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Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano

Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano. Maria Luisa Chiusano chiusano@unina.it Maria Raffaella Ercolano ercolano@unina.it University “Federico II” of Naples (Unina). Bioinformatics. Sequencing. Italy: tomato chr. 12

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Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano

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  1. Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Maria Luisa Chiusano chiusano@unina.it Maria Raffaella Ercolano ercolano@unina.it University “Federico II” of Naples (Unina) Bioinformatics Sequencing

  2. Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano

  3. Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Two groups: Principal Investigators: Prof. Luigi Frusciante(Unina) Naples Dr. Giovanni Giuliano (ENEA) Rome Actual fundings: Agronanotech project (Unina): 560,000 euro ENEA External Collaborators: Dr. Silvana Grandillo (IGV-CNR) Prof. Giorgio Valle (CRIBI UniPa)

  4. Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Two groups: Principal Investigators: Prof. Luigi Frusciante(Unina) Naples Dr. Giovanni Giuliano(ENEA) Rome Actual fundings: Agronanotech project (Unina): 560,000 euro ENEA External Collaborators: Dr. Silvana Grandillo (IGV-CNR) Prof. Giorgio Valle (CRIBI UniPa)

  5. Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Two groups: Principal Investigators: Prof. Luigi Frusciante(Unina) Naples Dr. Giovanni Giuliano(ENEA) Rome Actual fundings: Agronanotech project (Unina):560.000 euro ENEA External Collaborators: Dr. Silvana Grandillo (IGV-CNR) Prof. Giorgio Valle (CRIBI UniPa)

  6. Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Two groups: Principal Investigators: Prof. Luigi Frusciante(Unina) Naples Dr. Giovanni Giuliano(ENEA) Rome Actual fundings: Agronanotech project (Unina):560,000 euro ENEA External Collaborators: Dr. Silvana Grandillo (IGV-CNR) Prof. Giorgio Valle (CRIBI UniPa)

  7. Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Two groups: Principal Investigators: Prof. Luigi Frusciante(Unina) Naples Dr. Giovanni Giuliano(ENEA) Rome Actual fundings: Agronanotech project (Unina):560,000 euro ENEA External Collaborators: Dr. Silvana Grandillo(IGV-CNR) Prof. Giorgio Valle(CRIBI UniPa)

  8. o Euchromatin portion = 11Mb Projected # of BACs 113 Chromosome 12: Overgo probes #BACs/ probe Selected BAC 12 TM14B TG180 7.4 cLPT6E9 CT19A 6.4 TG68 T1487 14.4 T1481 T0028 CT79 T0989 4.3 CT211A 5.5 CT219 2.2 TG360 0.8 T1211 CD6A 1.6 T1093 TG283 4.5 T1045 TG394 T1078 T1622 13.4 T1451 P62 SSR44 CT287A SSR124 6.3 TG394 TG28A 1.0 T1266 CT239B 2.0 TG296 2.4 CT156 T1676 7.2 T1784 CT80B TG296 6.1 T0882 CT276 T0770 5.8 T1504 TG473 1.8 T0800 CD2 CD2

  9. o Euchromatin portion = 11Mb Projected # of BACs 113 Chromosome 12: Overgo probes #BACs/ probe Selected BAC 12 TM14B TG180 7.4 cLPT6E9 CT19A 6.4 TG68 T1487 14.4 T1481 T0028 CT79 T0989 4.3 CT211A 5.5 CT219 2.2 TG360 0.8 T1211 CD6A 1.6 T1093 TG283 4.5 T1045 TG394 T1078 T1622 13.4 T1451 P62 SSR44 CT287A SSR124 6.3 TG394 TG28A 1.0 T1266 CT239B 2.0 TG296 2.4 CT156 T1676 7.2 T1784 CT80B TG296 6.1 T0882 CT276 T0770 5.8 T1504 TG473 1.8 T0800 CD2 CD2

  10. o Euchromatin portion = 11Mb Projected # of BACs 113 Chromosome 12: Overgo probes #BACs/ probe Selected BAC 12 TM14B TG180 Five BACs were selected for the short arm 7.4 cLPT6E9 13 Le Hba 026c13 CT19A 6.4 TG68 LeHba260c13 T1487 6 LeHba075c18 14.4 14 T1481 T0028 14 Le Hba163o04 CT79 T0989 19 LeHba 032k07 4.3 CT211A 5.5 CT219 2.2 TG360 0.8 T1211 CD6A 1.6 T1093 TG283 4.5 T1045 TG394 T1078 T1622 13.4 T1451 P62 SSR44 CT287A SSR124 6.3 TG394 TG28A 1.0 T1266 CT239B 2.0 TG296 2.4 CT156 T1676 7.2 T1784 CT80B TG296 6.1 T0882 CT276 T0770 5.8 T1504 TG473 1.8 T0800 CD2 CD2

  11. o Euchromatin portion = 11Mb Projected # of BACs 113 Chromosome 12: Overgo probes #BACs/ probe Selected BAC 12 TM14B TG180 Five BACs were selected for the short arm Three of these seed BACs were mapped by PCR markers. 7.4 cLPT6E9 13 Le Hba 026c13 CT19A 6.4 TG68 LeHba260c13 T1487 6 LeHba075c18 14.4 14 T1481 T0028 14 Le Hba163o04 CT79 T0989 19 LeHba 032k07 4.3 CT211A 5.5 CT219 2.2 TG360 0.8 T1211 CD6A 1.6 T1093 TG283 4.5 T1045 TG394 T1078 T1622 13.4 T1451 P62 SSR44 CT287A SSR124 6.3 TG394 TG28A 1.0 T1266 CT239B 2.0 TG296 2.4 CT156 T1676 7.2 T1784 CT80B TG296 6.1 T0882 CT276 T0770 5.8 T1504 TG473 1.8 T0800 CD2 CD2

  12. o Euchromatin portion = 11Mb Projected # of BACs 113 Chromosome 12: Overgo probes #BACs/ probe Selected BAC 12 TM14B TG180 Five BACs were selected for the short arm Three of these seed BACs were mapped by PCR markers. 7.4 cLPT6E9 13 Le Hba 026c13 CT19A 6.4 TG68 LeHba260c13 T1487 6 LeHba075c18 14.4 14 T1481 T0028 14 Le Hba163o04 CT79 T0989 19 LeHba 032k07 4.3 CT211A 5.5 CT219 2.2 TG360 0.8 T1211 CD6A 1.6 T1093 TG283 4.5 T1045 TG394 T1078 T1622 13.4 T1451 P62 Seed BACs from the long arm are under selection SSR44 CT287A SSR124 6.3 TG394 TG28A 1.0 T1266 CT239B 2.0 TG296 2.4 CT156 T1676 7.2 T1784 CT80B TG296 6.1 T0882 CT276 T0770 5.8 T1504 TG473 1.8 T0800 CD2 CD2

  13. Sequencing work Actual status since the last meeting: Sequencing has began: three BACs located on short arm of chr. 12 are currently in the sequencing pipeline.

  14. Sequencing work Actual status since the last meeting: Sequencing has began: three BACs located on short arm of chr. 12 are currently in the sequencing pipeline. Mapping confirmation of the other two Bacs is in progress.

  15. Sequencing work Actual status since the last meeting: Sequencing has began: three BACs located on short arm of chr. 12 are currently in the sequencing pipeline. Mapping confirmation of the other two Bacs is in progress. After a training in Hans de Jong’s laboratory a FISH mapping effort was initiated.

  16. Sequencing work Actual status since the last meeting: Sequencing has began: three BACs located on short arm of chr. 12 are currently in the sequencing pipeline. Mapping confirmation of the other two Bacs is in progress. After a training in Hans de Jong’s laboratory a FISH mapping effort was initiated. • Bioinformatics Pipeline under construction and testing

  17. Status reported in Wageningen September 2004

  18. Naples group BAC selection Evaluating External Sequencing Services Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Structural characterization Re-sequencing Annotation by similarity Annotation by prediction Bioinformatic Analyses (setup According to the SOL-pipeline) Conflictsresolution and manual curation Project specific analysis: Comparative genomics and Phylogenetics Identification and characterization of gene of specific interest Identification of Molecular Markers SNPs Microarray design …….. Wageningen September 2004

  19. Naples group BAC selection Evaluating External Sequencing Services Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Structural characterization Re-sequencing Annotation by similarity Annotation by prediction Bioinformatic Analyses (setup According to the SOL-pipeline) Conflictsresolution and manual curation Project specific analysis: Comparative genomics and Phylogenetics Identification and characterization of gene of specific interest Identification of Molecular Markers SNPs Microarray design …….. Wageningen September 2004

  20. Actual Status San Diego January 2005

  21. 70 BACs (in 12 months) Naples 5 BACs (ready by February 2005) BAC selection CRIBI Sequencing Service Evaluating External Sequencing Services Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Structural characterization Re-sequencing Annotation by similarity Annotation by prediction Bioinformatic Analyses (setup According to the SOL-pipeline) Conflictsresolution and manual curation Project specific analysis: Comparative genomics and Phylogenetics Identification and characterization of gene of specific interest Identification of Molecular Markers SNPs Microarray design …….. San Diego January 2005

  22. 70 BACs (in 12 months) Naples 5 BACs (ready by February 2005) BAC selection CRIBI Sequencing Service Enea Sequencing Service Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Structural characterization Re-sequencing Annotation by similarity Annotation by prediction Bioinformatic Analyses (setup According to the SOL-pipeline) Conflictsresolution and manual curation Project specific analysis: Comparative genomics and Phylogenetics Identification and characterization of gene of specific interest Identification of Molecular Markers SNPs Microarray design …….. San Diego January 2005

  23. 70 BACs (in 12 months) 5 BACs (ready by February 2005) BAC selection CRIBI Sequencing Service Enea Sequencing Service Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Structural characterization Re-sequencing Annotation by similarity Annotation by prediction Bioinformatic Analyses (setup According to the SOL-pipeline) Conflictsresolution and manual curation Project specific analysis: Comparative genomics and Phylogenetics Identification and characterization of gene of specific interest Identification of Molecular Markers SNPs Microarray design …….. will be available at ftp://agronanotech.unina.it/ San Diego January 2005

  24. Thanks!

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