BARLEY ESTS: A RESOURCE FOR SYSTEMATIC GENOME ANALYSIS

Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben

The partial sequencing of cDNA clones allows a systematic identification of genes and, in conjunction with the fast evolving information content of public databases, the in silico assignment of putative functions. Moreover, ESTs form a valuable resource for the development of genetic markers and are a prerequisite for the implementation of multiparallel expression analyses. Currently we are sequencing cDNAs of the high malting quality spring barley cultivar `BarkeĽ. Libraries were made from etiolated seedlings, roots, and developing caryopses. At this time, 8514 quality controled ESTs have been generated. Preliminary estimations including clones from all three libraries reveal a redundancy of app. 50 %. For the assignment of putative functions BLASTX2 similarity searches have been performed against the SwissPirPlus database. Based on BlastX2 outputs a BARLEY EST-DATABASE (BEST) was created containing both the raw sequences and BlastX2 documents converted into HTML-format. In this way a search using any alphanumeric string can be carried out to link all documents containing the search pattern. Based on the barley EST sequences a local BLAST search can be perfomed in BEST to quickly identify the barley homologue to any given cDNA sequence. BEST is currently available as an intranet solution but will be put into the public domain shortly. Apart from continued sequencing further goals include the development of new libraries, the advancement of the BEST, the implementation of bioinformatic tools (e.g. analysis of redundancy) and the generation of rearrayed libraries and filters.