Figure 1.
G-type Barbarea vulgaris and samples used for transcriptome sequencing.
A. Plant status. A whole plant and leaf samples are shown before the experiment (left) and 1, 4, 8, 12, 24, and 48 h after being infested by Plutella xylostella (right), respectively. B. Sketch showing sampling times.
Table 1.
Sequence and assembly summary of Barbarea vulgaris transcriptomes.
Figure 2.
Gene Ontology distribution of functional categories of genes in the transcriptome of Barbarea vulgaris.
Figure 3.
COG function classification of the Barbarea vulgaris transcriptome.
Figure 4.
Heatmap of overall changes in the Barbarea vulgaris transcriptome in response to Plutella xylostella.
The color scales represent the log2-transformed reads per kilobases per million reads ratios of plants 1, 4, 8, 12, 24, and 48 h after diamondback moth herbivory compared with the uneaten. The inset (upper left) shows the color bar. The trees on the left were generated using Cluster 3.0.
Table 2.
Summary of differentially expressed genes in Barbarea vulgaris herbivorized by Plutella xylostella.
Figure 5.
Distribution of differentially expressed genes in Barbarea vulgaris based on Gene Ontology functional categories.
The differentially expressed genes are those displaying a more than twofold change with a false discovery rate less than 10−3 in at least one time point.
Figure 6.
Heatmap of differentially expressed transcription factors in Barbarea vulgaris herbivorized by Plutella xylostella.
The transcription factor-encoding genes were retrieved from the annotated Gene Ontology. The heatmap shows genes that are differentially expressed in at least three time points. The color bar is shown at the upper right. Gene IDs and names are on the right (see Table S1 for detailed gene information).
Figure 7.
Heatmap of differentially expressed phytohormone and immune-related genes in Barbarea vulgaris herbivorized by Plutella xylostella.
Genes involved in metabolism, signal transduction, and responses to phytohormone signaling were identified based on their annotated Gene Ontology categories. Genes differentially expressed in at least three time points were used to generate the heatmap. The color bar is at the upper right. Gene IDs and names are on the right (see Table S1 for detailed gene information).
Figure 8.
Heatmap of differentially expressed secondary metabolism pathway genes in Barbarea vulgaris herbivorized by Plutella xylostella.
Genes involved in the secondary metabolic pathways of terpenoids, glucosinolates, and phenylpropanoids were isolated based on their Gene Ontology annotations. Genes differentially expressed in at least three time points were used to generate the heatmap. The color bar is at the upper right. Gene IDs and names are on the right (see Table S1 for detailed gene information).
Figure 9.
Differentially expressed genes potentially involved in the triterpene saponin synthetic pathway in Barbarea vulgaris.
Heatmaps represent relative expression levels of different genes/families determined by RNA-seq. The color bar is at the top right. Data represent log2 scale ratios of reads per kilo bases per million reads of plants treated 1, 4, 8, 12, 24, and 48 h after DBM feeding compared with non-feeding controls. The cytochrome P450 (P450) and glycosyltransferase (GT) families were analyzed using Cluster 3.0. HMG-CoA, 3-hydroxy-3-methylglutaryl CoA; MVA, mevalonic acid; MVAP, mevalonic acid 5-phosphate; PMVK, phosphomevalonate kinase; MVD, MVA diphosphate decarboxylase; G3P, glyceraldehyde 3-phosphate; DOXP, deoxy-D-xylulose 5-phosphate; MEP, 2-C-methyl-D-erythritol 4-phosphate; CMS, 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase; CDP-ME, 4-diphosphocytidyl-2-C-methylerythritol; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; CDP-MEP, 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; MCS, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; MEcPP, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate; HMB-PP, hydroxy-2-methyl-2-diphosphate; IPP, isopentenyl diphosphate; DMAPP, dimethylallyl diphosphate; GPS, geranylgeranyl pyrophosphate synthase; FPS, farnesyl pyrophosphate synthase; GPP, geranyl diphosphate; FPP, farnesyl diphosphate; SS, squalene synthase; SE, squalene epoxidase; 2,3-OSCs, 2,3-oxidosqualene cyclases; β-AS, β-amyrin synthase.
Figure 10.
Neighbor-joining bootstrap tree of CYP450 proteins in plants.
Amino acid sequences of 148 plant cytochrome P450s (CYPs), including 105 sequences representative of the 10 CYP families in land plant and 41 P450s from the B. vulgaris transcriptome (marked with dots), were used to construct the phylogenetic tree. Multiple alignments were performed with Clustal W, and the tree was generated with MEGA 5. The 10 CYP clades are labeled. Bootstrap values are shown at the nodes. Al, Arabidopsis lyrata; As, Avena strigosa; At, Arabidopsis thaliana; Bs, Berberis stolinifera; Cj, Coptis japonica; Ct, Catharanthus roseus; El, Euphorbia lagascae; Gu, Glycyrrhiza uralensis; Lj, Lotus japonicas; Me, Manihot esculenta; Mi, Micromonas pusilla; Mt, Medicago truncatula; Nt, Nicotiana tabacum; Os, Oryza sativa; Ph, Petunia hybrida; Po, Populus trichocarpa; Pp, Physcomitrella patens; Pt, Pinus taeda; Py, Pyrus communis; Sb, Sorghum bicolor; Sm, Selaginella moellendorffii; Ta, Triticum aestivum; Tm, Triglochin maritime; Vs, Vicia sativa; Zm, Zea mays.
Figure 11.
Neighbor-joining bootstrap tree of UGT proteins.
The PROSITE consensus sequence of the 11 significantly up-regulated Barbarea vulgaris UGTs transcripts (red), as well as 41 UGTs representative of the Arabidopsis genome (black) and six reported to be involved in saponin biosynthesis (blue), were used to construct the phylogenetic tree. Multiple alignments were performed with Clustal W, and the tree was generated with MEGA 5. Bootstrap values above 50% are shown at the nodes.
Figure 12.
Venn diagram showing unique and shared gene families in five crucifer species.
Table 3.
Comparison of transcriptome data in five crucifer species.
Table 4.
Functional distribution of Barbarea vulgaris-specific genes responded to diamondback moth herbivory.
Figure 13.
Comparison of real-time RT–PCR and RNA sequencing expression data.
Eight secondary metabolic genes with different expression patterns were analyzed for RNA abundance using real-time RT–PCR. The relative expression levels in RNA sequencing (solid lines) were determined as the ratio of the reads per kilo bases per million reads of samples of Barbarea vulgaris 1, 4, 8, 12, 24, and 48 h after continuous herbivory by Plutella xylostella relative to the non-herbivorized control. Real-time RT–PCR results (dotted lines) were calculated with 2−ΔΔCT using similarly-treated samples. Gene IDs and names are labeled on each panels (see Table S1 for detailed gene information).