Transcript US Tomato sequencing project http://sgn.cornell.edu/

US Tomato sequencing project
update
http://sgn.cornell.edu/
January 14, 2007
US Tomato Genome sequencing
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BAC libraries
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Made two BAC libraries (EcoRI & MboI) in
addition to HindIII library
BAC end sequence
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400,000 BAC end sequence reads
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340,000 high quality insert sequences
Chromosomes to be sequenced
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1, 10, 11
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Sequenced 17 full BACs to date
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> 40 successful FISH hybridizations
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$1.8 million in support from NSF (Fall, 06)
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Pending proposal for full sequencing of
Chromosomes 1, 10, 11
BAC libraries and BAC end sequences
Library Name /
enzyme
HindIII
MboI
EcoRI
Sheared library
Total Number of
Approx number of
Cloning Vector
clones
clones seqenced
129024
76000
pBeloBAC11
100,000
50688
25344
pEC BAC I
50,000
50,000
75000
25344
pIndigoBAC-5
N.A.
4800
PUC18-SW
Additional ordered libraries:
S. cheesmannii
S. pennellii
HindIII
HindIII
S. lycopersicum Sau3A
S. lycopersicum Sau3A
pBeloBAC11
pBeloBAC11
100,000 clones
100,000 clones
cosmid
cosmid
200,000 clones 20 kb avg.
>100,000 clones > 20 kb avg.
S. lycopersicum sheared fosmid
>100kb avg.
>100kb avg.
>150,000 clones 40 kb avg.
(400,000 target)
SSR125
cLEC7H4
SSR331
SSR580
cLET1I9
SSR103
T1201
T634
cLER17N11
TG154
Fw2.2
T1480
T1566
T347
CT9
T1665
CT38
SSR50
T147
SSR32
T1494
SSR26
T562
SSR5
SSR349A
T697
SSR605
T1706
T1117
TG31
SSR57
SSR356
CT255
SSR96
SSR66
SSR40
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SSR586
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cLEC7P21
T1616
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
FISH Image
Bioinformatics
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BAC registry database
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SGN Data repository
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Central database at SGN that keeps track
of the status of every BAC sequenced in
the project
All sequences, including all primary data
(chromatograms and assemblies) are
uploaded to the central data repository
Participation in ITAG annotation
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Structural Annotation pipeline
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Functional Annotation pipeline
Hetero/euchromatin BAC repeat annotation
Euchromatin: Gene rich, repeat poor
Genes
Heterochromatin: Gene poor, repeat rich (red)
Repeats
Future plans
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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
Acknowledgments
Steven Tanksley
Yimin Xu
Nancy Eanetta
Jim Giovannoni
Ruth White
Julia Vrebalov
Joyce van Eck
Stephen Stack
Suzanne Royer
SGN:
Lukas Mueller
Naama Menda
Rob Buels
Marty Kreuter
Chenwei Lin
John Binns
Beth Skwarecki