| Abstract Detail
Bioinformatics - Afternoon Torre, Sara [1], D Agostino, Nunzio [2], Chiusano, Maria Luisa [2], Frusciante, Luigi [1], Alessandra, Traini [2], Barone, Amalia [1]. “BAC sequencing and annotation driven by experimental data: an application for a serine-threonine kinase on chromosome 12.”. IN the frame of the International Tomato Sequencing Project, the first BAC of chromosome 12 (Le_HBa0032K07) has been sequenced and submitted at the Solanaceae (SOL) Genomics Network. A preliminary annotation was based on experimental data derived from TomatESTdb, a database of about 215,000 expressed sequences from tomato species and computational defined tentative consensus. Considering EST-genome alignments, eleven gene tags were located on this BAC. A partial matching at the 3’ end of the BAC with a tentative consensus from TomatESTdb assembling 24 ESTs was identified. In order to validate the gene localization we based successive analyses on the predicted consensus. The tentative consensus sequence revealed sequence similarity with various serine-threonine protein kinases as annotated at TomatEST db. In particular, a significant similarity (E=9e-27) was found with the serine-threonine protein kinase Q8GV29 of Oryza sativa and with the dual specificity kinase Q9ZQ31 (E=3e-23) of Arabidopsis thaliana. In rice, the protein kinase was reported to be involved in response to salt stress (Gu et al., Plant Sci. 2005). In order to verify the occurrence of this gene in the tomato genome and its expression as cDNA, PCR were carried out designing primers on the consensus sequence retrieved from the TomatESTdb. One 5000 bp fragment was amplified on genomic DNA, while a 1000 bp fragment was obtained from cDNA amplification, as expected from primer designed on the tentative consensus structure. The sequencing of the cDNA fragment and its alignment with the consensus sequence confirmed the tentative consensus and the expression of the gene. Afterwords, using the SGN BAC ends database, 4 BACs were selected to extend the sequencing at the 3’ end of BAC Le_HBa0032K07 and to cover the full length of the consensus. Furthermore, tomato mutants are being used to investigate on possible roles of this gene in abiotic stress response.
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1 - University \"Federico II\", Department of Soil, Plant and Environmental Sciences, Naples, Italy, 80055
2 - University \"Federico II\", Department of Structural and Functional Biology, Naples, Italy,
Keywords:
Sequence finishing
BAC extension
Assembly
Experimental annotation.
Session: Poster-63
Location: Ballroom CD/Monona Terrace
Date: Tuesday, July 25th, 2006
Time: 8:00 AM
Abstract ID:107 |
