Plant Transcription factor database - Universität Potsdam
version: 3.0

Populus trichocarpa 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 104 gene models in this family



Gene modelDescriptionDomains
174550 gw1.I.3150.1 WRKY
177280 gw1.I.5880.1 WRKY
177701 gw1.I.6301.1 WRKY
197570 gw1.IV.2659.1 WRKY
198942 gw1.IV.4031.1 WRKY
208696 gw1.V.4097.1 WRKY
226173 gw1.X.870.1 WRKY
233382 gw1.XI.1362.1 WRKY
234796 gw1.XI.2776.1 WRKY
242989 gw1.XIII.3238.1 WRKY
246962 gw1.XIV.3705.1 WRKY
249063 gw1.XIX.1463.1 WRKY
249075 gw1.XIX.1475.1 WRKY
249258 gw1.XIX.1658.1 WRKY
256681 gw1.XVI.2620.1 WRKY
259824 gw1.XVIII.365.1 WRKY
261634 gw1.XVIII.2175.1 WRKY
267181 gw1.127.187.1 WRKY
274535 gw1.166.31.1 WRKY
278925 gw1.212.69.1 WRKY
281810 gw1.28.384.1 WRKY
287143 gw1.40.903.1 WRKY
298129 gw1.88.251.1 WRKY
409145 gw1.II.480.1 WRKY
413677 gw1.III.780.1 WRKY
415314 gw1.III.2417.1 WRKY
417465 gw1.VI.1838.1 WRKY
417508 gw1.VI.1881.1 WRKY
417600 gw1.VI.1973.1 WRKY
418833 gw1.VIII.261.1 WRKY
424440 gw1.87.54.1 WRKY
550164 eugene3.00012605 WRKY
552620 eugene3.00021935 WRKY
552777 eugene3.00002092 WRKY
555180 eugene3.00031813 WRKY
559484 eugene3.00051099 WRKY
561985 eugene3.00061944 WRKY
562723 eugene3.00070661 WRKY
562724 eugene3.00070662 WRKY
571055 eugene3.00130419 WRKY
571679 eugene3.00131043 WRKY
572520 eugene3.00140565 WRKY
572606 eugene3.00140651 WRKY
577093 eugene3.00161228 WRKY
577692 eugene3.00170434 WRKY
578746 eugene3.00180970 WRKY
581356 eugene3.01290013 WRKY
588876 eugene3.02690004 LRR_1 NB-ARC WRKY
590547 eugene3.32050001 WRKY
591760 eugene3.00400105 WRKY
594801 eugene3.06680002 WRKY
640058 grail3.0008011601 WRKY
643201 grail3.0003036201 WRKY
646672 grail3.0018034701 WRKY
653213 grail3.0023037401 WRKY
654913 grail3.0011025901 WRKY
655096 grail3.0019002001 WRKY
656500 grail3.0010023001 WRKY
662175 grail3.0015029001 WRKY
663578 grail3.0092008201 WRKY
664330 grail3.0061011101 WRKY
665964 grail3.0094006501 WRKY
666695 grail3.0005030601 WRKY
669155 grail3.0007034202 WRKY
674772 grail3.0204000201 WRKY
710033 estExt_Genewise1_v1.C_LG_II0718 WRKY
710455 estExt_Genewise1_v1.C_LG_II1638 WRKY
711034 estExt_Genewise1_v1.C_LG_II2783 WRKY
715111 estExt_Genewise1_v1.C_LG_V1110 WRKY
716013 estExt_Genewise1_v1.C_LG_V3133 WRKY
732261 estExt_Genewise1_v1.C_LG_XIV3374 WRKY
744845 estExt_Genewise1_v1.C_1400026 WRKY
751667 fgenesh4_pg.C_LG_I001270 WRKY
755334 fgenesh4_pg.C_LG_II001514 WRKY
755339 fgenesh4_pg.C_LG_II001519 WRKY
757358 fgenesh4_pg.C_LG_III000900 WRKY
760201 fgenesh4_pg.C_LG_V000253 WRKY
772348 fgenesh4_pg.C_LG_XII000123 WRKY
774432 fgenesh4_pg.C_LG_XIV000342 WRKY
777667 fgenesh4_pg.C_LG_XVI000909 WRKY
778465 fgenesh4_pg.C_LG_XVII000344 WRKY
779120 fgenesh4_pg.C_LG_XVIII000488 WRKY
779126 fgenesh4_pg.C_LG_XVIII000494 WRKY
782119 fgenesh4_pg.C_scaffold_44000249 WRKY
789260 fgenesh4_pg.C_scaffold_537000002 WRKY
797318 fgenesh4_pm.C_LG_I000321 WRKY
800701 fgenesh4_pm.C_LG_IV000388 WRKY
802026 fgenesh4_pm.C_LG_VI000373 WRKY
803420 fgenesh4_pm.C_LG_VIII000375 WRKY
806176 fgenesh4_pm.C_LG_XI000451 WRKY
816178 estExt_fgenesh4_pg.C_LG_II0549 WRKY
816628 estExt_fgenesh4_pg.C_LG_II1537 WRKY
819104 estExt_fgenesh4_pg.C_LG_VI0537 WRKY
819471 estExt_fgenesh4_pg.C_LG_VI1508 WRKY
822219 estExt_fgenesh4_pg.C_LG_X1328 WRKY
822926 estExt_fgenesh4_pg.C_LG_XI0756 WRKY
823993 estExt_fgenesh4_pg.C_LG_XIV0332 WRKY
825419 estExt_fgenesh4_pg.C_LG_XVI1289 WRKY
827299 estExt_fgenesh4_pg.C_700041 WRKY
828718 estExt_fgenesh4_pg.C_2080026 WRKY
830461 estExt_fgenesh4_pm.C_LG_II0899 WRKY
830963 estExt_fgenesh4_pm.C_LG_III0624 WRKY
833697 estExt_fgenesh4_pm.C_LG_X0626 WRKY
834779 estExt_fgenesh4_pm.C_LG_XIV0172 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