## 3 Results
### Manipulating FaHMGR Expression Caused Changes in Strawberry Transcription and Metabolism
Principal component analysis (PCA) was employed to evaluate the overall metabolic differences between samples (Figure 7A,D), revealing thatHMGROE was more closely related to HMGRC than to HMGRR. In positive ion mode, 63 differential metabolites were common to both HMGROE vs. HMGRC and HMGRR vs. HMGRC. Additionally, 70 and 128 unique metabolites were identified in each pairwise comparison, respectively (Figure 7B,E). In the negative ion mode, 30 differential metabolites were shared in the two pairs, with 34 and 70 metabolites uniquely present in each. Further analysis showed that in HMGROE vs. HMGRC, 20 differential metabolites were upregulated and 52 were downregulated in negative ion mode, while 133 were upregulated and 131 were downregulated in positive ion mode. For HMGRR vs. HMGRC, 116 differential metabolites were upregulated and 115 were downregulated in negative ion mode, while 191 were upregulated and 189 were downregulated in positive ion mode. KEGG pathway analysis indicated that most metabolites mapped to the item \"Global and overview maps\", with four specific substances associated with the \"Metabolism of terpenids and polyketides\" pathway in both negative and positive ion modes (Figure 7C,F). Figure 5: Differentially expressed genes (DEGs) in strawberries after the overexpression and suppression of _FaHMGR_ in strawberry fruits. (**A**). Principal component analysis (PCA) scatter plot of transcriptomic profiles from different samples. (**B**). Correlation coefficient graph showing the relationships among all samples, demonstrating the degree of similarity in gene expression profiles. (**C**). Venn diagram illustrating the number of DEGs in comparison pairs HMGROE vs. HMGRC and HMGRR vs. HMGRC. (**D**). Expression patterns of DEGs. The \(Y\)-axis represents the \(p\)-value and the \(X\)-axis represents samples. KEGG analysis of differentially accumulated metabolites (DAMs) identified 30 enriched pathways in HMGROE vs. HMGRC, with significant enrichment in the phenylpropanol biosynthesis pathway (\(p\) value = 0.029) (Table S7). It is worth noting that the DEGs were enriched in the diterpenoid biosynthesis pathway (\(p\) value = 0.228), indicating that _HMGR_ overexpression caused DAMs to decrease and affected terpenoid metabolism. For HMGRR vs. HMGRC, 56 pathways were enriched, including ubiquinone and other terpenoid-quinone biosynthesis pathways (\(p\) value = 0.500), with specific metabolites such as shikonin linked to the HMGR metabolic pathway. This group was also enriched in the anthocyanin biosynthesis pathway (\(p\) value = 0.126), involving metabolites like keracyanin and pelargonidin, which is likely one reason for the enhanced coloration in strawberries under  
Figure 6: Gene Ontology (GO) categories (**A**) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis (**B**) of significantly enriched DEGs in the comparisons HMGRR vs. HMGRC and HMGOE vs. HMGRC. the HMGRR condition. Notably, both HMGROE vs. HMGRC and HMGRR vs. HMGRC were enriched in methyl jasmonate-related pathways, including alpha-linolenic acid metabolism and plant hormone signal transduction (_p_ value = 0.500). Figure 7: Differentially accumulated metabolites (DAMs) in negative and positive ion modes (NEG, POS) in strawberries after the overexpression and suppression of _FaHMGR_ in fruits. (**A**,**D**). PCA analyses in NEG and POS. Quality control (QC) was an equivalent standard to evaluate the stability and signal response strength of the instrument during metabolite detection. (**B**,**E**). Venn diagrams and volcano maps illustrating the differential metabolites and their quantities. (**C**,**F**). Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation of identified metabolites in samples.