Solanum lycopersicum Chromosome 4

Sequencing Update

SOL Germany– October 2008

Wellcome Trust Medical Photographic Library

Summary of Project Status at WTSI

WTSI will be leaving the project on 31st Oct 2008

Transfer of BAC selection/contig building QC-checking is on the move to Imperial College London

Introduction

WTSI Tomato Clone Pipeline

Pipeline Stage Number of BACs 2007

Number of BACs 2008

Subcloning 34 0

Shotgun 21 1

Assembly Start 7 0

Auto-prefinishing 3 0

Finishing 11 33

QC Checking 4 2

Finished 63 147

Total 143 183

Phase 3

Phase 1+2

HTGS:

Chromosome 4Sequence Generated

Total Sequence Available 19,815,026 bp

Total Unique Sequence 19,527,597 bp

Total amount of Finished Sequence = 15,244,914 bp

Some facts and figures

We have 81 contigs on chr4 (80 contigs with sequence available).

Average contig length is just under 250 kb.

The average number of BACs per contig is 2.3.

The largest sequence contigs are in the range of 450kb-500kb with 5 or 6 BACs.

Distribution of tomato Chromosome BACs and sequence content

Centromere

= Euchromatin

= Heterochromatin

62 markers 41 markers 124 markers

30 contigs 11 contigs 36 contigs

56 BACs 59 BACs 63 BACs

SSR markers 4 contigs 5 BACs

UNORDERED

27 markers 16 markers 61 markers

Summary of Progress on Chromosome 4

81 map contigs have been built on chromosome 4 (AGP files)

119 BACs/44 contigs definitely on chr4 in FISH/ IL mapped

58 BACs under confirmation but have chr4 marker sequence

~60 Markers for which BACs have not been identified.

~13 BACs have been sequenced to HTGS3 and placed on chr0, definitely not on chr4 (others initiated, in same contig etc but stopped in pipeline).

22 Missing markers missing sequence?

Summary of what we will do next

1) Confirm chr4 location of BACs that lack chr4 marker sequence and or have conflicting map location. IL mapping.

2) Use missing marker sequences to identify further BACs (3D pools) and confirm chr4 location using IL mapping.

3) Use 3D BAC pools to identify BACs to extend current contigs.

4) Analyse output from X2 GS-FLX and X2 Illumina sequencing runs on cDNA from chr4 IL and parental lines to identify SNPs and further chr4 markers.

5) Use any markers from (4) to isolate further BACs for sequencing.

Acknowledgements

Wellcome Trust Sanger Institute:Carol ChurcherJane RogersSean HumphrayClare Riddle and Mapping Core GroupKaren McLaren and Finishing Team 46Stuart McLaren and Pre-finishing Team 58Christine Lloyd and QC Team 57Karen OliverMatt JonesCarol Scott

Imperial College London:Gerard BishopDaniel BuchanJames AbbottSarah ButcherRosa Lopez-Cobollo

University of Nottingham:Graham Seymour

Scottish Crop Research Institute:Glenn Bryan

Cornell University: Lukas MuellerJim Giovannoni

MIPS/IBI Institute for Bioinformatics:Klaus MayerRemy Bruggmann

FISH ResourcesStephen Stack Group (Colorado)Hans de Jong (Wageningen)Dora Szinay (Wageningen)

FUNDING