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

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

Maria Luisa Chiusano [email protected]

Maria Raffaella [email protected]

University “Federico II” of Naples (Unina)

Bioinformatics

Sequencing

mailto:[email protected]

mailto:[email protected]


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)





Actual fundings:

Agronanotech project (Unina): 560.000 euro

ENEA






Actual fundings:

Agronanotech project (Unina): 560,000 euro

ENEA


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:


Three of these seed BACs were mapped by PCR markers. LeHba075c18

LeHba260c13



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:


Three of these seed BACs were mapped by PCR markers. LeHba075c18

LeHba260c13



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



Mapping confirmation of the other two Bacs is in progress.

Sequencing work




After a training in Hans de Jong’s laboratory a FISH mapping effort was initiated.

Sequencing work




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






BioinformaticAnalyses

(setupAccording to the

SOL-pipeline)




Re-sequencing

BAC selection

Wageningen September 2004

Naples group


Annotation by similarity

Actual Status

San Diego January 2005








SOL-pipeline)




Re-sequencing

5 BACs (ready by February 2005)BAC selection


70 BACs (in 12 months)

CRIBISequencing Service

Naples









SOL-pipeline)




Re-sequencing




EneaSequencing Service

Naples










SOL-pipeline)




Re-sequencing




EneaSequencing Service

will be available atftp://agronanotech.unina.it/




Thanks!

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

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