Open Access

Nomenclature report on rice WRKY's - Conflict regarding gene names and its solution

  • Rice WRKY Working Group
Rice20125:3

DOI: 10.1186/1939-8433-5-3

Received: 22 November 2011

Accepted: 27 February 2012

Published: 27 February 2012

Abstract

Background

Since whole genome sequences of rice were made publically accessible, the number of articles onnew rice genes has increased remarkably. The Committee on Gene Symbolization, Nomenclature and Linkage(CGSNL) of the Rice Genetics Cooperative published the gene nomenclature system for rice and encouragedresearchers to follow the rules before publishing their results. The CGSNL provides an on-line registration systemfor newly identified rice genes to prevent conflicts and/or duplication of gene name in journal articles.

Findings

Recently, the CGSNL surveyed genes in the rice WRKY family in published journal articles and foundseveral duplicated gene names.

Conclusions

To discuss and resolve inconsistencies in WRKY gene nomenclature, the rice WRKY working groupwas established and redefined the nomenclature. This report announces the conclusion.

Keywords

Gene nomenclature WRKY family gene rice

Since 2004, when whole genome sequences of rice were made publically accessible (Goff et al. 2002; Yu et al. 2002; IRGSP 2005; Yuan et al. 2003, 2005), the number of articles on new rice genes, including genome-wide studies of rice gene families, has increased remarkably. Although vigorous research activity is promising, the conflicts with regard to the duplication of gene names in journal articles can occur. Therefore, the CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative) published the "Gene Nomenclature System for Rice" in 2008 (CGSNL 2008) and encouraged researchers to follow the nomenclature rules before publication of their results.

The WRKY family is one of the largest families of transcription factors in higher plants and WRKY genes have key roles in plant development and responses to environmental stresses (see Rushton et al. 2010 and Chen et al. 2011 for recent reviews). Recently, the CGSNL surveyed genes in the rice WRKY family in published journal articles and found several duplicated gene names (Additional file 1: Table S1). Several reasons account for such duplications. For example, if two research groups independently performed their studies and submitted the results to different journals at the same time, neither group would be aware of the results of the other research group until the studies were published. In some cases, a sequence in the DNA data banks and/or in the genome databases was updated after the publication of a study, and only the older version of the sequence contained the WRKY domain, indicating that the gene became obsolete (retired from new gene list, e.g. WRKY78 in Additional file 1: Table S1). Hence, researchers would not be able to find the original sequence of that gene in the database. Alternatively, a researcher might name a new gene by placing a prefix "Os (Oryza sativa)" followed by the name of the orthologous Arabidopsis gene, and another researcher might name the same new gene according to the rice nomenclature rule; this would cause the new gene to have two or more different names. Moreover, if an obsolete gene name was reused for a new gene by other researchers, it might lead to confusion. In a remarkably rapidly advancing field of research, although such conflicts are apt to happen, it may mislead researchers who attempt to utilize published but misused gene names.

To resolve the conflicts and confusion in WRKY gene names and symbols, the CGSNL established a rice WRKY-working group that includes corresponding authors (Qiu et al. 2004; Zhang et al. 2004; Wu et al 2005; Xie et al. 2005; Zhang and Wang 2005; Ryu et al. 2006; Ross et al. 2007; Berri et al. 2009), and redefined the gene names as CGSNL proposal main genes, as shown in Table S1. First, based on the CGSNL rules, the gene names were arranged in numerical order according to the date of publication and assigned gene names on the basis of the numerical order. To document the publication records, we started from Zhang et al. (2004) as this is the first publication on rice WRKY family genes (numbered from 1 to 77). The second paper, Qui et al. (2004), published 97 WRKY genes. Based on our investigation, WRKY38, -44, -59, -63, and WRKY78 to -97 were novel genes. Hence, new numbers were assigned for WRKY38, -44, -59, and -63 because these numbers have been already used. In such a way, we have examined publications in chronological order and assigned new numbers when necessary. Columns B and C show the locus numbers recently provided by RAP and MSU (TIGR), respectively. Blanks in these columns mean obsolete genes, unannotated genes, or genes present only in the indica subspecies. We stress here that the objective of this proposal is to resolve the nomenclature of published gene names, but not to review if a specified gene is a bona fide WRKY gene or not. Also, it is very likely that the genome sequence will be updated going forward. Therefore, the naming system proposed here needs to be revised in the future.

Table S1 lists the gene names as per this convention for the rice WRKY gene family members. We request authors utilize this gene nomenclature and bring to our attention any concerns if a gene name has not been allocated according to its first reported instance. We hope that all researchers will submit new gene names through the online submission system (http://www.shigen.nig.ac.jp/rice/oryzabase_submission/gene_nomenclature/) prior to publishing their results and add a sentence in future publications. For example, "WRKY genes in the present study are named according to the CGSNL nomenclature" as part of either the footnote, acknowledgements and/or methods section as deemed fit by the journal publishers. We hope that this practice will become generally acceptable to the scientific community. We also request that journal editors discourage authors from publishing duplicate names for the same genes by encouraging authors to register and/or confirm their gene names and symbols by contacting the CGSNL via the online portal. Your cooperation will greatly contribute to a productive research progress and consistency in reporting.

List of abbreviations

RAP: 

Rice Annotation Project

TIGR: 

The Institute for Genomic Research

MSU: 

Michigan State University.

Declarations

Acknowledgements

Qingxi J Shen - School of Life Sciences, University of Nevada, M/S 4004,4505 Maryland Parkway, Las Vegas, NV 89154, USA

Diqiu Yu - Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical BotanicalGarden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

Jong-Seong Jeon, Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea

Pietro Piffanelli, Pamela Abbruscato - Rice GenomicsUnit, Parco Tecnologico Padano, Via Einstein Loc. Cascina Codazza, 26900 Lodi, Italy

Ze-Jian Guo - College of Agronomy and Biotechnology, China Agricultural University, Beijing 100094, PR China

Yuanji Zhang - Monsanto Company, Chesterfield Village Research Center, 700 Chesterfield Parkway North, Chesterfield, MO 63017

Takeshi Itoh, Sung Shin Lee - Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

C Robin Buell - Department of Plant Biology, Michigan State University, East Lansing MI 48824, USA

Yasuo Nagato - Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo 113-0032, Japan; Susan McCouch - Department of Plant Bredding & Genetics, Cornell University, Ithaca, New York, USA

Masahiro Yano - National Institute of Agrobiological Sciences, 1-2 Ohwashi, Tsukuba, Ibaraki 305-8634, Japan; Guo-liang Wang - Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210, USA

Kshirod K Jena - Plant Breeding, Genetics and Biotechnology Division, The International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

Lizhong Xiong - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China

Blake Meyers - Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711, USA

Pankaj Jaiswal - Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA

Yukiko Yamazaki - Center for Genetic Resource Information, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.

References

  1. Berri S, Abbruscato P, Faivre-Rampant O, Brasileiro AC, Fumasoni I, Satoh K, Kikuchi S, Mizzi L, Morandini P, Pè ME, Piffanelli P: Characterization of WRKY co-regulatory networks in rice and Arabidopsis. BMC Plant Biol 2009, 9: 120. 10.1186/1471-2229-9-120PubMed CentralView ArticlePubMedGoogle Scholar
  2. CGSNL: Gene Nomenclature System for Rice. Rice 2008, 1: 72–84. 10.1007/s12284-008-9004-9View ArticleGoogle Scholar
  3. Chen L, Song Y, Li S, Zhang L, Zou C, Yu D: The role of WRKY transcription factors in plant abiotic stresses. Biochim Biophys Acta 2012. doi:10.1016/j.bbagrm.2011.09.002 doi:10.1016/j.bbagrm.2011.09.002Google Scholar
  4. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002,296(5565):92–100. 10.1126/science.1068275View ArticlePubMedGoogle Scholar
  5. IRGSP: The map-based sequence of the rice genome. Nature 2005,436(7052):793–800. 10.1038/nature03895View ArticleGoogle Scholar
  6. Qiu Y, Jing S, Fu J, Li L, Yu D: Cloning and analysis of expression profile of 13 WRKY genes in rice. Chinese Science Bulletin 2004,49(20):2159–2168.Google Scholar
  7. Ross CA, Liu Y, Shen QJ: The WRKY Gene Family in Rice (Oryza sativa). J Int Plant Biol 2007,49(6):827–842. 10.1111/j.1744-7909.2007.00504.xView ArticleGoogle Scholar
  8. Rushton PJ, Somssich IE, Ringler P, Shen QJ: WRKY transcription factors. Trends in Plant Science 2010,15(5):247–258. 10.1016/j.tplants.2010.02.006View ArticlePubMedGoogle Scholar
  9. Ryu HS, Han M, Lee SK, Cho JI, Ryoo N, Heu S, Lee YH, Bhoo SH, Wang GL, Hahn TR, Jeon JS: A comprehensive expression analysis of the WRKY gene superfamily in rice plants during defense response. Plant Cell Rep 2006,25(8):836–47. 10.1007/s00299-006-0138-1View ArticlePubMedGoogle Scholar
  10. Wu KL, Guo ZJ, Wang HH, Li J: The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res 2005,12(1):9–26. 10.1093/dnares/12.1.9View ArticlePubMedGoogle Scholar
  11. Xie Z, Zhang ZL, Zou X, Huang J, Ruas P, Thompson D, Shen QJ: Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiol 2005,137(1):176–89. 10.1104/pp.104.054312PubMed CentralView ArticlePubMedGoogle Scholar
  12. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, et al.: A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002,296(5565):79–92. 10.1126/science.1068037View ArticlePubMedGoogle Scholar
  13. Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR: The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res 2003,31(1):229–33. 10.1093/nar/gkg059PubMed CentralView ArticlePubMedGoogle Scholar
  14. Yuan Q, Ouyang S, Wang A, Zhu W, Maiti R, Lin H, Hamilton J, Haas B, Sultana R, Cheung F, Wortman J, Buell CR: The institute for genomic research Osa1 rice genome annotation database. Plant Physiol 2005,138(1):18–26. 10.1104/pp.104.059063PubMed CentralView ArticlePubMedGoogle Scholar
  15. Zhang Y, Wang L: The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol Biol 2005, 5: 1. 10.1186/1471-2148-5-1PubMed CentralView ArticlePubMedGoogle Scholar
  16. Zhang ZL, Xie Z, Zou X, Casaretto J, Ho TH, Shen QJ: A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol 2004,134(4):1500–13. 10.1104/pp.103.034967PubMed CentralView ArticlePubMedGoogle Scholar

Copyright

© Shen et al; licensee Springer. 2012

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.