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Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata

Tomato Sequencing Project Meeting at SOL 2008, Oct. 15, 2008. Status of tomato genome sequence in Japan: chromosome 8 sequencing and selected BAC mixture sequencing. Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata. 92 165 1.8. 79 143 1.8. 67 171 2.6.

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Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata

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  1. Tomato Sequencing Project Meeting at SOL 2008, Oct. 15, 2008 Status of tomato genome sequence in Japan: chromosome 8 sequencing and selected BAC mixture sequencing Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata

  2. 92 165 1.8 79 143 1.8 67 171 2.6 62 137 2.2 40 119 3.0 63 101 1.6 51 112 2.2 33 87 2.6 40 116 2.9 41 87 2.1 43 103 2.4 39 120 3.1 # anchors cM chr length cM per anchor Distribution of Anchor Markers on Chromosomes Initial seeds on Chr.8

  3. Summary of EST-SSR Marker analysis 712 markers have been mapped on EXPEN2000 chr1 78 chr7 56 chr2 66 chr8 62 chr3 74 chr9 52 chr4 60 chr10 49 chr5 62 chr11 50 chr6 52 chr12 51 34 new seed clones have been selected

  4. Status of Chr.8 Sequencing (86% of initial target) (106% of initial target) Finished length without overlap:14,906,592 bp 67 seed points (34 contigs, 11 single clones)

  5. Gap Filling by Whole Genome Shotgun Sequencing • Selected BAC Mixture (SBM) shotgun • Select BACs whose end sequences do not contain undesired (repeat) sequences • Mix the BACs and sequence by shotgun BAC Gene space Repeat

  6. BLASTN BES vs. RepeatDB 402,012 end sequences from 177,408 BAC clones vs. 14,229 repeat sequences (TIGR_SolAth_repeat, mips_repeat_collection, SGN repeat collection) Source of the 1st BAC mixture

  7. Selected BAC Mixture (SBM) shotgun sequencing <1st set> 10,000 clones from HBa library 5,000 clones from EcoRI library 5,000 clones from MboI library 20,000 BAC clones A total of 2.9 million sequences were accumulated by August. (total length is ~1.7 Gbp)

  8. BLASTN BES vs. RepeatDB 402,012 end sequences from 177,408 BAC clones vs. 14,229 repeat sequences (TIGR_SolAth_repeat, mips_repeat_collection, SGN repeat collection) Source of the 2nd BAC mixture Source of the 1st BAC mixture

  9. Selected BAC Mixture (SBM) shotgun sequencing <2nd set> 5,400 clones from HBa library 2,700 clones from EcoRI library 2,700 clones from MboI library 10,800 BAC clones Sequencing has started in September 2008.

  10. Status of SBM Shotgun Sequences ・As of Oct. 2008, 3.0 million sequences has been accumulated. (total length is 1.9 Gbp) 3rd Assemble ・Assembled into 205,091 contigs. Total size of the contigs is ~ 580 Mbp. longest contig: 127,384 bp(17,702bp in 2nd Assemble) > 5kb contigs: 24,774(21,230 in 2nd Assemble)

  11. 74% SBM + Finished BAC (34,546 hits) Status of SBM Shotgun Assembly EST coverage :Tomato Gene Index (46,849 unigenes) 71% SBM (33,089 hits)

  12. Blast DB of the SBM contigs > We are pleased to provide the blast DB of the SBM contigs to other groups of tomato genome sequence project for the purpose of contig extension. http://plant1.kazusa.or.jp/TBAC/blast.html user name: SOLseq password: ConExDB0804 > Please contact Shusei Sato (ssato@kazusa.or.jp) for the sequence information on the matched contigs.

  13. National Institute of Vegetable and Tea Science Dept. Plant Genome Research Satoshi Tabata Erika Asamizu Shusei Sato Molecular Genetics and Physiology team Sequencing Marker Hiroyuki Fukuoka Satomi Negoro Yumika Kitamura Takakazu Kaneko Akiko Watanabe Akiko Ono Naomi Nakazaki Midori Kato Kumiko Kawashima Yoshimi Shimizu Chiharu Minami Chika Takahashi Shigemi Sasamoto Tsuyuko Wada Ai Matsuno

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