1. Tomato Sequencing Project Meeting at SOL 2008, Oct. 15, 2008
Status of tomato genome sequence in Japan: chromosome 8 sequencing and selected BAC mixture sequencing
Shusei Sato, Erika Asamizu, Takakazu Kaneko,
Hiroyuki Fukuoka, Satoshi Tabata

2. Distribution of Anchor Markers on Chromosomes
Initial seeds on Chr.8 92
165
1.8 79
143 67
171
2.6 62
137
2.2 40
119
3.0 63
101
1.6 51
112 33 87
116
2.9 41
2.1 43
103
2.4 39
120
3.1
# anchors
cM chr length
cM per anchor

3. Summary of EST-SSR Marker analysis
712 markers have been mapped on EXPEN2000
chr1 78
chr7 56
chr2 66
chr8 62
chr3 74
chr9 52
chr4 60
chr10 49
chr5 62
chr11 50
chr6 52
chr12 51
34 new seed clones have been selected

4. Status of Chr.8 Sequencing
Nr. BACs
Finished
151
Phase 2 5
Assembling 11
Sequencing 18
Total
185
(86% of initial target)
(106% of initial target)
Finished length without overlap: 14,906,592 bp
67 seed points (34 contigs, 11 single clones)

5. Gap Filling by Whole Genome Shotgun Sequencing
Selected BAC Mixture (SBM) shotgun
Select BACs whose end sequences do not contain undesired (repeat) sequences
Mix the BACs and sequence by shotgun
BAC
Repeat
Gene space

6. Both ends are NOT repeat
BLASTN BES vs. RepeatDB
Percentage
LTR
49.7
Unknown
30.3
rRNA
7.4
Satellite
1.6
Simple repeat
1.5
DNA
1.4
LINE
1.3
402,012 end sequences from 177,408 BAC clones
vs.
14,229 repeat sequences (TIGR_SolAth_repeat, mips_repeat_collection, SGN repeat collection)
Library
Both ends are repeat
One end is repeat
Both ends are NOT repeat
HBa
19,123
35,277
26,181
Eco RI
9,533
18,594
15,516
Mbo I
15,570
20,995
13,134
Total
44,226
74,866
54,831
Source of the 1st
BAC mixture

7. Selected BAC Mixture (SBM) shotgun sequencing
<1st set>
10,000 clones from HBa library
5,000 clones from EcoRI library
5,000 clones from MboI library
20,000 BAC clones
A total of 2.9 million sequences were accumulated by August.
(total length is ~ 1.7 Gbp)

8. Both ends are NOT repeat
BLASTN BES vs. RepeatDB
Percentage
LTR
49.7
Unknown
30.3
rRNA
7.4
Satellite
1.6
Simple repeat
1.5
DNA
1.4
LINE
1.3
402,012 end sequences from 177,408 BAC clones
vs.
14,229 repeat sequences (TIGR_SolAth_repeat, mips_repeat_collection, SGN repeat collection)
Library
Both ends are repeat
One end is repeat
Both ends are NOT repeat
HBa
19,123
35,277
26,181
Eco RI
9,533
18,594
15,516
Mbo I
15,570
20,995
13,134
Total
44,226
74,866
54,831
Source of the 2nd
BAC mixture
Source of the 1st
BAC mixture

9. Selected BAC Mixture (SBM) shotgun sequencing
<2nd set>
5,400 clones from HBa library
2,700 clones from EcoRI library
2,700 clones from MboI library
10,800 BAC clones
Sequencing has started in September 2008.

10. Status of SBM Shotgun Sequences
・As of Oct. 2008, 3.0 million sequences
　has been accumulated.
　(total length is 1.9 Gbp)
3rd Assemble
・Assembled into 205,091 contigs.
　Total size of the contigs is ~ 580 Mbp.
longest contig: 127,384 bp (17,702bp in 2nd Assemble)
> 5kb contigs: 24,774 (21,230 in 2nd Assemble)

11. Status of SBM Shotgun Assembly
EST coverage :Tomato Gene Index (46,849 unigenes)
74%
SBM +
Finished BAC
(34,546 hits)
71%
SBM
(33,089 hits)

12. Blast DB of the SBM contigs
> We are pleased to provide the blast DB of the SBM contigs to other groups of tomato genome sequence project for the purpose of contig extension.
user name: SOLseq
password: ConExDB0804
> Please contact Shusei Sato
for the sequence information on the matched contigs.

13. Dept. Plant Genome Research
National Institute of Vegetable and Tea Science
Satoshi Tabata
Erika Asamizu
Shusei Sato
Molecular Genetics and Physiology team
Sequencing
Marker
Takakazu Kaneko
Akiko Watanabe
Akiko Ono
Naomi Nakazaki
Midori Kato
Kumiko Kawashima
Yoshimi Shimizu
Chiharu Minami
Chika Takahashi
Shigemi Sasamoto
Tsuyuko Wada
Ai Matsuno
Hiroyuki Fukuoka
Satomi Negoro
Yumika Kitamura