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

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Presentation transcript:

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

Korea China France India Italy Japan Spain The Netherlands UK Foundation Resources Libraries Clones Maps Anchoring FISH SGN Sequencing Troubleshooting

Species Orthologous markers COSII markers Total map distance (cM)Mapping population Tomato cM83 F2 plants (S. lycopersicum X S. pennellii) Eggplant cM58 F2 plants (S. linnaeanum X S. melongena) Pepper cM94 F2 plants (C. annuum X C. frutescens) Tobacco84 NA55 F2 plants (N. tomentosiformis X N. otophora) Table – Statistics of comparative mapping in the family Solanaceae Figure – Comparative maps of Pepper (P) and Eggplant (E) against Tomato (T) T1 T2 T3 T4 T5 T6 T7 T8 T9 T10 T11 T12 Wu and Tanksley, unpublished

An example of conserved synteny in the family Solanaceae and coffee (Rubiaceae) Note: The tobacco chromosome may be incomplete due to the on-going mapping process. Wu and Tanksley, unpublished

' C 12 12’ A B E A F 5 D annotated gene pseudogene homolog most similar to tomato gene At3 petunia eggplant tomato potato pepper At4 At2 At1 At5-A At5-B

Progress in FISHing Tomato BACs in the USA - August 2007  171 BAC clones FISHed  120 positive results  107 unique localizations (see SGN web site)  ~10 multiple locations (generally in pericentric heterochromatin and telomeres)  17 located on “wrong” chromosome  1 located on “wrong” arm  With a few exceptions, the order of BACs on the FISH map corresponds to the order of loci on the linkage map  At least one BAC has been localized in every chromosome arm

Total number raw reads 1 2,304 Number of low quality reads Vector/E. coli contamination 2 Chloroplast/mitochondria contamination 250 Ribosomal RNA contamination 84 Total number of high quality reads 3 1,821 Tomato Fosmid Library Currenty over 150,000 ordered clones Sheared inserts (avg kb) Three test plates end sequences (1152 clones) 17 fosmids have one end hitting a sequenced BAC ( ,868 bases from end) 9 fosmids reside on existing BAC clones (ends map 30, ,363 bases apart) 5 fosmids fill existing BAC gaps (ie, connect two BACs) 50,000 sent to Sanger Center for end sequencing

Korea China France India Italy Japan Spain The Netherlands UK Foundation Resources Libraries Clones Maps Anchoring FISH SGN Sequencing Troubleshooting

Status of Tomato sequencing Project Funding in the US NSF proposal for sequencing 3 chromosomes - declined Current NSF project through September, 2008 USDA proposal for SGN expansion - $400,000 awarded L. Mueller USDA proposal for annotation support - $300,000 awarded B. Barbazuk USDA proposal for 454 sequencing of ESTs - $400,000 J. Rose and J. Giovannoni