Fig 1.
Phylogenetic relationships of the 60 species investigated in the present study.
Phylogenetic relationships (branch lengths are arbitrary) among these species have been described previously (http://www.phytozome.net/). The total number of cytochrome P450 93 (CYP93) proteins identified in each genome is indicated on the right.
Fig 2.
Phylogenetic tree and classification of 214 plant CYP93 proteins.
The neighbor joining (NJ) tree includes 214 CYP93 proteins from 60 eukaryotes. Proteins are clustered into eight subfamilies (e.g., CYP93A). The colored lines and names symbolize the species to which the proteins in each clade belong. The black dots represent the major clades in the phylogenetic tree, and the corresponding bootstrap support values from 1000 replications are shown beside the black dots. Bootstrap values <50% are shown as black circles, and those >50% are shown as black dots in the phylogenetic tree. The numbers in brackets indicate the dN/dS value for each subfamily or branch. The information of species abbreviations used for the tree of Fig 2 is listed in S2 Table. The scale bar represents amino acid substitutions per site.
Fig 3.
Sequence logos of the multiple alignments of the 214 CYP93 proteins in plants.
The sequence logos of plant CYP93 proteins based on amino acid alignment using MAFFT are shown. The logos were generated using Weblogo. The bit score indicates the information content for each position in the sequence. The height of the letter designating the amino acid residue at each position represents the degree of conservation. The key conserved motifs are underlined; the red lines indicate the less conserved regions; the black ones, the P450 motifs; and the blue ones, the substrate recognition sites (SRSs). The white triangles indicate the conserved intron insertion location of plant CYP93 genes; the numbers within the triangles indicate the splicing phase of the intron (0 refers to phase 0). The red and black dots indicate the conserved amino acid insertion or deletion sites, respectively, in a given subfamily and/or clade; the number below each dot indicates the corresponding subfamily, i.e., B indicates the CYP93B subfamily.
Fig 4.
Architecture of conserved protein motifs in the eight subgroups of the plant CYP93 family.
The sequence logos of the P450 transmembrane, I-helix, K-helix, PERF, and heme-binding motifs based on the amino acid alignments are shown. The bit score indicates the information content for each position in the sequence. A−K indicate subfamilies CYP93A−CYP93K.
Fig 5.
Weblogo of SRSs based on the amino acid alignments across the eight subgroups of the plant CYP93 family.
The bit score indicates the information content for each position in the sequence. A−K indicate subfamilies CYP93A−CYP93K.
Fig 6.
Expression profiles of CYP93 homologous genes in Arabidopsis, soybean, rice, and maize.
(A) Expression profiles of the AtCYP93D1 gene in Arabidopsis. (B) and (C) expression profiles of GmCYP93 genes in soybean expression dataset1[46] and dataset2[47]. (D) and (E) expression profiles of OsCYP93 genes in rice expression dataset1 (GSE14304) and dataset2 (GSE19024)[31]. (F) expression profiles of ZmCYP93 genes in maize[48]. Color bar at the base represents log2 expression values.
Fig 7.
qRT-PCR analyses of the expression profiles of CYP93 homologous genes in Arabidopsis, soybean, rice, and maize.
(A) Expression profiles of CYP93 genes in soybean. (B) Expression profiles of the AtCYP93D1 gene in Arabidopsis. (C) Expression profiles of CYP93 genes in maize. (D) Expression profiles of CYP93 genes in rice.
Fig 8.
Expression profiles of plant CYP93 genes in response to abiotic stresses.
(A) Expression profiles of AtCYP93 and representative P450 genes in response to abiotic stresses. (B) Expression profiles of eight probe sets representing eight soybean CYP93 genes based on four microarray datasets of abiotic stresses. (C) Expression profiles of rice CYP93 genes based on four microarray datasets of abiotic stresses. Color bar at the base represents log2 expression values.
Fig 9.
Expression profiles of GmCYP93 genes in response to biotic stresses.
(A) Expression profiles of GmCYP93 genes after infection with root-knot nematode (GSE33410). (B) Expression profiles of GmCYP93 genes after infection with Phytophthora sojae (GSE9687). (C) Expression profiles of GmCYP93 genes after aphid infestation (GSE35427). Color bar at the base represents log2 expression values.
Table 1.
Summary of functionally characterized CYP93 genes in plants.