*2.4. Transcriptome Profiles of Mycorrhizal and Non-Mycorrhizal A. roxburghii*

The expression profiles of M and NM grown for six months were also analyzed using RNA-sequencing (RNA-seq). The Q20 and Q30 base percentages were greater than or equal to 97.79% and 93.61%, respectively (Table 1). The GC contents of the M and NM were in the range of 48.10–49.06% and 47.93–48.43%, respectively (Table 1). Compared with the control group, 4341 genes were shown to be differentially expressed, including 2915 upregulated genes and 1426 downregulated genes.


**Table 1.** Summary of the analysis of transcriptome sequences from the NM and M growth for six months.

NM: represents non-mycorrhizal *A. roxburghii*; M: represents mycorrhizal *A. roxburghii.*

Genes with |log2(fold change)| > 1 and *q* < 0.001 were defined as differentially expressed genes (DEGs). To further understand the functions of DEGs and the related biological processes they have a role in, gene ontology (GO) and KEGG analyses were conducted. The GO analysis classified DEGs into three categories: "molecular function", "cellular component", and "biological process" with a total of 45 GO terms (Figure 4A). The enriched GO terms were "binding" and "catalytic activity" within molecular function, "cell part", "cell", and "organelle" within cellular component and "cellular process", "metabolic process", and "response to stimulus" within biological process. The pathway enrichment analysis of the DEGs using KEGG identified significantly enriched "metabolic pathways" and "biosynthesis of secondary metabolites" (Figure 4B). As a result, the transcription analysis also showed that mycorrhizal fungus AR2 significantly affected the metabolic pathways in *A. roxburghii*.

**Figure 4.** The classification column of GO and KEGG from the DEGs between the NM and M growth for six months. (**A**) GO classification of DEGs. The x-axis represents the secondary GO item. The y-axis represents the proportion of the DEGs in the total number of DEGs. The labels above the columns is the number and proportion of DEGs of this GO item. (**B**) KEGG classification of DEGs. The x-axis represents the name of KEGG pathway. The y-axis represents the proportion of genes annotated to the pathway in the total of annotated genes. The labels above the columns represent the classification of KEGG pathway.
