Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Phylogenomic Approaches For Gene Function Prediction In Crops

Nandini Krishnamurthy , Kimmen V. Sjölander

  Dept. of Bioengineering, University of California, Berkeley Berkeley, CA -94720

Several crop genomes are being sequenced with the principal aim of identifying genes involved in pathways of agronomic importance such as defense signaling and stress tolerance. With the explosion in sequence information, accurate prediction of protein function has become a vital task to aid biologists in the selection of gene families for experimental characterization. In this talk we present phylogenomic strategies for function prediction that have a lower error rate than using only BLAST, PFAM and other popular approaches. Phylogenomic approaches utilize the evolutionary conservation of residues in proteins to find close and distant homologs. We discuss the strategies employed in phylogenomic analysis such as homolog gathering, multiple sequence alignments, phylogenetic tree construction and integration of experimental information for better function prediction. These approaches are being employed by the Berkeley Phylogenomics Group in the construction of a library of protein families that will complement the genomics effort. Phylogenomic analysis of receptor-like proteins from Arabidopsis and rice is presented as an illustration of the methods.