Table 1.
List of the 58 RcWRKY genes identified in this study.
Fig 1.
Comparison of the WRKY domain sequences from 58 RcWRKY proteins.
WRKY..N/C represents the N or C-terminal WRKY domain of group I members, respectively. “-” has been inserted for the optimal alignment. Conserved amino acid residues are shown in gray and the highly conserved WRKYGQ/KK heptapeptide and C2H2/C and residues are indicated by “*”. The four β-strands are indicated by right arrows. For each (sub)group, the position of a conserved intron is indicated by a down arrow.
Fig 2.
Phylogenetic analysis of RcWRKY proteins with Arabidopsis and physic nut homologs.
The WRKY domains (WRKY..N/C representing the N and C-termini of group I members, respectively) extracted from deduced amino acid sequences were performed using MUSCLE and the phylogenetic tree adopting DdWRKY1C as an outgroup was constructed using bootstrap maximum likelihood tree (1000 replicates) method and MEGA6 software. The distance scale denotes the number of amino acid substitutions per site. The name of each (sub)group is indicated next to the corresponding group. Species and accession numbers are listed in Table 1 and S1 Table.
Fig 3.
Distribution of the 58 RcWRKY genes and their Arabidopsis and physic nut homologs in subgroups.
Fig 4.
Exon-intron structures of the 58 identified RcWRKY genes.
The graphic representation of the optimized gene models is displayed using GSDS.
Table 2.
Motif sequences of 58 RcWRKY proteins identified by the MEME tools.
Fig 5.
Structural and phylogenetic analysis of RcWRKY proteins.
The unrooted phylogenetic tree resulting from the full-length amino acid alignment of all the RcWRKY proteins is shown on the left side of the figure. The different colored balls at the bottom of the figure indicate different groups. The distribution of conserved motifs among the RcWRKY proteins is shown on the right side of the figure. Different motif types are represented by different color blocks as indicated at the bottom of the figure. The same color in different proteins indicates the same group or motif.
Fig 6.
Expression profiles of the 58 RcWRKY genes in leaf, flower, endosperm II/III, endosperm V/VI and seed.
Color scale represents RPKM normalized log2 transformed counts and red indicates low expression and yellow indicates high expression.