Progress tomato chromosome 6 René Klein Lankhorst.

Slides:



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

The Role of Fluorescence in situ hybridization (FISH) in Sequencing the Tomato Genome.
Progress on the sequencing of the euchromatic gene rich space of chromosome 6 of Solanum lycopersicum cv. Heinz 1706 Sander Peters Cologne Oct 2008.
The International Tomato Sequencing Project: The first Cornerstone of the SOL Project Lukas Mueller on behalf of International SOL Tomato Sequencing Project.
A high throughput workflow management system Cyrille2 Mark Fiers NBIC practical course on web services and workflow management december 2007.
US Tomato sequencing project update January 14, 2007.
Progress on the sequencing of the euchromatic gene rich space of chromosome 6 of Solanum lycopersicum cv. Heinz 1706 Sander Peters Sep 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.
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.
Use of FISH in sequencing tomato chromosome 6 René Klein Lankhorst Hans de Jong Korea meeting 2007.
Sequencing activities in EU-SOL René Klein Lankhorst PAG 2007.
Tomato Chromosome 8 sequencing at Kazusa DNA Research Institute Erika Asamizu.
EU-SOL 2008 November 13-16, Toulouse, FRANCE CHROMOSOME 7 SEQUENCING Current status and perspective TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497.
Chromosome 8 Sequencing: Current Status and Future Prospects toward Finishing Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata.
Tomato genome annotation pipeline in Cyrille2
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.
Update tomato chr. 6 Roeland van Ham Centre for BioSystems Genomics The Netherlands.
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.
Progress on sequencing tomato chromosome 12 Mara Ercolano.
WGP Tomato EU-SOL meeting July 15, 2009 Antoine Janssen.
Mapping and sequencing chromosome 6 of Solanum lycopersicum cv
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.
BAC FISH and repeat bar-coding technology for tomato and potato San Diego, January – 2008 Hans de Jong, Dóra Szinay Laboratory of Genetics Wageningen University.
Finishing tomato chromosomes #6 and #12 using a Next Generation whole genome shotgun approach Roeland van Ham, CBSG, NL René Klein Lankhorst, EUSOL Giovanni.
Chromosome 2 Doil Choi, Sunghwan Jo KOREA. Cytological architecture of chromosome kb/µm DAPI (4’-6-diamidino-2-phenylindole) stained pachytene chromosome.
INDIAN INITIATIVE FOR TOMATO GENOME SEQUENCING Nagendra Singh National Research Centre on Plant Biotechnology Indian Agricultural Research Institute New.
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.
Wageningen, April 24-25, 2008 II Tomato Finishing Workshop Chromosome 12 Update ENEA, Rome University of Naples ‘Federico II’ CRIBI and Univ. of Padua.
HeterochromatinEuchromatin Relative chromosome length Relative bivalent diameter X 1.23 X 1.00 Relative area Relative optical density.
1.Data production 2.General outline of assembly strategy.
2nd TOMATO FINISHING WORKSHOP chromosome 9 Wageningen, April 24-25, 2008.
Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Maria Luisa Chiusano Maria Raffaella Ercolano University.
The Genome Assemblies of Tasmanian Devil Zemin Ning The Wellcome Trust Sanger Institute.
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.
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.
Cross_genome: Assembly Scaffolding using Cross-species Synteny Zemin Ning High Performance Assembly.
Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Contribution from Naples Funding Agency: Italian Ministry of Agriculture (MiPAF) Project.
CURRENT STATUS ON SEQUENCING OF CHROMOSOME 12 Mara Ercolano Ischia, 2005.
Tomato Sequencing Project Meeting at SOL 2008, Oct. 15, 2008
Plant & Animal Genome Conference
Development of genome sequencing infrastructure and progress toward sequencing of chromosomes 1, 10 and 11 Steve Tanksley, Cornell U Steve Stack, Colorado.
Sequencing Chromosome 2
Status of the US contribution to the international
Progress on sequencing tomato chromosome 12
Progress in sequencing chromosome 6
Current Sequencing Effort of Tomato Chromosome 2 - Chromosome assembly - Finishing workshop April KRIBB/SNU, Korea.
Progress in sequencing chromosome 6
Assembly of BAC ends on P250I21
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
Tomato FISH Song-Bin Chang Suzanne Royer Lorrie Anderson Steve Stack.
Sequence the 3 billion base pairs of human
The Role of Fluorescence in situ hybridization (FISH)
SOL Jeju Island, Korea 14th September 2007
Presentation transcript:

Progress tomato chromosome 6 René Klein Lankhorst

155 BACs sequenced (64 seeds plus 91 extension BACs), 140 BACs arranged into 12 major contigs Short arm completely covered –3 small gaps remain Long arm has 5 major gaps left 16 Mb of BAC DNA sequenced from the euchromatin These BACs assembled into 12 Mb unique DNA Total euchromatine in chr.# 6 is approx. 20 Mb  60% done 76 BACs available on SGN –69 Phase 1 /2 –8 Phase 3 Status chromosome #6 TG193

Targeting the gaps on the long arm 3 novel seed BACs resulted from a targeted screening of the MboI BAC library with overgo markers (Joyce van Eck) 21 AFLP markers plus 10 SNP markers have been selected for the different gaps (Keygene). Currently, 16 BACs have been retrieved with these markers

GAP closure of chr.#6 BACs 130 Phase 1/2 BACs are/were in the finishing pipeline In total, more than 800 gaps were present in these 130 BACs (average ~6 gaps / BAC) In the past 6 months ~400 gaps have been closed resulting in the finishing of 37 BACs.

The Dutch chromosome 6 sequencing team Sander Peters Marleen Henkens Marjo van Staveren José van der Belt Dorá Szinay Erwin Datema Yulin Bai Roeland van Ham Hans de Jong Willem Stiekema René Klein Lankhorst Sequence providers: Funding: