Diapositiva 1

1
Italy tomato chr. 12 Country
Representative Dr. Giovanni Giuliano
Maria Luisa Chiusano chiusano_at_unina.it Maria
Raffaella Ercolano ercolano_at_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
Euchromatin portion 11Mb Projected of BACs
113
Chromosome 12
BACs/ probe
Overgo probes
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
Euchromatin portion 11Mb Projected of BACs
113
Chromosome 12
BACs/ probe
Overgo probes
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
Euchromatin portion 11Mb Projected of BACs
113
Chromosome 12
BACs/ probe
Overgo probes
Selected BAC
12
TM14B
TG180
Five BACs were selected for the short arm
7.4
cLPT6E9
Le Hba 026c13
13
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
Euchromatin portion 11Mb Projected of BACs
113
Chromosome 12
BACs/ probe
Overgo probes
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
Le Hba 026c13
13
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
Euchromatin portion 11Mb Projected of BACs
113
Chromosome 12
BACs/ probe
Overgo probes
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
Le Hba 026c13
13
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 Jongs 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 Jongs 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)
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 ..
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)
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 ..
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)
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 ..
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)
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 ..
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)
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 ..
will be available at ftp//agronanotech.unina.it/
San Diego January 2005
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Thanks!