Phylogenetic Analyses Of WRKY Gene Family And The Expression Profiles Of Rice WRKY Genes

WRKY proteins are regulatory transcription factors with a binding preference for the W box, originally isolated from plants contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif. Evidence is accumulating to suggest that the WRKY proteins play significant roles in responses to biotic and abiotic stresses, and in development.Genome-Wide analysis of the WRKY transcription factor family in rice: Rice WRKY genes were obtained by multiple BLAST searches of the rice genome database using the WRKY domain sequences. Based on an extensive search of the sequence of the rice genome, we found 102 predicted WRKY genes in the genome. During annotation analyses of the DNA sequences, we found that most of the OsWRKY genes contained conserved intron splicing positions in their WRKY domains.Phylogentic analysis of the rice WRKY gene family: The unrooted phylogenetic tree was depicted by the CLUSTAL W program using WRKY domains and WRKY genes respectively. The genes were clustered in a manner similar to the clusters obtained by analyses of the WRKY domains. The classification system is based on both of the features of WRKY domains and their phylogenies. The rice WRKY gene family can be classified as three group and eight subgroup (Subgroup Ia and Ib in group I, subgroup IIa, IIb, IIc and IId in group II, subgruop IIIa and IIIb in group III).Gene duplications and rearrangements were also analyzed.Comparative WRKY gene family of rice and Arabidopsis: For comparison, we also collected data for the AtWRKY gene superfamily from the ArabidopsisInformation Resource. The WRKY genes from rice and Arabidopsis were divided into similar groups with subgroups. The phylogenetic trees generated from the WDs and the genes indicate that the WRKY gene family arose during evolution through duplication and that the dramatic amplification of rice WRKY genes in group III is due to tandem and segmental gene duplication compared with those of Arabidopsis. The result suggests that some of the rice WRKY genes in group III are evolutionarily more active than those in the Arabidopsis, and may have specific roles for the monocotyledonous plants.Phylogenetic analysis of the WRKY domains from plants and protists: Further, it was possible to identify the presence of WRKY like genes in protists (Giardia lamblia and Dictyostelium discoideum) and green algae (Chlamydomonas reinhardtii) through database research, demonstrating the ancient origin of the gene family. The results obtained by alignments of the WDs from different species and other analysis imply that domain gain and loss is a divergent force for expansion of the WRKY gene family, and that a rapid amplification of the WRKY genes predate the divergence of monocots and dicots. On the basis of these results, we believe that genes encoding a single WD may have been derived from the C-terminal WD of the genes harboring two WDs. The conserved intron splicing positions in the WDs of higher plants offer clues about WRKY gene evolution, annotation, and classification.Expression profile analysis of WRKY genes in rice: 89 WRKY genes cDNA macroarray were prepared. Macroarray analysis indicated that 13 WRKY genes were induced by rice blast pathogen strongly, and 19 WRKY genes were induced by Jasmonic acids quickly. Among them, there are five genes induced by rice blast pathogen and Jasmonic acids. The result suggests that these genes play a role in defence or JA signaling pathway.