Genome-Wide Identification, Characterisation, and Evolution of the Transcription Factor WRKY in Grapevine (Vitis vinifera): New View and Update

Abstract

WRKYs are a multigenic family of transcription factors that are plant-specific and involved in the regulation of plant development and various stress response processes. However, the evolution of WRKY genes is not fully understood. This family has also been incompletely studied in grapevine, and WRKY genes have been named with different numbers in different studies, leading to great confusion. In this work, 62 Vitis vinifera WRKY genes were identified based on six genomes of different cultivars. All WRKY genes were numbered according to their chromosomal location, and a complete revision of the numbering was performed. Amino acid variability between different cultivars was assessed for the first time and was greater than 5% for some WRKYs. According to the gene structure, all WRKYs could be divided into two groups: more exons/long length and fewer exons/short length. For the first time, some chimeric WRKY genes were found in grapevine, which may play a specific role in the regulation of different processes: VvWRKY17 (an N-terminal signal peptide region followed by a non-cytoplasmic domain) and VvWRKY61 (Frigida-like domain). Five phylogenetic clades A-E were revealed and correlated with the WRKY groups (I, II, III). The evolution of WRKY was studied, and we proposed a WRKY evolution model where there were two dynamic phases of complexity and simplification in the evolution of WRKY.

Keywords: Vitis vinifera; WRKY transcription factor; genome-wide analyses; grape; grape cultivars; phylogeny.

Figure 1

The characterisation of the WRKY family of plant transcription factors. The investigation of the influence of abiotic and biotic factors on WRKY TF expression (A). The distribution of WRKY gene number in different plant species (B) and WRKY protein length distribution (C) based on PlantTFDB database data.

Figure 2

The evolutionary relationship, exon-intron structure, and motif analysis of WRKY transcription factor family members in V. vinifera (a). The midpoint-rooted phylogenetic tree was constructed with the Maximum Likelihood (ML) method and the VT + F + R4 substitution model (on the left) based on the complete amino acid sequences. The different colours and letters (A–E) note the five phylogenetic groups; the letters with numbers indicate the subgroups. The accepted type of WRKY classification is indicated on the right (I, IIa–IIe, III). The yellow boxes represent exons, and lines represent introns (in the middle). All exon and intron lengths are drawn to scale. The 23 different coloured boxes represent diverse conserved motifs identified with MEME (on the right). The numbering of conservative motifs is noted below (b).

Figure 3

Chromosomal location of 62 genes of transcriptional factor WRKY on the nineteen grape chromosomes.

Figure 4

The topology of the phylogenetic tree associated with domain characteristics. The midpoint-rooted phylogenetic tree was constructed with the Maximum Likelihood (ML) method and the Q.plant + G4 substitution model based on the domain amino acid sequences. The different colours and letters (A–E) indicate the five phylogenetic groups according to Figure 2. The coloured boxes note the features of different groups of WRKY genes.

Figure 5

The analysis of length and gene structure. The distribution of VvWRKY protein length (A) and exon number (C) in grapevine. The mean values of protein length (B) and exon number (D) according to belonging to different phylogenetic clades and WRKY groups. The data are presented as mean ± SD.

Figure 6

The suggested evolutionary model of the WRKY transcriptional factor family according to the phylogenetic studies in grapevine.