Post on 17-Jan-2016
Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano
Maria Luisa Chiusano chiusano@unina.it
Maria Raffaella Ercolanoercolano@unina.it
University “Federico II” of Naples (Unina)
Bioinformatics
Sequencing
Italy: tomato chr. 12 Country Representative: Dr. Giovanni Giuliano
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)
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)
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)
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)
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)
CT211A
TG180
7.4
CT19A 6.4
TG68
14.4
CT79 4.3
5.5CT219 2.2 TG360 0.8 CD6A 1.6 TG283 4.5TG394
13.4
CT287A
6.3
TG28A 1.0CT239B 2.0TG296 2.4CT156
7.2
CT80B
6.1
CT276 5.8
TG473 1.8CD2
12
o
TM14B
#BACs/probe
Overgoprobes
cLPT6E9
T1487
T1481 T0028
T0989
T1211 T1093 T1045
T1078T1622T1451P62SSR44SSR124TG394
T1266
T1676
T1784TG296T0882
T0770
T1504T0800
CD2
Chromosome 12:Euchromatin portion = 11Mb Projected # of BACs 113
Selected BAC
CT211A
TG180
7.4
CT19A 6.4
TG68
14.4
CT79 4.3
5.5CT219 2.2 TG360 0.8 CD6A 1.6 TG283 4.5TG394
13.4
CT287A
6.3
TG28A 1.0CT239B 2.0TG296 2.4CT156
7.2
CT80B
6.1
CT276 5.8
TG473 1.8CD2
12
o
TM14B
#BACs/probe
Overgoprobes
cLPT6E9
T1487
T1481 T0028
T0989
T1211 T1093 T1045
T1078T1622T1451P62SSR44SSR124TG394
T1266
T1676
T1784TG296T0882
T0770
T1504T0800
CD2
Chromosome 12:Euchromatin portion = 11Mb Projected # of BACs 113
Selected BAC
Le Hba 026c13
CT211A
TG180
7.4
CT19A 6.4
TG68
14.4
CT79 4.3
5.5CT219 2.2 TG360 0.8 CD6A 1.6 TG283 4.5TG394
13.4
CT287A
6.3
TG28A 1.0CT239B 2.0TG296 2.4CT156
7.2
CT80B
6.1
CT276 5.8
TG473 1.8CD2
12
o
TM14B
#BACs/probe
Overgoprobes
cLPT6E9 13
T1487 6
T1481 14 T0028 14
T0989 19
T1211 T1093 T1045
T1078T1622T1451P62SSR44SSR124TG394
T1266
T1676
T1784TG296T0882
T0770
T1504T0800
CD2
Chromosome 12:
Five BACs were selected for the short arm
LeHba075c18
LeHba260c13
LeHba 032k07Le Hba163o04
Euchromatin portion = 11Mb Projected # of BACs 113
Selected BAC
Le Hba 026c13
CT211A
TG180
7.4
CT19A 6.4
TG68
14.4
CT79 4.3
5.5CT219 2.2 TG360 0.8 CD6A 1.6 TG283 4.5TG394
13.4
CT287A
6.3
TG28A 1.0CT239B 2.0TG296 2.4CT156
7.2
CT80B
6.1
CT276 5.8
TG473 1.8CD2
12
o
TM14B
#BACs/probe
Overgoprobes
cLPT6E9 13
T1487 6
T1481 14 T0028 14
T0989 19
T1211 T1093 T1045
T1078T1622T1451P62SSR44SSR124TG394
T1266
T1676
T1784TG296T0882
T0770
T1504T0800
CD2
Chromosome 12:
Five BACs were selected for the short arm
Three of these seed BACs were mapped by PCR markers. LeHba075c18
LeHba260c13
LeHba 032k07Le Hba163o04
Euchromatin portion = 11Mb Projected # of BACs 113
Selected BAC
Le Hba 026c13
CT211A
TG180
7.4
CT19A 6.4
TG68
14.4
CT79 4.3
5.5CT219 2.2 TG360 0.8 CD6A 1.6 TG283 4.5TG394
13.4
CT287A
6.3
TG28A 1.0CT239B 2.0TG296 2.4CT156
7.2
CT80B
6.1
CT276 5.8
TG473 1.8CD2
12
o
TM14B
#BACs/probe
Overgoprobes
cLPT6E9 13
T1487 6
T1481 14 T0028 14
T0989 19
T1211 T1093 T1045
T1078T1622T1451P62SSR44SSR124TG394
T1266
T1676
T1784TG296T0882
T0770
T1504T0800
CD2
Chromosome 12:
Five BACs were selected for the short arm
Three of these seed BACs were mapped by PCR markers. LeHba075c18
LeHba260c13
LeHba 032k07Le Hba163o04
Euchromatin portion = 11Mb Projected # of BACs 113
Selected BAC
Seed BACs from the long arm are under selection
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.
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.
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.
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
Status reported in Wageningen
September 2004
Evaluating External Sequencing Services
Chromatogram (.abi,.scf)
Phred scores (fasta)
Raw sequence (fasta)
LocalBioinformatic Center
BioinformaticAnalyses(setup
According to the SOL-pipeline)
Structural characterization
Annotation by prediction
Conflicts resolution and manual curation
Project specific analysis:Comparative genomics and PhylogeneticsIdentification and characterization of gene of specific interestIdentification of Molecular MarkersSNPs Microarray design……..
Re-sequencingAnnotation by similarity
BAC selection
Wageningen September 2004
Naples group
Evaluating External Sequencing Services
Chromatogram (.abi,.scf)
Phred scores (fasta)
Raw sequence (fasta)
LocalBioinformatic Center
BioinformaticAnalyses
(setupAccording to the
SOL-pipeline)
Structural characterization
Conflicts resolution and manual curation
Project specific analysis:Comparative genomics and PhylogeneticsIdentification and characterization of gene of specific interestIdentification of Molecular MarkersSNPs Microarray design……..
Re-sequencing
BAC selection
Wageningen September 2004
Naples group
Annotation by prediction
Annotation by similarity
Actual Status
San Diego January 2005
Evaluating External Sequencing Services
Chromatogram (.abi,.scf)
Phred scores (fasta)
Raw sequence (fasta)
LocalBioinformatic Center
BioinformaticAnalyses
(setupAccording to the
SOL-pipeline)
Structural characterization
Conflicts resolution and manual curation
Project specific analysis:Comparative genomics and PhylogeneticsIdentification and characterization of gene of specific interestIdentification of Molecular MarkersSNPs Microarray design……..
Re-sequencing
5 BACs (ready by February 2005)BAC selection
San Diego January 2005
70 BACs (in 12 months)
CRIBISequencing Service
Naples
Annotation by prediction
Annotation by similarity
Chromatogram (.abi,.scf)
Phred scores (fasta)
Raw sequence (fasta)
LocalBioinformatic Center
BioinformaticAnalyses
(setupAccording to the
SOL-pipeline)
Structural characterization
Conflicts resolution and manual curation
Project specific analysis:Comparative genomics and PhylogeneticsIdentification and characterization of gene of specific interestIdentification of Molecular MarkersSNPs Microarray design……..
Re-sequencing
5 BACs (ready by February 2005)BAC selection
70 BACs (in 12 months)
CRIBISequencing Service
EneaSequencing Service
Naples
San Diego January 2005
Annotation by prediction
Annotation by similarity
Chromatogram (.abi,.scf)
Phred scores (fasta)
Raw sequence (fasta)
LocalBioinformatic Center
BioinformaticAnalyses
(setupAccording to the
SOL-pipeline)
Structural characterization
Conflicts resolution and manual curation
Project specific analysis:Comparative genomics and PhylogeneticsIdentification and characterization of gene of specific interestIdentification of Molecular MarkersSNPs Microarray design……..
Re-sequencing
5 BACs (ready by February 2005)BAC selection
70 BACs (in 12 months)
CRIBISequencing Service
EneaSequencing Service
will be available atftp://agronanotech.unina.it/
San Diego January 2005
Annotation by prediction
Annotation by similarity
Thanks!