Transcriptome analysis of WRKY gene family in Oryza officinalis Wall ex Watt and WRKY genes involved in responses to Xanthomonas oryzae pv. oryzae stress

Abstract

Oryza officinalis Wall ex Watt, a very important and special wild rice species, shows abundant genetic diversity and disease resistance features, especially high resistance to bacterial blight. The molecular mechanisms of bacterial blight resistance in O. officinalis have not yet been elucidated. The WRKY transcription factor family is one of the largest gene families involved in plant growth, development and stress response. However, little is known about the numbers, structure, molecular phylogenetics, and expression of the WRKY genes under Xanthomonas oryzae pv. oryzae (Xoo) stress in O. officinalis due to lacking of O. officinalis genome. Therefore, based on the RNA-sequencing data of O. officinalis, we performed a comprehensive study of WRKY genes in O. officinalis and identified 89 OoWRKY genes. Then 89 OoWRKY genes were classified into three groups based on the WRKY domains and zinc finger motifs. Phylogenetic analysis strongly supported that the evolution of OoWRKY genes were consistent with previous studies of WRKYs, and subgroup IIc OoWRKY genes were the original ancestors of some group II and group III OoWRKYs. Among the 89 OoWRKY genes, eight OoWRKYs displayed significantly different expression (>2-fold, p<0.01) in the O. officinalis transcriptome under Xoo strains PXO99 and C5 stress 48 h, suggesting these genes might play important role in PXO99 and C5 stress responses in O. officinalis. QRT-PCR analysis and confirmation of eight OoWRKYs expression patterns revealed that they responded strongly to PXO99 and C5 stress 24 h, 48 h, and 72 h, and the trends of these genes displaying marked changes were consistent with the 48 h RNA-sequencing data, demonstrated these genes played important roles in response to biotic stress and might even involved in the bacterial blight resistance. Tissue expression profiles of eight OoWRKY genes revealed that they were highly expressed in root, stem, leaf, and flower, especially in leaf (except OoWRKY71), suggesting these genes might be also important for plant growth and organ development. In this study, we analyzed the WRKY family of transcription factors in O.officinalis. Insight was gained into the classification, evolution, and function of the OoWRKY genes, revealing the putative roles of eight significantly different expression OoWRKYs in Xoo strains PXO99 and C5 stress responses in O.officinalis. This study provided a better understanding of the evolution and functions of O. officinalis WRKY genes, and suggested that manipulating eight significantly different expression OoWRKYs would enhance resistance to bacterial blight.

Genome-Wide Identification of WRKY Transcription Factors in the Asteranae

“…Group Ib includes CcWRKY25 and HaWRKY67 genes. Previous studies have reported the presence of group Ib in some monocotyledonous plants; for example, eight WRKY genes found in rice, six in O. officinalis Wall ex Watt, and one ( PheWRKY61 ) in moso bamboo [9,24,31]. The only WRKY genes in group Ib uncovered in our study were in globe artichoke and sunflower (all dicotyledonous plants).…”

“…Although CcWRKY25 and HaWRKY67 genes fell into group III in the phylogenetic tree, they contain two WRKY domains and thus belong to group I. Group Ib has arisen from group III via the duplication of WRKY genes [19]; this WRKY transcription factor’s evolutionary patterns has also been confirmed in wild rice [31]. Although PgWRKY42 and PgWRKY122 of ginseng cannot be classified into any of the three groups in the phylogenetic tree, they cluster with group I and may have originated through the loss of the WRKY domain during the course of evolution.…”

“…Two, one, five, and two tandem clusters (gene clusters) were found in globe artichoke, carrot, sunflower, and lettuce, respectively. Gene clusters have been found in radish, O. officinalis , and other species [31,45]. Duplicated genes may have different expressions.…”

WRKY transcription factors: evolution, binding, and action

“…Members in group II have a CX 5 CX 23 HXH zinc finger motif, except subgroup IIc, which has a CX 4 CX 23 HXH zinc finger that is the same as that in the C-terminal WD (CTWD) of group I WRKY proteins. The subgroup IIc members can be clustered into separated clades, in which the ancient IIc clade neighbors the CTWD clade (Xu et al 2016;Jiang et al 2017b), suggesting a close evolutionary relationship between genes in group I and subgroup IIc. Subgroup IIc has also been proposed to be a separate group by Zhang and Wang (2005) or subgroup Ib by Wu et al (2005).…”

“…Subgroup IIc has also been proposed to be a separate group by Zhang and Wang (2005) or subgroup Ib by Wu et al (2005). In addition to variations in zinc finger motifs, mutations in the consensus WRKYGQK sequence often appear in various plant species, and frequently observed variants include WRKYGKK and WRKYGEK (Wu et al 2005;Yao et al 2015;Jiang et al 2017b;Yang et al 2017;Song et al 2018).…”