1. 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

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

3. 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

4. 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

5. 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

12. Summary of New US Tomato Sequencing Project
$1.8 million
October 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