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