Plant & Animal Genomes XI Conference Plant & Animal Genomes XI ConferenceJanuary 11-15, 2003
Town & Country Convention Center
San Diego, CA
Workshop: Citrus
The overall objective is to integrate genetic mapping with studies on functional and comparative genomics (ESTs) of sweet orange, mandarin and Poncirus trifoliata growing under limiting biotic (CVC, canker, tristeza, leprosis, and gummosis) and abiotic (drought) factors. Functional genomic studies of citrus pathogens whose genomes have been fully sequenced (CTV, Xylella fastidiosa and Xanthomonas axonopodis pv. citri) are also planned. An experimental field network for testing hybrids of sweet orange and mandarins will be the foundation for the validation of genetic maps and inheritance studies. So far (October, 2002), from the 240,000 planned ESTs, we have sequenced more than 40,000 clones, producing over 17,000 clusters. Libraries from healthy and pathogen-inoculated sweet orange plants have been constructed and sequenced. We have also started sequencing ESTs obtained from fruits. The Bioinformatics facility has set up an automated analysis pipeline that extracts sequence trace files from compressed zip files, converts them into fasta sequences, masks vector sequences, removes all traces of contaminating sequences, assembles non-redundant clusters, and finally compares those to the GenBank protein database. Automatic categorization of completely sequenced libraries is being carried out by comparing our clusters to a locally built database composed by already cured protein databases from different plant species.