The large soybean (Glycine max) WRKY TF family expanded by segmental duplication events and subsequent divergent selection among subgroups

Abstract

BackgroundWRKY genes encode one of the most abundant groups of transcription factors in higher plants, and its members regulate important biological process such as growth, development, and responses to biotic and abiotic stresses. Although the soybean genome sequence has been published, functional studies on soybean genes still lag behind those of other species.ResultsWe identified a total of 133 WRKY members in the soybean genome. According to structural features of their encoded proteins and to the phylogenetic tree, the soybean WRKY family could be classified into three groups (groups I, II, and III). A majority of WRKY genes (76.7%; 102 of 133) were segmentally duplicated and 13.5% (18 of 133) of the genes were tandemly duplicated. This pattern was not apparent in Arabidopsis or rice. The transcriptome atlas revealed notable differential expression in either transcript abundance or in expression patterns under normal growth conditions, which indicated wide functional divergence in this family. Furthermore, some critical amino acids were detected using DIVERGE v2.0 in specific comparisons, suggesting that these sites have contributed to functional divergence among groups or subgroups. In addition, site model and branch-site model analyses of positive Darwinian selection (PDS) showed that different selection regimes could have affected the evolution of these groups. Sites with high probabilities of having been under PDS were found in groups I, II c, II e, and III. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean.ConclusionsIn this work, all the WRKY genes, which were generated mainly through segmental duplication, were identified in the soybean genome. Moreover, differential expression and functional divergence of the duplicated WRKY genes were two major features of this family throughout their evolutionary history. Positive selection analysis revealed that the different groups have different evolutionary rates. Together, these results contribute to a detailed understanding of the molecular evolution of the WRKY gene family in soybean.

Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)

“…The P -values of groups I and II, I and IV, II and IV, II and V were less than 0.05, reaching a significant level. To avoid the occurrence of false positives, we determined the sites of posterior probability (Qk) > 0.9 to be key amino acid sites leading to functional divergence according to previous research methods (Yin et al, 2013). The results showed there were significant type I functional differences in the 295th amino acid between I and II, in the 231st and 326th amino acid sites between I and IV, and in the 295th amino acid site between II and IV.…”

High‐Density Mapping of Resistance QTL Toward Phytophthora sojae, Pythium irregulare, and Fusarium graminearum in the Same Soybean Population

“…irregulare and F. graminearum compared with P. sojae. Many of these belonged to families that have previously been implicated in defense, such as WRKY transcription factors (Yin et al, 2013), which have previously been shown to be involved in the salicylic acid defense pathway and in salicylic acid-jasmonic acid cross talk both in Arabidopsis and in soybean (Euglem and Somssich, 2007;Liu et al, 2011). MYB transcription factors have also been shown to play a role in defense against the soybean rust pathogen Phakopsora pachyrhizi Syd.…”

The expression patterns of Cucumis sativus WRKY (CsWRKY) family under the condition of inoculation with Phytophthora melonis in disease resistant and susceptible cucumber cultivars

“…Since the first WRKY gene, SPF1, was cloned from sweet potato (Ishiguro and Nakamura 1994), a large number of WRKY genes were identified and characterized from different plant species, such as tobacco (Yang et al 1999;Chen and Chen 2000), Arabidopsis (Eulgem et al 2000;Dong et al 2003), parsley (Cormack et al 2002), barley (Sun et al 2003), rice (Xie et al 2005;Ross et al 2007), coffee (Ramiro et al 2010), cucumber (Ling et al 2011), poplar (He et al 2012), soybean (Yin et al 2013), physic nut (Xiong et al 2013), brachypodium distachyon (Wen et al 2014), and grape (Guo et al 2014).…”