Plant Transcription factor database - Universität Potsdam
version: 3.0

Arabidopsis lyrata 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 79 gene models in this family



Gene modelDescriptionDomains
313633 fgenesh1_pm.C_scaffold_1002413 WRKY
317082 fgenesh1_pm.C_scaffold_3000098 WRKY
320036 fgenesh1_pm.C_scaffold_4000093 WRKY
321760 fgenesh1_pm.C_scaffold_4001817 WRKY
321761 fgenesh1_pm.C_scaffold_4001818 WRKY
322266 fgenesh1_pm.C_scaffold_4002323 WRKY
324601 fgenesh1_pm.C_scaffold_5002145 WRKY
325325 fgenesh1_pm.C_scaffold_6000545 WRKY
327396 fgenesh1_pm.C_scaffold_6002616 WRKY
328547 fgenesh1_pm.C_scaffold_7000774 WRKY
328625 fgenesh1_pm.C_scaffold_7000852 FLYWCH Ribosomal_L21p WRKY
329038 fgenesh1_pm.C_scaffold_7001265 WRKY
329411 fgenesh1_pm.C_scaffold_7001638 WRKY
335144 fgenesh1_pg.C_scaffold_1001709 WRKY
336031 fgenesh1_pg.C_scaffold_1002596 WRKY
337643 fgenesh1_pg.C_scaffold_1004208 WRKY
338870 fgenesh1_pg.C_scaffold_2000969 WRKY
339216 fgenesh1_pg.C_scaffold_2001315 WRKY
343891 fgenesh1_pg.C_scaffold_4000233 Plant_zn_clust WRKY
351629 fgenesh1_pg.C_scaffold_6002222 WRKY
471557 fgenesh2_kg.1__1511__AT1G13960.1 WRKY
474956 fgenesh2_kg.2__86__AT1G64000.1 WRKY
475116 fgenesh2_kg.2__246__AT1G62300.1 WRKY
476056 fgenesh2_kg.2__1186__AT1G69310.1 WRKY
477161 fgenesh2_kg.2__2291__AT1G80840.1 WRKY
477731 fgenesh2_kg.3__432__AT3G04670.1 Plant_zn_clust WRKY
481313 fgenesh2_kg.4__373__AT2G24570.1 Plant_zn_clust WRKY
481352 fgenesh2_kg.4__412__AT2G25000.1 WRKY
481938 fgenesh2_kg.4__998__AT2G30250.1 WRKY
482446 fgenesh2_kg.4__1506__AT2G34830.1 WRKY
482718 fgenesh2_kg.4__1778__AT2G37260.1 WRKY
482857 fgenesh2_kg.4__1917__AT2G38470.1 WRKY
483604 fgenesh2_kg.4__2664__AT2G44745.1 WRKY
483794 fgenesh2_kg.4__2854__AT2G46400.1 WRKY
484242 fgenesh2_kg.5__234__AT2G03340.1 WRKY
486080 fgenesh2_kg.5__2072__AT3G56400.1 WRKY
486325 fgenesh2_kg.5__2317__AT3G58710.2 WRKY
486738 fgenesh2_kg.5__2730__AT3G62340.1 WRKY
488124 fgenesh2_kg.6__1258__AT5G13080.1 WRKY
489268 fgenesh2_kg.6__2402__AT5G24110.1 WRKY
489657 fgenesh2_kg.6__2791__AT5G28650.1 Plant_zn_clust WRKY
489946 fgenesh2_kg.6__3080__AT4G11070.1 WRKY
490404 fgenesh2_kg.6__3538__AT4G01720.1 WRKY
490447 fgenesh2_kg.6__3581__AT4G01250.1 WRKY
490719 fgenesh2_kg.7__152__AT4G39410.1 WRKY
492487 fgenesh2_kg.7__1920__AT4G23810.1 WRKY
492514 fgenesh2_kg.7__1947__AT4G23550.1 WRKY
493050 fgenesh2_kg.7__2483__AT4G18170.1 WRKY
493831 fgenesh2_kg.7__3264__AT5G41570.1 WRKY
494337 fgenesh2_kg.8__153__AT5G46350.1 WRKY
495347 fgenesh2_kg.8__1163__AT5G52830.1 WRKY
496697 fgenesh2_kg.8__2513__AT5G64810.1 WRKY
497253 fgenesh2_kg.97__1__AT5G43290.1 WRKY
859664 Al_scaffold_0007_3163 WRKY
860504 Al_scaffold_0006_13 WRKY
867069 Al_scaffold_0005_2548 WRKY
870142 Al_scaffold_0004_2305 WRKY
871269 Al_scaffold_0004_3432 WRKY
874313 Al_scaffold_0003_2954 WRKY
876639 Al_scaffold_0002_1233 WRKY
876849 Al_scaffold_0002_1443 WRKY
884073 Al_scaffold_0008_337 LRR_3 NB-ARC WRKY
884135 Al_scaffold_0008_399 LRR_3 NB-ARC WRKY
884150 Al_scaffold_0008_414 LRR_3 NB-ARC WRKY
884408 Al_scaffold_0008_672 WRKY
884549 Al_scaffold_0008_813 WRKY
890619 scaffold_103413.1 WRKY
896042 scaffold_300012.1 WRKY
902048 scaffold_401549.1 Plant_zn_clust WRKY
909483 scaffold_601540.1 WRKY
910251 scaffold_602308.1 WRKY
913314 scaffold_701056.1 Plant_zn_clust WRKY
913892 scaffold_701634.1 WRKY
914166 scaffold_701908.1 Plant_zn_clust WRKY
917333 scaffold_800733.1 WRKY
917334 scaffold_800734.1 WRKY
917932 scaffold_801332.1 WRKY
918771 scaffold_802171.1 WRKY
921120 scaffold_9700001.1 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