Plant Transcription factor database - Universität Potsdam
version: 3.0

Sorghum bicolor WRKY Family

Description

Wu et al. 2005: WRKY transcription factors, 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. In this research, we identified 102 putative WRKY genes from the rice genome and compared them with those from Arabidopsis. The WRKY genes from rice and Arabidopsis were divided into three groups with several subgroups on the basis of phylogenies and the basic structure of the WRKY domains (WDs). 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 Arabidopsis, and may have specific roles in monocotyledonous plants. 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.

Members of this family
  SHOULD possess WRKY domain

Domain alignments

Benchmark against A. thaliana

The Sensitivity and Positive Predictive Value (PPV) were assessed for this family. The data reported by Ulker & Somssich 2004 for A. thaliana were taken as gold standard.

The gold standard reported 71 members for this family, 71 of which are present in ArabTFDB, giving a PPV of 0.99. One additional member not present in ArabTFDB might be false negative, giving a Sensitivity of 0.99.

This family is also present in:

References

There are 94 gene models in this family



Gene modelDescriptionDomains
125759 fgenesh1_pm.C_chr_3000790 WRKY
127069 fgenesh1_pm.C_chr_4000372 WRKY
143186 estExt_fgenesh1_pm.C_chr_30497 WRKY
144221 estExt_fgenesh1_pm.C_chr_40198 WRKY
148837 estExt_fgenesh1_kg.C_chr_50021 WRKY
149661 estExt_fgenesh1_kg.C_chr_90104 WRKY
149797 estExt_fgenesh1_kg.C_chr_90242 WRKY
3993906 gw1.5.843.1 WRKY
3993912 gw1.5.845.1 WRKY
4003449 gw1.3.1719.1 WRKY
4003998 gw1.1.1984.1 WRKY
4094464 gw1.6.11296.1 WRKY
4102469 gw1.5.11592.1 WRKY
4104349 gw1.10.11778.1 WRKY
4114272 gw1.10.12778.1 WRKY
4130585 gw1.9.14616.1 WRKY
4133329 gw1.3.15280.1 WRKY
4134451 gw1.7.14992.1 WRKY
4143588 gw1.6.15991.1 WRKY
4144047 gw1.9.16060.1 WRKY
4153199 gw1.9.16728.1 WRKY
4154004 gw1.4.16639.1 WRKY
4154284 gw1.9.16822.1 WRKY
4162836 gw1.3.19431.1 WRKY
4163469 gw1.3.19553.1 WRKY
4169133 gw1.3.21047.1 WRKY
4756235 estExt_Genewise1.C_chr_44693 Plant_zn_clust WRKY
4762157 estExt_Genewise1.C_chr_67443 Plant_zn_clust WRKY
4775979 e_gw1.1.3652.1 WRKY
4776346 e_gw1.1.12974.1 WRKY
4776612 e_gw1.1.14704.1 WRKY
4783620 e_gw1.1.731.1 WRKY
4786052 e_gw1.2.646.1 WRKY
4812036 e_gw1.4.18423.1 WRKY
4841359 e_gw1.7.3777.1 WRKY
4849205 e_gw1.9.1817.1 WRKY
4858234 e_gw1.10.14745.1 WRKY
4865573 e_gw1.10.15356.1 WRKY
4867461 estExt_Genewise1Plus.C_chr_11028 Plant_zn_clust WRKY
4874328 estExt_Genewise1Plus.C_chr_26654 WRKY
4888873 estExt_Genewise1Plus.C_chr_67358 WRKY
4891803 estExt_Genewise1Plus.C_chr_77950 WRKY
4898070 estExt_Genewise1Plus.C_chr_107179 WRKY
4964177 fgenesh1_pg.C_chr_1000779 WRKY
4969704 fgenesh1_pg.C_chr_2001020 LRR_1 NB-ARC Tryp_alpha_amyl WRKY
4970819 fgenesh1_pg.C_chr_2002135 WRKY
4975141 fgenesh1_pg.C_chr_3002256 WRKY
4976178 fgenesh1_pg.C_chr_3003293 WRKY
4976179 fgenesh1_pg.C_chr_3003294 WRKY
4980770 fgenesh1_pg.C_chr_5000130 WRKY
4980773 fgenesh1_pg.C_chr_5000133 WRKY
4986598 fgenesh1_pg.C_chr_7000688 WRKY
4992581 fgenesh1_pg.C_chr_9002309 WRKY
4995093 fgenesh1_pg.C_chr_10002270 WRKY
4999627 estExt_fgenesh1_pg.C_chr_21266 WRKY
5000715 estExt_fgenesh1_pg.C_chr_23499 WRKY
5001331 estExt_fgenesh1_pg.C_chr_30352 WRKY
5002076 estExt_fgenesh1_pg.C_chr_31981 WRKY
5002784 estExt_fgenesh1_pg.C_chr_33273 WRKY
5004879 estExt_fgenesh1_pg.C_chr_43004 WRKY
5008532 estExt_fgenesh1_pg.C_chr_80572 WRKY
5008708 estExt_fgenesh1_pg.C_chr_81141 WRKY
5010463 estExt_fgenesh1_pg.C_chr_100311 WRKY
5030891 Sb10g004000 WRKY
5033621 Sb02g022280 WRKY
5034929 Sb03g000240 WRKY
5036539 Sb03g032800 WRKY
5036837 Sb03g038170 WRKY
5036853 Sb03g038510 WRKY
5039381 Sb05g001220 WRKY
5044459 Sb08g002520 WRKY
5044462 Sb08g002540 WRKY
5044464 Sb08g002560 WRKY
5044465 Sb08g002570 WRKY
5044466 Sb08g002590 WRKY
5046723 Sb09g023500 WRKY
5048172 Sb01g008550 Plant_zn_clust WRKY
5048510 Sb01g014180 Plant_zn_clust WRKY
5049476 Sb01g036180 WRKY
5051187 Sb02g024760 WRKY
5051349 Sb02g027950 WRKY
5052251 Sb02g043030 WRKY
5053449 Sb03g029920 WRKY
5053477 Sb03g030480 WRKY
5053650 Sb03g033640 WRKY
5053712 Sb03g034670 WRKY
5053921 Sb03g038200 WRKY
5057358 Sb06g019710 WRKY
5058547 Sb07g006230 WRKY
5058662 Sb07g016330 WRKY
5059759 Sb08g020270 Plant_zn_clust WRKY
5060215 Sb09g005700 WRKY
5060976 Sb09g028660 WRKY
5061044 Sb09g029850 WRKY

General references

Eulgem, T; Rushton, PJ; Robatzek, S; Somssich, IE. 2000. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5(5):199-206 PUBMEDID:10785665
Ulker, B; Somssich, IE. 2004. WRKY transcription factors: from DNA binding towards biological function. Curr. Opin. Plant Biol. 7(5):491-8 PUBMEDID:15337090
Zhang, Y; Wang, L. 2005. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol. Biol. 5(1):1 PUBMEDID:15629062