1. Tomato Chromosome 2 PAG 2009 Doil Choi, Korea

2. Summary of chromosome 2 sequencing 142 cM 129cM CNR (?) 13.0 40.048.0 78.0100.0120.0 142.0 Markers (cM) T1554 (142.0) cLEC-7-P21 (0) T1616 (1.0) TG276 (14.0) CT140 (16.0)T1706 (18.0)CT213 (24.0) T1668 (37.0) C2_At2g34470 (38.5) cLEC-27-M9 (46.0) ? rcr3 (?) CT103 (63.7) T1438 (70.0)T1395 (72.0)TM34 (73.0) T1537 (74.5) SSR26 (77.5) cLET-1-A5 (79.0) CLER-5-N18 (86.0) T1535 (89.0)TG645R (90.0)U146494 (90.0)TG373 (94.0) CT9 (101.0) T1480 (106.0) d (108.0)T1158 (111.5) f.w.2. 2 (116.0) U214677 (126.5) cTOB-6-13 (140.0) ? 13 cM NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere Contig regions 1234 5/6 7 8/9 10/11 12/13 1617 18/19 20/21 23/24 2025 26272829 30/31 3233 34 35/36 3722 Big GAP 1 14/15 Big GAP 2  Sequencing progress  194 BACs in total (20.7Mb)  183 in phase 3 with ABI 3730  11 In phase 1 with GS FLX  Confirmation  184 BACs mapped on chromosome 2  10 BACs on chromosome 0  Assembly (14.6Mb, 66%)  29 contigs (13.8Mb) - 172 BACs  8 single BAC (754kb) - 44 Hind, 7 Eco, 18 Mbo  37 gaps

3. Marker (cM) BACCandidateOverlap (bp) Marker (cM) BACCandidateOverlap (bp) 16.0 LE_HBa0163K16F183F16-F F269A06-F 33,106 31,574 72.5 LE_HBa0323A14 F119B09-R24,820 18.0 LE_Hba0190N21 F272G05-F F166I01-F 25,146 16,961 72.0 LE_HBa0167J21 F225P01-F31,674 36.9 SL_MboI0045L06 F039M08-R 35,825 SL_MboI0008E03 F207I07-F F198L16-F 19,390 24,270 38.3 LE_HBa0185P07 F250N24-F F183O09-F 14,392 4,377 74.5 LE_HBa0320D04 No Fosmid 44.0 LE_HBa0091J18 F085I24-F F159B09-F F190E10-F 26,789 31,935 30,955 77.0 SL_MboI0020N15 No Fosmid 48.0 LE_HBa0125L12 No Fosmid 78.0 LE_HBa0172H10 F279N10-R9,691 LE_HBa00209I20 F136L07-F17,374 89 (90) LE_HBa0164H08 No Fosmid ? LE_HBa0122E16 F134I04-F24,339 120.0 LE_HBa0073P13 F275H06-F F007D18-F F158G07-R 21,612 955 30,725 SL_EcoRI0005F12 F245M20-F F105L22-R 18,289 28,921 135.0 SL_EcoRI0017H17 F037I11-R20,684 68.0 LE_HBa0090O01 No Fosmid # of Contig end # of Hit < 20kb overlap < 10kb overlap Average overlap 19 147 3(16%) 23kb Contig end (query) - Fosmid End Sequence (subject)

4. Markers (cM)Contig regions Big GAP 1 Big GAP 2 T0888 (13cM) CT205 (13cM) SSR40 (22cM) cLEC-27-E17 (36.7cM) SSR103 (51cM) SSR5 (53cM) T0710 (62cM) cLEF-41-C3 (62cM) SSR50 (70.5cM) T0784 (74cM) cLEG-36-B2 (75.5cM) P18 (87cM) cLEM-23-E21 (89.7cM) cLED-19-B24 (90/100cM) CT106 (99cM) New Marker39 No FES hit34 FES Hit5 Candidate Fosmid 4(10%) C2_At2g34560 (38cM) T1256 (40cM) C2_At1g65720 (45cM) cLPT-1-E8 (47cM) SSR605 (48.5cM) T1665 (49cM) U242666 (49cM) TG14 (54cM) cLEW-17-M24 (55cM) TG139 (57cM) cLEG-29-A13 (63cM) C2_At4g30930 (63.1cM) CT244 (64cM) C2_At1g11430 (70.1cM) U143788 (70.3cM) cLET-3-K13 (72cM) cLEF-50-C16 (72cM) cLEC-7-H4 (87cM) cLES-3-G11 (111cM) TG140 (122cM) cLEZ-17-J15 (124cM) cLER-17-N11 (124cM) TG151 (126cM) cLEX-2-I9 (133cM) 142 cM 129cM 13 cM 1 2 3 4 5/6 7 8/9 10/11 12/13 16 17 18 19 22 23/24 25 26 27 28 29 30/31 32 33 34 35/36 37 20/21 14/15 NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere New markers – FES (Query) (subject)

5. Markers (cM) 142 cM 129cM 13 cM Contig regions Big GAP 2 13cMBACMIX_r3_Contig104380.1 14cMBACMIX_r3_Contig86792.1 16cMBACMIX_r3_Contig185075.1 24cMBACMIX_r3_Contig3426.1 35cMBACMIX_r3_Contig19336.1 36.6cMBACMIX_r3_Contig6903.1 40cMBACMIX_r3_Contig10192.1 40cMBACMIX_r3_Contig6231.1 ?cMBACMIX_r3_Contig5976.1 ?cMBACMIX_r3_Contig13752.1 72cMBACMIX_r3_Contig701.1 73cMBACMIX_r3_Contig49928.1 86cMBACMIX_r3_Contig26801.1 89.3cMBACMIX_r3_Contig3257.1 89.3cMBACMIX_r3_Contig6865.1 94cMBACMIX_r3_Contig57741.1 94cMBACMIX_r3_Contig21461.1 100cMBACMIX_r3_Contig3397.1 111cMBACMIX_r3_Contig17772.1 108cMBACMIX_r3_Contig873.1 Contig ends74 No SBM Hit48 SBM Hit21 Candidate BAC 4 (5%) 1 2 3 4 5/6 7 8/9 10/11 12/13 16 17 18/19 20/21 23/24 20 25 26 27 28 29 30/31 32 33 34 35/36 37 22 Big GAP 1 14/15 NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere Contig ends – SBM (query) (subject)

6. Markers (cM)Contig regions Big GAP 1 Big GAP 2 T0888 (13cM) CT205 (13cM) SSR40 (22cM) cLEC-27-E17 (36.7cM) SSR103 (51cM) SSR5 (53cM) T0710 (62cM) cLEF-41-C3 (62cM) SSR50 (70.5cM) T0784 (74cM) cLEG-36-B2 (75.5cM) P18 (87cM) cLEM-23-E21 (89.7cM) cLED-19-B24 (90/100cM) CT106 (99cM) New Marker39 No SBM hit27 SBM Hit11 Candidate Extension BAC 7(18%) (BAC: 2 / Fosmid:5) C2_At2g34560 (38cM) T1256 (40cM) C2_At1g65720 (45cM) cLPT-1-E8 (47cM) SSR605 (48.5cM) T1665 (49cM) U242666 (49cM) TG14 (54cM) cLEW-17-M24 (55cM) TG139 (57cM) cLEG-29-A13 (63cM) C2_At4g30930 (63.1cM) CT244 (64cM) C2_At1g11430 (70.1cM) U143788 (70.3cM) cLET-3-K13 (72cM) cLEF-50-C16 (72cM) cLEC-7-H4 (87cM) cLES-3-G11 (111cM) TG140 (122cM) cLEZ-17-J15 (124cM) cLER-17-N11 (124cM) TG151 (126cM) cLEX-2-I9 (133cM) 142 cM 129cM 13 cM 1 2 3 4 5/6 7 8/9 10/11 12/13 16 17 18 19 22 23/24 25 26 27 28 29 30/31 32 33 34 35/36 37 20/21 14/15 NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere New markers – SBM (Query) (subject)

7. 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.