| Abstract Detail
Tomato sequencing - Morning Granel, Antonio [1], Fernandez, Vicky [2], Zuniga, Sheila [2], Perez, Angela [2], Botella Mesa, Miguel Angel [3], Camara, Francisco [4], Guigo, Roderic [4]. Sequencing of euchromatic regions of Chr9 of tomato: a progress report. TWELVE seed-BACclones were selected based on his predicted position in the F2-2000 map. The selected clones were confirmed to contain the anchored marker by PCR and sequencing, and Chr9 position verified by both sequence polimorfism in the S.pennelli x S esculentum ILs mapping population generated by Zamir, and by FISH (Chang and Stack). The first BAC has been finished and 6 additional BACs are in phase 2, and 3 in library construction phase. The Phred/Phrap/Consed package is used for the assembly and editing of contigs. We are using the quality standards recommended in the “Tomato genome sequencing standards and guidelines” and finished sequences have been submitted to the SGN database and to the IMIM for additional quality control and annotation. IMIM/CRG is also developing and optimizing tools for gene prediction in tomato. One of those is Geneid, a fast genome-scale ab initio gene prediction tool developed for finding genes in anonymous DNA sequences. Geneid performance depends on a parameter file to build the predictions. The parameter file contains mostly the description of the probabilistic model on which the predictions are based. Development of a parameter file requires the “training” of geneid to predict genes in a particular genome, in this case tomato. We are currently using a geneid parameter file that was trained on a set of 112 Solanaceae protein-coding genes (53 of which were tomato sequences), and expect to get a more complete set from Shibatas’s group (Kazusa) and European colleagues. While this parameter file performs already better in predicting tomato sequences than another related plant´s geneid parameter file (Arabidopsis thaliana) we expect it to perform significantly better once a larger tomato training set is available. Once we have the gene predictions we have in-house tools (i.e. gff2ps) which allows for their visualization on a chromosomal-scale.
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1 - Consejo Superior de Investigaciones Científicas, Instituto de Biolgia Molecular y Celular de Plantas, Universidad Politecnica de Valencia, Avda Tarongers s/n, Valencia, V alencia, 46022, Spain
2 - Sistemas Genomicos,
3 - Universidad de Malaga, Biología Molecular y Bioquímica, Edificio I + D, 3ª planta. Campus te Teatinos s/nº, Malaga, Malaga, 29071, Spain
4 - Institut Municipal Investigació Medica (IMIM), Genome Bioinformatics Laboratory,
Keywords:
tomato
geneid
DNA sequence.
Session: SAT04-10
Location: Hall of Ideas Room E/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 10:30 AM
Abstract ID:208 |
