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Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Maria Luisa Chiusano Maria Raffaella Ercolano University.

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Presentation on theme: "Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano Maria Luisa Chiusano Maria Raffaella Ercolano University."— Presentation transcript:

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

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

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

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

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

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 Evaluating External Sequencing Services Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Bioinformatic Analyses (setup According to the SOL-pipeline) Structural characterization Annotation by prediction Conflicts resolution 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 …….. Re-sequencing Annotation by similarity BAC selection Wageningen September 2004 Naples group

19 Evaluating External Sequencing Services Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Bioinformatic Analyses (setup According to the SOL-pipeline) Structural characterization Conflicts resolution 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 …….. Re-sequencing BAC selection Wageningen September 2004 Naples group Annotation by prediction Annotation by similarity

20 Actual Status San Diego January 2005

21 Evaluating External Sequencing Services Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Bioinformatic Analyses (setup According to the SOL-pipeline) Structural characterization Conflicts resolution 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 …….. Re-sequencing 5 BACs (ready by February 2005) BAC selection San Diego January 2005 70 BACs (in 12 months) CRIBI Sequencing Service Naples Annotation by prediction Annotation by similarity

22 Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Bioinformatic Analyses (setup According to the SOL-pipeline) Structural characterization Conflicts resolution 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 …….. Re-sequencing 5 BACs (ready by February 2005) BAC selection 70 BACs (in 12 months) CRIBI Sequencing Service Enea Sequencing Service Naples San Diego January 2005 Annotation by prediction Annotation by similarity

23 Chromatogram (.abi,.scf) Phred scores (fasta) Raw sequence (fasta) Local Bioinformatic Center Bioinformatic Analyses (setup According to the SOL-pipeline) Structural characterization Conflicts resolution 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 …….. Re-sequencing 5 BACs (ready by February 2005) BAC selection 70 BACs (in 12 months) CRIBI Sequencing Service Enea Sequencing Service will be available at ftp://agronanotech.unina.it/ San Diego January 2005 Annotation by prediction Annotation by similarity

24

25

26 Thanks!

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