Tomato Chromosome 2 PAG 2009 Doil Choi Korea

Tomato Chromosome 2 PAG 2009 Doil Choi, Korea

Summary of chromosome 2 sequencing c. TO ) (14 2. 0 T 15 54 (14 26. 5) 146 77 (1 CT 103 T 14 (63. 7 ) 38 T 13 (70. 0 ) 95 TM (72. 0 ) 34 (73. 0) T 15 37 (74. 5) SSR 26 (77. 5) c. LE T-1 -A 5 (79. 0) CL ER -5 -N 18 T 15 (86. 0) TG 35 (8 645 9. 0) R( 90. 0) ? U 1 46 TG 494 ( 90 373 (94. 0) CT 9( T 14 101. 0) 80 d (1 (106. 0) 08. T 11 0) 58 (11 1. 5 ) f. w. 2. 2 (11 6. 0 ) 0. 0 ) 142 c. M 129 c. M c. LE T 16 C-7 -P 2 16 (1. 0 1 (0) ) TG 2 CT 76 140 (14 T 17 (16. . 00) ) 06 CT (18. 0 213 ) (24. 0) T 16 68 (37. 0) C 2_ At 2 g 34 470 c. LE (38 C-2. 5) 7 M ? 9 (4 6. 0 ) rcr 3 (? ) 13 c. M TEL: telomere -13 CEN: centromere B-6 PH: pericentromeric heterochromatin U 2 NOR: nucleolar organizing region Markers (c. M) 13. 0 40. 0 48. 0 CNR (? ) 78. 0 100. 0 142. 0 120. 0 Contig regions 4 5/6 7 11 13 8/9 10/ 12/ 15 3 14 / 1 2 16 17 19 18/ /21 22 20 4 23/2 20 25 26 27 28 29 /31 32 30 33 34 Big GAP 1 Ø Sequencing progress § 194 BACs in total (20. 7 Mb) § 183 in phase 3 with ABI 3730 § 11 In phase 1 with GS FLX Ø Confirmation § 184 BACs mapped on chromosome 2 § 10 BACs on chromosome 0 6 /3 35 37 Big GAP 2 Ø Assembly (14. 6 Mb, 66%) § 29 contigs (13. 8 Mb) § § - 172 BACs 8 single BAC (754 kb) - 44 Hind, 7 Eco, 18 Mbo 37 gaps

Contig end (query) - Fosmid End Sequence (subject) Marker (c. M) BAC 16. 0 LE_HBa 0163 K 16 Candidate Overlap (bp) 33, 106 31, 574 72. 5 LE_HBa 0323 A 14 F 272 G 05 -F F 166 I 01 -F 25, 146 16, 961 72. 0 LE_HBa 0167 J 21 LE_Hba 0190 N 21 36. 9 SL_Mbo. I 0045 L 06 38. 3 LE_HBa 0185 P 07 44. 0 LE_HBa 0091 J 18 48. 0 LE_HBa 0125 L 12 No Fosmid LE_HBa 00209 I 20 F 136 L 07 -F 17, 374 F 134 I 04 -F 24, 339 SL_Eco. RI 0005 F 12 F 245 M 20 -F F 105 L 22 -R 18, 289 28, 921 LE_HBa 0090 O 01 No Fosmid 68. 0 LE_HBa 0122 E 16 BAC F 183 F 16 -F F 269 A 06 -F 18. 0 ? Marker (c. M) F 039 M 08 -R 14, 392 4, 377 26, 789 31, 935 30, 955 Overlap (bp) F 119 B 09 -R 24, 820 F 225 P 01 -F 31, 674 SL_Mbo. I 0008 E 03 F 207 I 07 -F F 198 L 16 -F 74. 5 LE_HBa 0320 D 04 No Fosmid 77. 0 SL_Mbo. I 0020 N 15 78. 0 LE_HBa 0172 H 10 F 279 N 10 -R 89 (90) LE_HBa 0164 H 08 No Fosmid 120. 0 LE_HBa 0073 P 13 F 275 H 06 -F F 007 D 18 -F F 158 G 07 -R 21, 612 955 30, 725 135. 0 SL_Eco. RI 0017 H 17 F 037 I 11 -R 20, 684 35, 825 F 250 N 24 -F F 183 O 09 -F F 085 I 24 -F F 159 B 09 -F F 190 E 10 -F Candidate 19, 390 24, 270 No Fosmid 9, 691 # of Contig end # of Hit < 20 kb overlap < 10 kb overlap Average overlap 19 14 7 3(16%) 23 kb

Contig regions 1 2 3 4 T 0888 (13 c. M) CT 205 SSR 40 (13 c. M) (22 c. M) c. LEC-27 -E 17 (36. 7 c. M) C 2_At 2 g 34560 (38 c. M) T 1256 (40 c. M) C 2_At 1 g 65720 (45 c. M) c. LPT-1 -E 8 (47 c. M) 5/6 7 13 c. M 8/9 10/11 12/13 14/15 Big GAP 1 16 17 18 19 129 c. M 20/21 22 23/24 25 26 27 28 29 30/31 32 34 35/36 Big GAP 2 37 NOR: nucleolar organizing region SSR 605 (48. 5 c. M) T 1665 (49 c. M) U 242666 (49 c. M) SSR 103 (51 c. M) SSR 5 (53 c. M) TG 14 (54 c. M) c. LEW-17 -M 24 (55 c. M) TG 139 (57 c. M) T 0710 (62 c. M) c. LEF-41 -C 3 (62 c. M) c. LEG-29 -A 13 (63 c. M) C 2_At 4 g 30930 (63. 1 c. M) CT 244 (64 c. M) C 2_At 1 g 11430 (70. 1 c. M) U 143788 (70. 3 c. M) SSR 50 (70. 5 c. M) c. LET-3 -K 13 (72 c. M) c. LEF-50 -C 16 (72 c. M) T 0784 (74 c. M) c. LEG-36 -B 2 (75. 5 c. M) c. LEC-7 -H 4 (87 c. M) P 18 (87 c. M) c. LEM-23 -E 21 (89. 7 c. M) New markers – FES (Query) 39 No FES hit 34 FES Hit 5 Candidate Fosmid c. LES-3 -G 11 (111 c. M) TG 140 (122 c. M) c. LEZ-17 -J 15 (124 c. M) c. LER-17 -N 11 (124 c. M) TG 151 (126 c. M) c. LEX-2 -I 9 (133 c. M) PH: pericentromeric heterochromatin CEN: centromere (subject) New Marker c. LED-19 -B 24 (90/100 c. M) CT 106 (99 c. M) 33 142 c. M Markers (c. M) TEL: telomere 4(10%)

Contig regions 1 2 3 4 5/6 7 13 c. M 8/9 10/11 12/13 14/15 Markers (c. M) 13 c. M 14 c. M 16 c. M 24 c. M 35 c. M BACMIX_r 3_Contig 104380. 1 BACMIX_r 3_Contig 86792. 1 BACMIX_r 3_Contig 185075. 1 BACMIX_r 3_Contig 3426. 1 BACMIX_r 3_Contig 19336. 1 36. 6 c. M BACMIX_r 3_Contig 6903. 1 40 c. M ? c. M BACMIX_r 3_Contig 10192. 1 BACMIX_r 3_Contig 6231. 1 BACMIX_r 3_Contig 5976. 1 BACMIX_r 3_Contig 13752. 1 Big GAP 1 16 17 72 c. M 73 c. M BACMIX_r 3_Contig 701. 1 BACMIX_r 3_Contig 49928. 1 20 25 26 86 c. M BACMIX_r 3_Contig 26801. 1 27 89. 3 c. M BACMIX_r 3_Contig 3257. 1 BACMIX_r 3_Contig 6865. 1 94 c. M BACMIX_r 3_Contig 57741. 1 BACMIX_r 3_Contig 21461. 1 100 c. M BACMIX_r 3_Contig 3397. 1 111 c. M 108 c. M BACMIX_r 3_Contig 17772. 1 BACMIX_r 3_Contig 873. 1 18/19 20/21 129 c. M 22 23/24 28 29 30/31 32 33 34 35/36 142 c. M Big GAP 2 37 NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere Contig ends – SBM (query) (subject) Contig ends 74 No SBM Hit 48 SBM Hit 21 Candidate BAC 4(5%)

Contig regions 1 2 3 4 T 0888 (13 c. M) CT 205 SSR 40 (13 c. M) (22 c. M) c. LEC-27 -E 17 (36. 7 c. M) C 2_At 2 g 34560 (38 c. M) T 1256 (40 c. M) C 2_At 1 g 65720 (45 c. M) c. LPT-1 -E 8 (47 c. M) 5/6 7 13 c. M 8/9 10/11 12/13 14/15 Big GAP 1 16 17 18 19 129 c. M 20/21 22 23/24 25 26 27 28 29 30/31 32 33 34 35/36 142 c. M Big GAP 2 37 NOR: nucleolar organizing region Markers (c. M) SSR 605 (48. 5 c. M) T 1665 (49 c. M) U 242666 (49 c. M) SSR 103 (51 c. M) SSR 5 (53 c. M) TG 14 (54 c. M) c. LEW-17 -M 24 (55 c. M) TG 139 (57 c. M) T 0710 (62 c. M) c. LEF-41 -C 3 (62 c. M) c. LEG-29 -A 13 (63 c. M) C 2_At 4 g 30930 (63. 1 c. M) CT 244 (64 c. M) C 2_At 1 g 11430 (70. 1 c. M) U 143788 (70. 3 c. M) SSR 50 (70. 5 c. M) c. LET-3 -K 13 (72 c. M) c. LEF-50 -C 16 (72 c. M) T 0784 (74 c. M) c. LEG-36 -B 2 (75. 5 c. M) c. LEC-7 -H 4 (87 c. M) P 18 (87 c. M) c. LEM-23 -E 21 (89. 7 c. M) c. LED-19 -B 24 New markers – SBM (Query) New Marker 39 No SBM hit 27 SBM Hit 11 Candidate Extension BAC (90/100 c. M) CT 106 (99 c. M) c. LES-3 -G 11 (111 c. M) TG 140 (122 c. M) c. LEZ-17 -J 15 (124 c. M) c. LER-17 -N 11 (124 c. M) TG 151 (126 c. M) c. LEX-2 -I 9 (133 c. M) PH: pericentromeric heterochromatin CEN: centromere (subject) TEL: telomere 7(18%) (BAC: 2 / Fosmid: 5)

Summary and Plan • Fosmid end sequence (FES) and SBM were examined for finding further BACs. • New 13 fosmid and 6 BAC clones were found. • FES shows better result in contig ends but SBM is better in new markers. • Search synteny region of tomato chromosome 2 from grapevine genome.