ISHS Acta Horticulturae 603: VIII International Conference on Grape Genetics and Breeding
TOWARDS THE TRANSCRIPTOME OF GRAPEVINE (VITIS VINIFERA L.) |
| Authors: | A.J. Driesel, A. Lommele, B. Drescher, R. Töpfer, M. Bell, I. Cartharius, N. Cheutin, J.-F. Huck, J. Kubiak, P. Regnard, A. Steinmetz |
| Keywords: | annotation, bioinformatics, clustering and assembly, contig, cDNA sequences, full-length cDNAs, protein function, secondary metabolism, resistance, enzymes |
| Abstract:
In order to establish the transcriptome of grapevine (cv. Gewürztraminer), we have isolated and sequenced full-length cDNAs from different tissues (flowers, berries, mature berry skins, roots, buds, leaves and tendrils) at various developmental stages. Starting with 29,564 readings and following cleanup filtering for high quality sequences, 20,151 sequences were assembled into 2,834 contigs with an average of about 5 sequences per contig using clustering and assembly technology from Paracel (with a minimum sequence identity set to 90% between members of a contig). Additionally, 6,589 not assembled sequences were used as singlets. Contigs and singlets sum up to a minimum of 9,432 different transcripts. These individual transcripts were analysed using Blast and InterProScan. Using these data, a grapevine DNA chip with core sequences for the various transcripts was designed and will be available upon request. About 60% of the sequences share significant sequence similarities (score >50) with proteins of assigned function. More than 80% of the sequences (including coding sequences for proteins of up to 1,000 aminoacids) were found to be full length and were called Full Length Expressed Sequences (FLES). Using domain search algorithms ("dry approach") we could assign putative functions to unknown genes, allowing a functional categorization. We intend to use our collection of clones to study the profiling of proteins involved in secondary metabolism and fungal disease resistance/susceptibility. Information about our clones is available to the scientific community. Our searchable database can be used for sequence comparisons with our grapevine data. Clones can be ordered from VitiGen at the following | |
Download Adobe Acrobat Reader (free software to read PDF files) | |
