us tomato sequencing project update january 14, 2007
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US Tomato sequencing project update
http://sgn.cornell.edu/
January 14, 2007
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
BAC libraries and BAC end sequences
Library Name /enzyme
Total Number ofclones
Approx number ofclones seqenced
Cloning Vector
HindIII 129024 76000 pBeloBAC11
MboI 50688 25344 pEC BAC I
EcoRI 75000 25344 pIndigoBAC-5
Sheared library N.A. 4800 PUC18-SW
Additional ordered libraries:
S. cheesmannii HindIII pBeloBAC11 100,000 clones >100kb avg.S. pennellii HindIII pBeloBAC11 100,000 clones >100kb avg.
S. lycopersicum Sau3A cosmid 200,000 clones 20 kb avg.S. lycopersicum Sau3A cosmid >100,000 clones > 20 kb avg.
S. lycopersicum sheared fosmid >150,000 clones 40 kb avg.(400,000 target)
100,00050,00050,000
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
TG154SSR57
SSR5 SSR50
T1566
FISH Image
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
Hetero/euchromatin BAC repeat annotation
Euchromatin: Gene rich, repeat poor
Heterochromatin: Gene poor, repeat rich (red)
GenesGenes
Repeats
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
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