ARS | Publication request: The rice kinase phylogenomics database: a guide for systematic analysis of the rice kinase super-family

Submitted to: Trends in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 8, 2010
Publication Date: November 1, 2010
Citation: Jung, K., Cao, P., Seo, Y., Dardick, C.D., Ronald, P. 2010. The rice kinase phylogenomics database: a guide for systematic analysis of the rice kinase super-family. Trends in Plant Science. 15(11):595-599.

Interpretive Summary: Typical plant genomes are comprised of 30,000 to 40,000 genes, each of which encodes a unique protein. It is a primary goal of plant biologists to determine the function of each gene and how it contributes to plant development, metabolism, response to the environment, defense against pathogens, etc. However, in some cases, numerous highly similar genes appear over and over again in the genome, each being only slightly different from another. A group of similar genes that occur repeatedly is called a gene family. Some gene families are quite large encompassing over 1,500 genes. In these cases, determining the function of each family member is extremely difficult, since the functions are often redundant if you knock out any one gene by mutation. Others will take its place resulting in no obvious impacts on the plant. Here, we have developed an approach which utilizes different kinds of data from high-throughput functional genomics experiments that allows us to functionally classify genes within large gene families. This method provides guidance to researchers allowing them to make more educated guesses as to which family members are most important and what conditions to evaluate.

Technical Abstract: Determination of gene function is particularly problematic when studying large-gene families because redundancy limits the ability to experimentally assess the contributions of individual genes. Phylogenomics, now referred to as phylomics, is a phylogenetic approach used in comparative genomics to predict biological functions of members of large gene families by assessing the similarity among gene products. Recently, we reported the development of two phylomics databases for 1,508 rice kinases (rice kinase database, RKD; http://rkd.ucdavis.edu) and 769 glycosyltransferases (rice glycosyltransferase database, RGTD; http://ricephylogenomics.ucdavis.edu/cellwalls/gt/). Currently, about 1,000 microarray hybridizations are integrated into these phylomics databases, and more than 250 protein-protein interactions are integrated into RKD. In this review, we introduce new elements of the rice phylomics databases and describe the application of RKD.