Thomson, Dr Mark Fiers, Dr.

Tomato Chromosome 4: A Mapping & Sequencing Update 28 th September 2005 Christine Nicholson Mapping Core Group Welcome Trust Sanger Institute, UK.

SOL 2008 October 12-16, Cologne, Germany CHROMOSOME 7 THE FRENCH CONTRIBUTION TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966.

Tomato Overgo Project and Seed BAC Selection Cornell Team Ying Eileen Wang, 2005 PAG.

Genome sequencing Haixu Tang School of Informatics.

BrGSP: the Brassica 'A' genome sequencing project Genetic map anchoring of sequenced BACs (Dec 2008) A01 JWF3 A01 VCS3MDH.

Genome Sequencing in the Legumes Le et al Phylogeny Major sequencing efforts Minor sequencing efforts ~14 MY ~45 MY.

Revision – Concept map.

Solanum lycopersicum Chromosome 4 Sequencing Update UK-SOL– Dec 2008 Wellcome Trust Medical Photographic Library.

Current Sequencing Status of Tomato Chromosome 2 PLANT GENOME RESEARCH CENTER, KRIBB, KOREA Sanghyeob Lee Sung-Hwan Jo Dal-Hoe Koo Chul-Goo Hur Hong-Seok.

4th Solanaceae Genome Workshop 2007, September 09th- 13th, Jeju Island, Korea THE FRENCH CONTRIBUTION TO THE INTERNATIONAL TOMATO GENOME SEQUENCING PROGRAM.

FINISHING WORKSHOP APRIL 2008 CHROMOSOME 7 THE FRENCH CONTRIBUTION TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966 T0731 TM15.

Theobroma cacao Integrated Physical and Genetic Map 2 BAC Libraries 250 Genetic Markers.

Chromosome 2 Doil Choi, Sunghwan Jo KOREA. Cytological architecture of chromosome kb/µm DAPI (4’-6-diamidino-2-phenylindole) stained pachytene chromosome.

Progress tomato chromosome 6 René Klein Lankhorst.

INDIAN INITIATIVE FOR TOMATO GENOME SEQUENCING Nagendra Singh National Research Centre on Plant Biotechnology Indian Agricultural Research Institute New.

中国农业科学院蔬菜花卉研究所 Institute of Vegetables and Flowers Chinese Academy of Agricultural Sciences Zhonghua Zhang Institute of Vegetables and Flowers, Chinese.

Chromosome 12 M. Pietrella 1, G. Falcone 1, E. Fantini 1, A. Fiore 1, C. Perla 1, M.R. Ercolano 2, A. Barone 2, M.L. Chiusano 2, S. Grandillo 3, N. D’Agostino.

Chromosome 12 M. Pietrella 1, G. Falcone 1, E. Fantini 1, A. Fiore 1, M.R. Ercolano 2, A. Barone 2, M.L. Chiusano 2, S. Grandillo 3, N. D’Agostino 2, A.

1.Data production 2.General outline of assembly strategy.

2nd TOMATO FINISHING WORKSHOP chromosome 9 Wageningen, April 24-25, 2008.

Solanum lycopersicum Chromosome 4 Mapping and Finishing Update SRC-UK and Wellcome Trust Sanger Institute SOL Korea – September 2007 Wellcome Trust Medical.

Lindsay A. Shearer1, Lorinda K

US Sequencing Project Funded by NSF Two-year project Start date: Sept 1, 2004 Follow-up project for full sequencing of chromosomes 1, 10 and 11.

70 µm 0 µm International Tomato Genome Sequencing Project Mb 85.6 Mb 83.6 Mb 82.1 Mb 80.0 Mb 53.8 Mb 80.3 Mb 64.7 Mb 81.8 Mb 88.5.

Mojavensis: Issues of Polymorphisms Chris Shaffer GEP 2009 Washington University.

13 th January 2008 Plant & Animal Genome Conference Progress with Sequencing Tomato Chromosome 4 Clare Riddle Tomato Project Group Wellcome Trust Sanger.

16 th April 2007 Christine Nicholson, Mapping Core Group Wellcome Trust Sanger Institute Tomato Chromosome 4 Mapping & Use of FPC Copyright Wellcome Trust.

26 th July 2006 Christine Nicholson, Mapping Core Group Karen McLaren, Finishing Group Leader Wellcome Trust Sanger Institute Sequencing the Gene Space.

Plan A Topics? 1.Making a probiotic strain of E.coli that destroys oxalate to help treat kidney stones in collaboration with Dr. Lucent and Dr. VanWert.

US Contribution to the International Tomato Genome Sequencing Effort Current structure of contributions Ongoing activity summary Funding issues.

CURRENT STATUS ON SEQUENCING OF CHROMOSOME 12 Mara Ercolano Ischia, 2005.

Genome Analysis. This involves finding out the: order of the bases in the DNA location of genes parts of the DNA that controls the activity of the genes.

BrGSP: the Brassica 'A' genome sequencing project

Tomato Sequencing Project Meeting at SOL 2008, Oct. 15, 2008

Pre-genomic era: finding your own clones

Biotech Tools Review

Plant & Animal Genome Conference

Sequencing Chromosome 2

Status of the US contribution to the international

Progress in sequencing chromosome 6

Progress in sequencing chromosome 6

TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966 T0731 TM15 T1347 T1257 T0848 THE FRENCH CONTRIBUTION TO THE INTERNATIONAL.

Sequencing update of tomato chromosome 3 Chinese Academy of Sciences

1 Point! 2 Points! 3 Points! 4 Points! 5 Points!!

Tomato FISH Song-Bin Chang Suzanne Royer Lorrie Anderson Steve Stack.

The Role of Fluorescence in situ hybridization (FISH)

The Potato Genome Sequencing Consortium: An Update

Presentation transcript:

Development of genome sequencing infrastructure and progress toward sequencing of chromosomes 1, 10 and 11 Steve Tanksley, Cornell U Steve Stack, Colorado State U Lukas Mueller, Cornell U Joyce Van Eck, Boyce Thompson Institute Jim Giovannoni, USDA-ARS

Table 2: Read statistics for the three BAC libraries and the sheared library.

BAC Resources for Tomato Euchromatin Sequencing HindIII BAC library - 15 X genome coverage MboI BAC Library - 7 X genome coverage EcoRI BAC Library - 9 X genome coverage HindIII clones anchored to genetic map via overgo probes A BAC end sequence for all libraries B C Fingerprint data for HindIII, EcoRI D Hybridization filters for all libraries

S. Korea X X X China X X Japan X X India X X X X United Kingdom X Distribution of Materials Full Libraries Individual Clones Verified Clones Filters S. Korea X X X China X X Japan X X India X X X X United Kingdom X Spain X X France X X Italy X X X The Netherlands X X X

Clone Verification Process Select BACs anchored via replicated high-quality overgo hybes. Single-colony purify (contamination a problem especially with HindIII clones) and isolate BAC miniprep DNA. Design sequencing oligo to the marker sequence from which the anchoring overgo sequence was derived but from a different area. 4. Sequence BAC DNA with marker-specific sequencing oligo and T7 T7 Anchor marker sequence BAC Marker-specific oligo Overgo probe

www.sgn.cornell.edu

Summary of New US Tomato Sequencing Project $1.8 million October 2006 - Sept 2007 Continued service to the international project - expansion of informatics team and SGN - emphasis on development of “end game tools” - methods and pipelines for creation of pseudomolecules - development of fosmid library - >40 kb average, 200,000 clones - end sequenced - continued BAC support - verification, mapping, FISH - continued sequencing of BACs from 1, 10, 11