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Progress in the sequencing of tomato chromosome 12. (See also poster number 39). The project is funded by the Italian Government (FIRB and Agronanotech projects) and by the European Union (EU-SOL project). Three main units are involved: ENEA, Rome (Prof. Giuliano)

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Presentation Transcript
slide1

Progress in the sequencing of tomato chromosome 12

(See also poster number 39)

The project is funded by the Italian Government (FIRB and Agronanotech projects) and by the European Union (EU-SOL project).

Three main units are involved:

ENEA, Rome (Prof. Giuliano)

University of Naples (Prof. Frusciante)

University of Padua (Prof. Valle)

PAG 2008, San Diego

slide2

Two sequencing pipelines are presently active, one at the University of Padua

and one at a private company.

To better organize and easily control all the information regarding the growing

number of BAC clones in processing, an SQL database has been generated.

PAG 2008, San Diego

slide3

Currently 67 BACs (around 60% of the projected gene-rich region) have been identified and are already placed at different stages of the two active sequencing pipelines.

PAG 2008, San Diego

slide4

For 15 seed BACs at least 1 round of extension has been performed and, thus,

small contigs consisting of overlapping BACs start to emerge.

Bioinformatics tools and molecular data are combined to choose suitable

overlapping clones for the sequencing walk. Good extension candidate BACsare selected using the software PABS-Select, which is complementary to the

SGN Online BLAST Interface.

(PABS is accessible at http://tomato.cribi.unipd.it)

PAG 2008, San Diego

slide5

Following selection based on bioinformatics analysis, and using the IL mapping strategy, chromosome location of the selected extending BACs is experimentally confirmed.

PAG 2008, San Diego

slide6

?What about these (and the other) sequenced BACs?

% coding DNA

Gene prediction by means of the platform already created for grapewine genome

PAG 2008, San Diego

slide7

Acknowledgments

ENEA - Rome

Giovanni Giuliano

Elio Fantini

Giulia Falcone

Marco Pietrella

CNR-IGV, Portici (Naples)

Silvana Grandillo

CRIBI & Univ. of Padua

Giorgio Valle

Alessandro Vezzi

Sara TodescoRiccardo SchiavonSilvia Pescarolo

Alessandro Zambon

Michela D’Angelo

University of Naples ‘Federico II’

(Dept. DISSPA & DSFB)

Luigi Frusciante

Amalia Barone

Mara Ercolano

Maria Luisa Chiusano

Rosa Paparo

Walter Sanseverino

Sara Torre

PAG 2008, San Diego