Current Sequencing Status of Tomato Chromosome 2 PLANT GENOME RESEARCH CENTER, KRIBB, KOREA...

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_HBa320M09





H167J21_T7

LE_HBa0323A14

LE_HBa0204D01

LE_HBa0320D04

M049G16

LE_HBa0198A03



H009K06



H134G09


LE_HBa0016A12

LE_HBa0011A02

E010H16


LE_HBa0046M08

SL_EcoRI0096G02_T7

LE_Hba00108N03


FW2.2

LE_HBa073P13

LE_HBa0155D20

SL_EcoRI0042D07_T7

LE_HBa0194L19


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_HBa320M09





H167J21_T7

LE_HBa0323A14

LE_HBa0204D01

LE_HBa0320D04

M049G16

LE_HBa0198A03



H009K06



H134G09


LE_HBa0016A12

LE_HBa0011A02

E010H16


LE_HBa0046M08

SL_EcoRI0096G02_T7

LE_Hba00108N03


FW2.2

LE_HBa073P13

LE_HBa0155D20

SL_EcoRI0042D07_T7

LE_HBa0194L19


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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Current Sequencing Status of Tomato Chromosome 2 PLANT GENOME RESEARCH CENTER, KRIBB, KOREA...

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