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US Tomato sequencing project update January 14, 2007.

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1 US Tomato sequencing project update http://sgn.cornell.edu/ January 14, 2007

2 US Tomato Genome sequencing ● BAC libraries  Made two BAC libraries (EcoRI & MboI) in addition to HindIII library ● BAC end sequence  400,000 BAC end sequence reads  340,000 high quality insert sequences ● Chromosomes to be sequenced  1, 10, 11  Sequenced 17 full BACs to date  > 40 successful FISH hybridizations  $1.8 million in support from NSF (Fall, 06)  Pending proposal for full sequencing of Chromosomes 1, 10, 11

3 BAC libraries and BAC end sequences Additional ordered libraries: S. cheesmanniiHindIIIpBeloBAC11100,000 clones >100kb avg. S. pennelliiHindIIIpBeloBAC11100,000 clones>100kb avg. S. lycopersicumSau3Acosmid200,000 clones20 kb avg. S. lycopersicumSau3A cosmid>100,000 clones> 20 kb avg. S. lycopersicumshearedfosmid>150,000 clones40 kb avg. (400,000 target) 100,000 50,000

4 Overgo Project ● anchor tomato BACs/contigs on the highly saturated genetic map (F2.2000) ● identify the minimum tiling path of BAC clones for BAC-by-BAC sequencing cLER17N11 cLEC7P21 SSR40 SSR356 cLET1I9 T562 SSR26 SSR32 T1494 cLEC7H4 Fw2.2 T1480 T634 T1201 SSR605 SSR96 SSR66 SSR586 T1616 SSR349A SSR103 SSR331 SSR580 SSR125 TG31 T1117 T1706 CT255 T697 T1665 CT38 T147 CT9 T347 TG154 SSR57 SSR5 SSR50 T1566

5 FISH Image

6 Bioinformatics ● BAC registry database  Central database at SGN that keeps track of the status of every BAC sequenced in the project ● SGN Data repository  All sequences, including all primary data (chromatograms and assemblies) are uploaded to the central data repository ● Participation in ITAG annotation  Structural Annotation pipeline  Functional Annotation pipeline

7 Hetero/euchromatin BAC repeat annotation Euchromatin: Gene rich, repeat poor Heterochromatin: Gene poor, repeat rich (red) Genes Repeats

8 Future plans ● Complete and End-sequence Fosmid library (400,000 clones) ● Full sequences of chromosome 1, 10 & 11 (estimated 550 BACs) ● Support international project partners with BAC libraries and FISH (10 hybes/country) ● Continue to run a central bioinformatics hub for data deposition (SGN), project tracking and running shared annotation pipeline

9 Acknowledgments SGN: Lukas Mueller Naama Menda Rob Buels Marty Kreuter Chenwei Lin John Binns Beth Skwarecki Steven Tanksley Yimin Xu Nancy Eanetta Jim Giovannoni Ruth White Julia Vrebalov Joyce van Eck Stephen Stack Suzanne Royer

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