Plant Transcription factor database - Universität Potsdam
version: 3.0

Oryza sativa subsp. indica 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 111 gene models in this family



Gene modelDescriptionDomains
OsIBCD000554 Chr01_830,219,,,1,219, WRKY
OsIBCD000573 Chr01_855,1524,,,1,1524, WRKY
OsIBCD000964 Chr01_1410,1773,,,1,1773, WRKY
OsIBCD001171 Chr01_1715,3012,,,1,3012, LRR_1 NB-ARC WRKY
OsIBCD001239 Chr01_1818,978,,,1,978, WRKY
OsIBCD002449 Chr01_3900,744,,,1,744, WRKY
OsIBCD002468 Chr01_3925,933,,,1,933, WRKY
OsIBCD002787 Chr01_4395,981,,,1,981, WRKY
OsIBCD002830 Chr01_4467,1158,,,1,1158, WRKY
OsIBCD003110 Chr01_4854,699,,,1,699, WRKY
OsIBCD003207 Chr01_5001,915,,,1,915, WRKY
OsIBCD003221 Chr01_5020,765,,,1,765, WRKY
OsIBCD003308 Chr01_5138,951,,,1,951, WRKY
OsIBCD003723 Chr01_5728,798,,,1,798, WRKY
OsIBCD003724 Chr01_5730,789,,,1,789, WRKY
OsIBCD003726 Chr01_5732,1224,,,1,1224, WRKY
OsIBCD003728 Chr01_5735,1071,,,1,1071, WRKY
OsIBCD003729 Chr01_5737,834,,,1,834, WRKY
OsIBCD003756 Chr01_5777,1668,,,1,1668, WRKY
OsIBCD003856 Chr01_5929,612,,,1,612, WRKY
OsIBCD004669 Chr01_7086,1239,,,1,1239, WRKY
OsIBCD005281 Chr02_839,1047,,,1,1047, WRKY
OsIBCD005786 Chr02_1559,1086,,,1,1086, WRKY
OsIBCD006331 Chr02_2575,762,,,1,762, WRKY
OsIBCD007429 Chr02_4330,639,,,1,639, WRKY
OsIBCD007658 Chr02_4689,1674,,,1,1674, WRKY
OsIBCD008109 Chr02_5316,1950,,,1,1950, WRKY
OsIBCD009967 Chr03_2002,651,,,1,651, WRKY
OsIBCD009971 Chr03_2006,1254,,,1,1254, WRKY
OsIBCD010058 Chr03_2121,1071,,,1,1071, WRKY
OsIBCD010317 Chr03_2509,1239,,,1,1239, WRKY
OsIBCD011432 Chr03_4539,429,,,1,429, WRKY
OsIBCD011933 Chr03_5316,1155,,,1,1155, WRKY
OsIBCD012035 Chr03_5455,696,,,1,696, WRKY
OsIBCD012043 Chr03_5463,1320,,,1,1320, WRKY
OsIBCD012272 Chr03_5789,1143,,,1,1143, WRKY
OsIBCD012691 Chr03_6317,1164,,,1,1164, WRKY
OsIBCD012743 Chr03_6409,993,,,1,993, WRKY
OsIBCD014663 Chr04_3264,2238,,,1,2238, WRKY
OsIBCD015153 Chr04_3960,603,,,1,603, WRKY
OsIBCD015155 Chr04_3962,411,,,1,411, WRKY
OsIBCD015442 Chr04_4409,1476,,,1,1476, WRKY
OsIBCD015494 Chr04_4475,930,,,1,930, WRKY
OsIBCD015891 Chr04_5003,1185,,,1,1185, WRKY zf-BED
OsIBCD016325 Chr05_277,879,,,1,879, WRKY
OsIBCD016330 Chr05_283,540,,,1,540, WRKY
OsIBCD016386 Chr05_357,1509,,,1,1509, WRKY
OsIBCD016683 Chr05_830,585,,,1,585, FAR1 WRKY
OsIBCD017493 Chr05_2379,1320,,,1,1320, WRKY
OsIBCD017495 Chr05_2382,969,,,1,969, WRKY
OsIBCD017574 Chr05_2541,1464,,,1,1464, WRKY
OsIBCD018348 Chr05_3724,1719,,,1,1719, WRKY
OsIBCD018370 Chr05_3760,1389,,,1,1389, WRKY
OsIBCD018371 Chr05_3761,987,,,1,987, WRKY
OsIBCD018669 Chr05_4208,543,,,1,543, WRKY
OsIBCD018727 Chr05_4283,666,,,1,666, WRKY
OsIBCD018899 Chr05_4519,927,,,1,927, WRKY
OsIBCD018903 Chr05_4525,1257,,,1,1257, WRKY
OsIBCD018914 Chr05_4540,1887,,,1,1887, WRKY
OsIBCD018946 Chr05_4587,684,,,1,684, WRKY
OsIBCD019015 Chr05_4692,1014,,,1,1014, WRKY
OsIBCD019021 Chr05_4703,903,,,1,903, WRKY
OsIBCD019399 Chr06_467,1875,,,1,1875, WRKY
OsIBCD019484 Chr06_591,1176,,,1,1176, WRKY
OsIBCD020816 Chr06_2866,648,,,1,648, WRKY
OsIBCD021599 Chr06_4142,1035,,,1,1035, WRKY
OsIBCD022163 Chr07_99,867,,,1,867, WRKY
OsIBCD023005 Chr07_1528,4416,,,1,4416, B3 LRR_1 NB-ARC WRKY
OsIBCD023315 Chr07_2212,906,,,1,906, WRKY
OsIBCD024023 Chr07_3289,1854,,,1,1854, WRKY
OsIBCD024095 Chr07_3407,1299,,,1,1299, WRKY
OsIBCD024610 Chr07_4146,1005,,,1,1005, WRKY
OsIBCD025277 Chr08_875,2586,,,1,2586, WRKY hATC zf-BED
OsIBCD025279 Chr08_878,2070,,,1,2070, WRKY hATC zf-BED
OsIBCD025280 Chr08_879,1698,,,1,1698, WRKY
OsIBCD025285 Chr08_884,2571,,,1,2571, WRKY hATC zf-BED
OsIBCD025288 Chr08_888,3381,,,1,3381, WRKY hATC zf-BED
OsIBCD025756 Chr08_1764,1704,,,1,1704, WRKY
OsIBCD026982 Chr08_3909,2025,,,1,2025, WRKY
OsIBCD027816 Chr09_726,915,,,1,915, WRKY
OsIBCD027904 Chr09_922,2127,,,1,2127, Na_H_Exchanger WRKY
OsIBCD028127 Chr09_1300,1086,,,1,1086, WRKY
OsIBCD028565 Chr09_1997,984,,,1,984, WRKY
OsIBCD028566 Chr09_1998,957,,,1,957, WRKY
OsIBCD028921 Chr09_2564,1902,,,1,1902, WRKY
OsIBCD030121 Chr10_1147,723,,,1,723, WRKY
OsIBCD031583 Chr10_3441,900,,,1,900, WRKY
OsIBCD031647 Chr11_88,1008,,,1,1008, WRKY
OsIBCD031649 Chr11_90,675,,,1,675, WRKY
OsIBCD031652 Chr11_93,792,,,1,792, WRKY
OsIBCD031653 Chr11_94,963,,,1,963, WRKY
OsIBCD031654 Chr11_96,984,,,1,984, WRKY
OsIBCD032867 Chr11_2165,483,,,1,483, WRKY
OsIBCD032868 Chr11_2166,738,,,1,738, WRKY
OsIBCD033614 Chr11_3339,3948,,,1,3948, NB-ARC WRKY
OsIBCD033616 Chr11_3341,783,,,1,783, WRKY
OsIBCD033620 Chr11_3345,2889,,,1,2889, NB-ARC WRKY
OsIBCD033752 Chr12_16,729,,,1,729, WRKY
OsIBCD033759 Chr12_24,1632,,,1,1632, WRKY
OsIBCD033762 Chr12_28,1788,,,1,1788, Peptidase_C48 WRKY
OsIBCD033861 Chr12_169,1014,,,1,1014, WRKY
OsIBCD033862 Chr12_172,693,,,1,693, WRKY
OsIBCD033864 Chr12_175,654,,,1,654, WRKY
OsIBCD033865 Chr12_176,966,,,1,966, WRKY
OsIBCD033866 Chr12_177,1488,,,1,1488, WRKY
OsIBCD035090 Chr12_2298,486,,,1,486, WRKY
OsIBCD035560 Chr12_2993,1092,,,1,1092, WRKY
OsIBCD035990 Chr01_856,648,,,1,648, FAR1 WRKY
OsIBCD043636 Chr08_1320,918,,,1,918, WRKY
OsIBCD044312 Chr09_468,1077,,,1,1077, WRKY
OsIBSD047308 Supscaffold123_4,960,,,1,960, 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