WRKY gene family evolution in Arabidopsis thaliana

Abstract

The Arabidopsis thaliana WRKY proteins are characterized by a sequence of 60 amino acids including WRKY domain. It is well established that these proteins are involved in the regulation of various physiological programs unique to plants including pathogen defense, senescence and response to environmental stresses, which attracts attention of the scientific community as to how this family might have evolved. We tried to satisfy this curiosity and analyze reasons for duplications of these gene sequences leading to their diversified gene actions. The WRKY sequences available in Arabidopsis thaliana were used to evaluate selection pressure following duplication events. A phylogenetic tree was constructed and the WRKY family was divided into five sub-families. After that, tests were conducted to decide whether positive or purified selection played key role in these events. Our results suggest that purifying selection played major role during the evolution of this family. Some amino acid changes were also detected in specific branches of phylogeny suggesting that relaxed constraints might also have contributed to functional divergence among sub-families. Sites relaxed from purifying selection were identified and mapped onto the structural and functional regions of the WRKY1 protein. These analyses will enhance our understanding of the precise role played by natural selection to create functional diversity in WRKY family.

The Beet Cyst Nematode Heterodera schachtii Modulates the Expression of WRKY Transcription Factors in Syncytia to Favour Its Development in Arabidopsis Roots

“…Arabidopsis contains 66 WRKY genes [45] with 59 represented by the ATH1 GeneChip. Of these, 6 were up-regulated in syncytia as compared to control root segments (Table 1).…”

“…Further information is available in the online methods (File S1). Tests were restricted to the 59 WRKY genes included on the GeneChip representing most of the 66 genes recognised by Wang et al [45] and containing the originally described WRKY gene subgroups [16]. This considerably increased the statistical power of the testing procedure as it reduces the necessary correction for massive multiple testing.…”

Chrysanthemum WRKY gene CmWRKY17 negatively regulates salt stress tolerance in transgenic chrysanthemum and Arabidopsis plants

“…Since Ishiguro and Nakamura isolated the first WRKY gene, SPF1, from Ipomoea batatas in 1994 (Ishiguro and Nakamura 1994), an increasing number of WRKY genes have been identified from a diverse variety of plants (Abbruscato et al 2012;Atamian et al 2012;Borrone et al 2004;Guo et al 2011;Zheng et al 2011;Lagacé and Matton 2004;Liu et al 2012;Marè et al 2004;Niu et al 2012;Pan et al 2009;Park et al 2006). Over 70 and 100 members of the family are known in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), respectively (Agarwal et al 2011;Kalde et al 2003;Wang et al 2011). On the basis of the primary structure, WRKY proteins have been classified into three groups (I, II, and II) and various subgroups (Eulgem et al 2000).…”

Novel Genomic and Evolutionary Insight of WRKY Transcription Factors in Plant Lineage

“…The WRKY TF gene family from various plant species, including A. thaliana 476, B. distachyon 14, G. raimondii 46, O. sativa 48, S. lycopersicum 51, T. aestivum 52 has been well elucidated. Surprisingly, when we combined the data from several published reports, none of them were found to be correlated with one another (Table 8).…”