Fig. 1

Leaf phenotype under glyphosate treatment"

Fig. 2

Shikimic acid accumulation under glyphosate treatment Different lowercase letters indicate significant difference (P<0.05)"

Table 1

Quality of the transcriptome data of each sample"

Fig. 3

Sample correlation and DEGs of tea plants under glyphosate treatment A: Correlation. B: The horizontal bar graph on the left represents the DEGs of each set. In the middle matrix, a single point represents the unique elements of a set, and the lines between points represent the unique intersection of different sets. In the vertical bar graph, the DEGs of corresponding intersection are respectively represented"

Fig. 4

KEGG enrichment analysis of DEGs The vertical axis represents the KEGG pathway enriched by multiple genes, the horizontal axis represents the Rich factor (the larger the Rich factor, the greater the degree of enrichment), the size of the dot represents the number of genes in this pathway, and the colors correspond to different ranges of P value"

Fig. 5

Phenylpropane, flavonoids and shikimic acid biosynthetic pathways and the expression levels of related DEGs The red border in the pathway indicates the DEGs annotated; the heat map indicates the expression level of all DEGS related to the pathway, which is generated by log2 conversion from the average value calculated by three repeated samples. The same as below"

Fig. 6

Phytohormone signal transduction pathway and the expression analysis of related DEGs A: The plant hormone signal pathway enriched by DEGs; B: The expression level of DEGs related to plant hormone signal transduction"

Fig. 7

Sample clustering, soft threshold screening and gene module construction A: The sample clustering tree; B: The scale-free fitness curve and the average connectivity curve; C: The gene clustering tree and module cutting, and each branch of the gene clustering tree corresponds to a module"

Fig. 8

Correlation analysis between modules and phenotypes The abscissa represents different phenotypes, and the ordinate represents different modules. The number in the left column of the figure represents the number of genes in the module, and each group of data on the right represents the r value of the correlation coefficient between the module and the phenotype and the significance P value (in parentheses). Red means the module has a greater correlation with the phenotype, and blue means the module has a lower correlation with the phenotype"

Fig. 9

KEGG enriched bubble diagram of green (A) and brown (B) module The vertical axis represents the name of the pathway, and the horizontal axis represents the rich factor; the size of the dot indicates the number of genes in the pathway, and the color of the dot corresponds to different P value ranges. The figure only shows the KEGG Pathway whose enrichment degree is in the top 20 under the premise of P-value<0.05"

Fig. 10

Gene co-expression network and hub genes in green (A) and brown (B) modules The triangle nodes are the top 3 genes in connectivity, and the black border nodes are transcription factor genes"

Fig. 11

Validation and correlation analysis of 15 DEGs Heat maps indicate the gene expression levels of RNA-Seq and qRT-PCR, respectively; the value between the two heat maps represents the correlation coefficient of the qRT-PCR and RNA-seq values of each gene"