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Tomato Chromosome 2

Tomato Chromosome 2. PAG 2009 Doil Choi, Korea. Summary of chromosome 2 sequencing. NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere. 142 cM. 13 cM. 129cM. C2_At2g34470 (38.5). CLER-5-N18 (86.0).

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Tomato Chromosome 2

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  1. Tomato Chromosome 2 PAG 2009 Doil Choi, Korea

  2. Summary of chromosome 2 sequencing NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere 142 cM 13 cM 129cM C2_At2g34470 (38.5) CLER-5-N18 (86.0) U214677 (126.5) T1554 (142.0) cLET-1-A5 (79.0) cLEC-27-M9 (46.0) cLEC-7-P21 (0) CT103 (63.7) cTOB-6-13 (140.0) T1438 (70.0) T1395 (72.0) TM34 (73.0) T1535 (89.0) TG645R (90.0) U146494 (90.0) TG373 (94.0) f.w.2. 2 (116.0) T1537 (74.5) ? CT140 (16.0) T1706 (18.0) CT213 (24.0) SSR26 (77.5) T1480 (106.0) TG276 (14.0) T1668 (37.0) CT9 (101.0) d (108.0) T1158 (111.5) rcr3 (?) ? T1616 (1.0) Markers (cM) 13.0 40.0 48.0 CNR (?) 142.0 78.0 100.0 120.0 Contig regions 18/19 5/6 23/24 8/9 20/21 35/36 10/11 12/13 14/15 30/31 1 2 3 4 7 16 17 22 20 25 26 27 28 29 32 33 34 37 Big GAP 1 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 • Assembly (14.6Mb, 66%) • 29 contigs (13.8Mb) • - 172 BACs • 8 single BAC (754kb) • - 44 Hind, 7 Eco, 18 Mbo • 37 gaps • Confirmation • 184 BACs mapped on chromosome 2 • 10 BACs on chromosome 0

  3. Contig end (query) - Fosmid End Sequence (subject)

  4. Contig regions Markers (cM) 1 2 T0888 (13cM) 3 CT205 (13cM) 4 SSR40 (22cM) cLEC-27-E17 (36.7cM) NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere 5/6 New markers – FES (Query) (subject) C2_At2g34560 (38cM) T1256 (40cM) 7 C2_At1g65720 (45cM) 13 cM cLPT-1-E8 (47cM) 8/9 SSR605 (48.5cM) 10/11 T1665 (49cM) 12/13 U242666 (49cM) 14/15 SSR103 (51cM) Big GAP 1 SSR5 (53cM) 16 TG14 (54cM) 17 cLEW-17-M24 (55cM) TG139 (57cM) 18 T0710 (62cM) 19 cLEF-41-C3 (62cM) cLEG-29-A13 (63cM) 129cM 20/21 C2_At4g30930 (63.1cM) 22 CT244 (64cM) C2_At1g11430 (70.1cM) 23/24 U143788 (70.3cM) 25 SSR50 (70.5cM) 26 cLET-3-K13 (72cM) cLEF-50-C16 (72cM) 27 T0784 (74cM) 28 cLEG-36-B2 (75.5cM) 29 cLEC-7-H4 (87cM) P18 (87cM) 30/31 cLEM-23-E21 (89.7cM) 32 cLED-19-B24 (90/100cM) 33 CT106 (99cM) 34 cLES-3-G11 (111cM) TG140 (122cM) 35/36 cLEZ-17-J15 (124cM) 142 cM Big GAP 2 cLER-17-N11 (124cM) TG151 (126cM) cLEX-2-I9 (133cM) 37

  5. Contig regions Markers (cM) 1 2 13cM BACMIX_r3_Contig104380.1 3 14cM BACMIX_r3_Contig86792.1 4 16cM BACMIX_r3_Contig185075.1 NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere 24cM BACMIX_r3_Contig3426.1 5/6 Contig ends – SBM (query) (subject) 35cM BACMIX_r3_Contig19336.1 7 36.6cM BACMIX_r3_Contig6903.1 13 cM 8/9 40cM BACMIX_r3_Contig10192.1 40cM BACMIX_r3_Contig6231.1 10/11 ?cM BACMIX_r3_Contig5976.1 12/13 ?cM BACMIX_r3_Contig13752.1 14/15 Big GAP 1 16 17 72cM BACMIX_r3_Contig701.1 18/19 73cM BACMIX_r3_Contig49928.1 20/21 129cM 22 23/24 20 86cM BACMIX_r3_Contig26801.1 25 26 89.3cM BACMIX_r3_Contig3257.1 27 89.3cM BACMIX_r3_Contig6865.1 28 29 94cM BACMIX_r3_Contig57741.1 94cM BACMIX_r3_Contig21461.1 30/31 100cM BACMIX_r3_Contig3397.1 32 33 111cM BACMIX_r3_Contig17772.1 108cM BACMIX_r3_Contig873.1 34 35/36 142 cM Big GAP 2 37

  6. Contig regions Markers (cM) 1 2 T0888 (13cM) 3 CT205 (13cM) 4 SSR40 (22cM) cLEC-27-E17 (36.7cM) NOR: nucleolar organizing region PH: pericentromeric heterochromatin CEN: centromere TEL: telomere 5/6 New markers – SBM (Query) (subject) C2_At2g34560 (38cM) T1256 (40cM) 7 C2_At1g65720 (45cM) 13 cM cLPT-1-E8 (47cM) 8/9 SSR605 (48.5cM) 10/11 T1665 (49cM) 12/13 U242666 (49cM) 14/15 SSR103 (51cM) Big GAP 1 SSR5 (53cM) 16 TG14 (54cM) 17 cLEW-17-M24 (55cM) TG139 (57cM) 18 T0710 (62cM) 19 cLEF-41-C3 (62cM) cLEG-29-A13 (63cM) 129cM 20/21 C2_At4g30930 (63.1cM) 22 CT244 (64cM) C2_At1g11430 (70.1cM) 23/24 U143788 (70.3cM) 25 SSR50 (70.5cM) 26 cLET-3-K13 (72cM) cLEF-50-C16 (72cM) 27 T0784 (74cM) 28 cLEG-36-B2 (75.5cM) 29 cLEC-7-H4 (87cM) P18 (87cM) 30/31 cLEM-23-E21 (89.7cM) 32 cLED-19-B24 (90/100cM) 33 CT106 (99cM) 34 cLES-3-G11 (111cM) TG140 (122cM) 35/36 cLEZ-17-J15 (124cM) 142 cM Big GAP 2 cLER-17-N11 (124cM) TG151 (126cM) cLEX-2-I9 (133cM) 37

  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.

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