current sequencing status of tomato chromosome 2 plant genome research center, kribb, korea...
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Current Sequencing Status of Current Sequencing Status of Tomato Chromosome 2Tomato Chromosome 2
PLANT GENOME RESEARCH CENTER,
KRIBB, KOREA
Sanghyeob Lee
Sung-Hwan Jo
Dal-Hoe Koo
Chul-Goo Hur
Hong-Seok Park
Doil ChoiJul 26, 2006
Madison, USA
Organization of chromosome 2Organization of chromosome 2
euchromatineuchromatin
heterochromatinheterochromatin
AT-rich satellite DNAAT-rich satellite DNA
226Mb*
Kor
ea
Chrom.
* Euchromatin portion (based on deJong and Stack)
NOR
PH
PH
CEN
TEL
Euchromatin
Heterochromatin
48.12 µm = 22.19 Mb
22.10 µm = 67.29 Mb
89.48 Mb
HK
NOR: nucleolar organizing region
PH: pericentromeric heterochromatin
HK: heterochromatic knob
CEN: centromere
TEL: telomere
A B CA B C
Overgo anchored BAC
A B C
Overgo anchored BAC
A B C
Overgo anchored BAC
A B C
Overgo anchored BAC
A B C
Overgo anchored BAC
A B C
Overgo anchored BAC
A B C
Overgo anchored BAC
A B C
Overgo anchored BAC
BAC to BAC SequencingBAC to BAC Sequencing
CENPH
PH
NOR
13 cM
142 cM
HK
TEL
10
20
30
40
50
60
70
80
90
100
110
140
120
130
0
H303I24
H163K16H190N21
H101G09
H162I09M045L06H160F05
H072A04
M018P14M019I01H323A14H204D01H320D04H198A03H291P19H060J03H009K06H164H08H213A01H134G09H016A12H011A02M014P22
M042B19H0461M08
H150M11H210D10
H073P13
H155D20
H064B17H194L19H257H21
LG2
142
13
H007F24
HK
Identification of Euchromatin Border
10
20
30
40
50
60
70
80
90
100
110
140
120
130
0
H303I24H163K16H190N21
H101G09
H162I09M045L06H160F05
H072A04
M018P14M019I01H323A14H204D01H320D04H198A03H291P19H060J03H009K06H164H08H213A01H134G09H016A12H011A02M014P22
M042B19H0461M08H150M11H210D10
H073P13
H155D20
H064B17H194L19H257H21
LG213
18
28
3738
H303I24
H025N15
H025A22
H155C04H160F05
13
18
28
373846
H303I24
H072A04
H025N15
H025A22
H155C04
H160F05H168N10
37
46
66
72
74.5
H072A04
H059M17
H167J21
H320D04
82
106
H013N18
H134G09
H172G12
6672
H059M17
H167J21H320D04
82
88
106
92
H013N18
H213A01
H016A12
H172G12
77.5
83.5 H009K06
89.3
9496
H011A02M014P22
108112
130140142
H046M08H111M10
H155D20H064B17H257H21
108112
130140142
H046M08H111M10
H155D20H064B17
H257H21H194L19141
120 H073P13114
110.9H210D10H150M11
H134G09
70 M019I01
H291P19
74.5
70 M019I01
H164H08
H204D0173
83.5
89.3
96
Chr.2 CGM.2
H009K06
H291P19
77.5
H213A01H164H08
8888
G1
G2
G3
G4
16 H163K16
M014P22
Selection & Confirmation of “Seed BACs“
Seed BACsSeed BACs BAC extensionBAC extension Finishing Finishing
(on pipeline)(on pipeline)
4040
Seed BAC Sequencing SummarySeed BAC Sequencing Summary
BAC ExtensionBAC ExtensionA B CA B CA B CA B C
Using Pachytene- / Fiber- FISH for Confirmation of Using Pachytene- / Fiber- FISH for Confirmation of Extended BACsExtended BACs
H066C13
H072A04
M045L06 H168N10
M045L06H168N10
M045L06
H168N10
Seed BACsSeed BACs BAC extensionBAC extension Finishing Finishing
(on pipeline)(on pipeline)
4040 4242 7676 (6) (6)
Total reading length : 8.2 Mb(31%)
Summary of BAC ExtensionSummary of BAC ExtensionE057O21LE_HBa0155E05M65K08
LE_HBa0303I24
LE_HBa0163K16
LE_Hba0190N21LE_HBa0025N15 LE_HBa0280E02
LE_HBa0209K17 LE_HBa0025A22 LE_HBa0101G09
LE_HBa320M09
LE_HBa0162I09_sp6LE_HBa0155C04 LE_HBa0168N10 SL_MboI0045L06
SL_MboI0064E19_T7LE_HBa0160F05
M100O21_T7LE_HBA0072A04LE_HBa0066C13
SL_MboI108P14_sp6LE_HBa0059M17 LE_HBa0031A21_T7LE_HBa0161P02 LE_HBa0329G05 SL_MboI0019I01LE_HBa0090O01_sp6
H167J21_T7
LE_HBa0323A14
LE_HBa0204D01
LE_HBa0320D04
M049G16
LE_HBa0198A03
LE_HBa0291P19 SL_EcoRI0033D19_T7
LE_HBa0159F19 LE_HBA0060J03LE_HBa0013N18_SP6 (30kb)
H009K06
H030A21LE_HBa0213A01
LE_HBa0164H08 SL_MboI0097L01_sp6
H134G09
LE_HBa0074A14_T7LE_HBa0023N04_T7BAC19(
LE_HBa0016A12
LE_HBa0011A02
E010H16
SL_MboI0025E22LE_HBa0172G12 SL_MboI0042B19_T7
LE_HBa0046M08
SL_EcoRI0096G02_T7
LE_Hba00108N03
LE_HBa0111M10SL_Mbo0066K03
FW2.2
LE_HBa073P13
LE_HBa0155D20
SL_EcoRI0042D07_T7
LE_HBa0194L19
LE_HBa0072B02SL_ECORI0034H10LE_HBa0064B17 SL_MboI0055O24
LE_HBa0032J10LE_HBa0177F12
LE_HBa0098J01
LE_HBa0257H21
8.2Mb, 76 BACs16 contigs17 Single BAC Sequence
Problem : No more extendible BACs
E057O21LE_HBa0155E05M65K08
LE_HBa0303I24
LE_HBa0163K16
LE_Hba0190N21LE_HBa0025N15 LE_HBa0280E02
LE_HBa0209K17 LE_HBa0025A22 LE_HBa0101G09
LE_HBa320M09
LE_HBa0162I09_sp6LE_HBa0155C04 LE_HBa0168N10 SL_MboI0045L06
SL_MboI0064E19_T7LE_HBa0160F05
M100O21_T7LE_HBA0072A04LE_HBa0066C13
SL_MboI108P14_sp6LE_HBa0059M17 LE_HBa0031A21_T7LE_HBa0161P02 LE_HBa0329G05 SL_MboI0019I01LE_HBa0090O01_sp6
H167J21_T7
LE_HBa0323A14
LE_HBa0204D01
LE_HBa0320D04
M049G16
LE_HBa0198A03
LE_HBa0291P19 SL_EcoRI0033D19_T7
LE_HBa0159F19 LE_HBA0060J03LE_HBa0013N18_SP6 (30kb)
H009K06
H030A21LE_HBa0213A01
LE_HBa0164H08 SL_MboI0097L01_sp6
H134G09
LE_HBa0074A14_T7LE_HBa0023N04_T7BAC19(
LE_HBa0016A12
LE_HBa0011A02
E010H16
SL_MboI0025E22LE_HBa0172G12 SL_MboI0042B19_T7
LE_HBa0046M08
SL_EcoRI0096G02_T7
LE_Hba00108N03
LE_HBa0111M10SL_Mbo0066K03
FW2.2
LE_HBa073P13
LE_HBa0155D20
SL_EcoRI0042D07_T7
LE_HBa0194L19
LE_HBa0072B02SL_ECORI0034H10LE_HBa0064B17 SL_MboI0055O24
LE_HBa0032J10
LE_HBa0177F12
LE_HBa0098J01
LE_HBa0257H21
Only 6 BAC clones (on the sequencing pipeline) Is available for further extension ????
E057O21LE_HBa0155E05M65K08
LE_HBa0303I24
LE_HBa0163K16
LE_Hba0190N21LE_HBa0025N15 LE_HBa0280E02
LE_HBa0209K17 LE_HBa0025A22 LE_HBa0101G09
LE_HBa320M09
LE_HBa0162I09_sp6LE_HBa0155C04 LE_HBa0168N10 SL_MboI0045L06
SL_MboI0064E19_T7LE_HBa0160F05
M100O21_T7LE_HBA0072A04LE_HBa0066C13
SL_MboI108P14_sp6LE_HBa0059M17 LE_HBa0031A21_T7LE_HBa0161P02 LE_HBa0329G05 SL_MboI0019I01LE_HBa0090O01_sp6
H167J21_T7
LE_HBa0323A14
LE_HBa0204D01
LE_HBa0320D04
M049G16
LE_HBa0198A03
LE_HBa0291P19 SL_EcoRI0033D19_T7
LE_HBa0159F19 LE_HBA0060J03LE_HBa0013N18_SP6 (30kb)
H009K06
H030A21LE_HBa0213A01
LE_HBa0164H08 SL_MboI0097L01_sp6
H134G09
LE_HBa0074A14_T7LE_HBa0023N04_T7BAC19(
LE_HBa0016A12
LE_HBa0011A02
E010H16
SL_MboI0025E22LE_HBa0172G12 SL_MboI0042B19_T7
LE_HBa0046M08
SL_EcoRI0096G02_T7
LE_Hba00108N03
LE_HBa0111M10SL_Mbo0066K03
FW2.2
LE_HBa073P13
LE_HBa0155D20
SL_EcoRI0042D07_T7
LE_HBa0194L19
LE_HBa0072B02SL_ECORI0034H10LE_HBa0064B17 SL_MboI0055O24
LE_HBa0032J10LE_HBa0177F12
LE_HBa0098J01
LE_HBa0257H21
7.28 µm = 2.29 Mb20 cM = 2.15 Mb
Problem : Big Gap
Problem : Redundant Sequences
C (34290bp)
B (128329bp)
A (115036bp)
9.1kb25.2kb
AB
C
Require large contig FPC
Waiting for Waiting for UK’s New FPC MapUK’s New FPC Map
Thanks for your attention.
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