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Towards an Integrated Physical Map of the Tomato Genome

Towards an Integrated Physical Map of the Tomato Genome. Mingsheng Chen Institute of Genetics and Developmental Biology Chinese Academy of Sciences January 13, 2008. Reassemble the fingerprint data of HindIII and MboI libraries generated by Arizona Genomics Institute and Sanger

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Towards an Integrated Physical Map of the Tomato Genome

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  1. Towards an Integrated Physical Map of the Tomato Genome Mingsheng Chen Institute of Genetics and Developmental Biology Chinese Academy of Sciences January 13, 2008

  2. Reassemble the fingerprint data of HindIII and MboI libraries generated by Arizona Genomics Institute and Sanger • Manual editing and contig merging • Marker data generation: 3D pool • FSD: Fingerprint Simulated Digest • Anchored contig information • WebFPC

  3. FPC build • Reassemble the fingerprint data of HindIII and MboI libraries • Cutoff value of e-12 tolerance 7 • Clone total 132,541 • Total contigs 4360 (Compare > 7000 of HindIII FPC build) • Genome coverage 658 Mb (avearge band size 4096 bp)

  4. Manual Editing • Contig merging by BAC end searching combined with marker information • 4156 contigs (we only merged the contigs with anchoring information) • 837 markers (781 framework)

  5. Marker • Overgo marker (provided by Ying Eileen Wang) • PCR-based approach: 3-D pool

  6. The pooling strategy for the tomato HindIII BAC library

  7. 985 markers • 245 markers of chr 1/5/12 (Chen) • 249 markers of chr 3/7/9 (Li) • 247 markers of chr 4/6/10 (Ling) • 244 markers of chr 2/8/11 (Wang)

  8. Example

  9. C2_At1g09760-group1 C2_At1g09760-group2 C2_At1g09760-group4 C2_At1g09760-group3 1-B6; 1-E6; 1-F5; 1-G12 5-B1; 5-E6; 5-G2 C2_At1g09760-group5 Control

  10. Fingerprint Simulated Digest (FSD) • Compare the position of the original BAC clone with sd clone; check the integrity of the physical map • Identify additional clones for sequencing • 531 sd clones

  11. 145kb 26kb 80% 107kb

  12. Anchored Contigs • Chr01 36 ctgs 10 Mb • Chr02 29 ctgs 6.8 Mb • Chr03 29 ctgs 10 Mb • Chr04 26 ctgs 9 Mb • Chr 05 24 ctgs 7 Mb • Chr06 29 ctgs 8.4 Mb

  13. Anchored Contigs • Chr07 36 ctgs 9.2 Mb • Chr08 38 ctgs 10.2 Mb • Chr09 27 ctgs 7.5 Mb • Chr10 11 ctgs 4.7 Mb • Chr11 14 ctgs 4.6 Mb • Chr12 19 ctgs 6.6Mb Total Coverage 187 Mb

  14. WebFPC http://tomato.genetics.ac.cn/

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