## 2 Results
### A Transcriptome Atlas of Finger Citron  
In an attempt to understand the changes in gene expression causing metabolite diversity during development, we sequenced the RNA libraries extracted from flower, leaf and fruit. Information about RNA-Seq quality is summarized in Table S2. The correlation coefficients of tested samples were listed in Figure S2. The correlation of the three biological replicates is above 0.7, with false discovery rate (FDR) value \(<\) 0.01 indicating the reliability of sampling. The relatively low correlation between organs indicates a selectively expression pattern of finger citron genes. A total of 1.5G clean data was generated, 95.80% of which was successfully mapped to the reference genome of C. medica. We assembled 32,579 genes, which were expressed in finger citron. For functional annotation, unigenes were searched against the Gene Ontology (GO) knowledgebase and the Kyoto encyclopedia of genes and genomes (KEGG). About 76% of the unigenes were assigned to GO terms and 42% of them were annotated with KEGG entries. This information establishes the foundation for further investigation into target genes. Fragments per kilobase of exon model per million mapped reads (FPKM) values were calculated to represent gene expression levels and the gene number and FPKM distribution are summarized in Figure S3. Most genes were expressed in the 0.3-3.57 and 3.57-15 intervals (Figure S3). In general, flowers had the most genes expressed and fruit had the least. As mentioned above, plant terpenids are synthesized from two independent pathways and the upstream genes and their functions are well studied [2]. Hence, we screened key structural genes involved in terpene biosynthesis by KEGG annotation. The values of their expression fold changes are listed in Table 1. \begin{table}
\begin{tabular}{l l c c c c c} \hline \hline
**Gene ID** & **Gene Name** & **FC (F2/F1)** & **DEG** & **FC (L2/L1)** & **DEG** & **FC (S6/S1)** & **DEG** \\ \hline
**MEP Pathway** & & & & & & \\ Cm152440 & DXS & 1.21 & 0.49 & yes, down & 0.20 & yes, down \\ Cm165980 & DXS & 0.97 & 1.24 & & 0.12 & yes, down \\ Cm165990 & DXS & 1.42 & 2.03 & & 1.34 & \\ Cm219000 & DXS & 1.09 & 1.72 & & 1.32 & \\ Cm104830 & DXS & 0.88 & 2.08 & yes, up & 1.49 & \\ Cm018790 & DXR & 0.95 & 1.25 & & 0.93 & \\ Cm018780 & DXR & 1.43 & 0.86 & & 1.22 & \\ Cm191510 & MCT & 1.39 & 0.61 & & 0.90 & \\ Cm162030 & CMK & 1.34 & 0.88 & & 0.91 & \\ Cm015360 & MDS & 0.88 & 1.60 & & 2.53 & yes, up \\ Cm131750 & HDS & 1.20 & 2.67 & yes, up & 1.52 & \\ Cm315300 & HDR & 0.31 & - & & - & \\ Cm315660 & HDR & 0.24 & - & & - & \\ Cm219660 & HDR & 0.99 & 0.80 & & 0.42 & yes, down \\ Cm276630 & HDR & 1.41 & 2.10 & yes, up & 0.93 & \\ Cm318240 & HDR & 1.05 & - & & 0.61 & \\
**MVA Pathway** & & & & & & \\ Cm183050 & AACT & 0.92 & 1.03 & & 1.28 & \\ Cm042040 & AACT & 1.04 & 0.60 & & 2.90 & yes, up \\ Cm014300 & HMGS & 1.17 & 0.82 & & 1.24 & \\ Cm248930 & HMGS & 0.98 & 0.38 & yes, down & 1.47 & \\ Cm197870 & HMGR & 0.93 & 0.91 & & 1.42 & \\ Cm212470 & HMGR & 0.72 & 0.86 & & 0.66 & \\ Cm122170 & HMGR & 1.56 & 0.33 & yes, down & 5.51 & yes, up \\ Cm268880 & MVK & 1.23 & 0.97 & & 0.55 & \\ Cm034040 & PMK & 1.10 & 0.52 & & 1.08 & \\ Cm235330 & MVD & 1.13 & & 0.55 & 0.65 & \\ \hline \hline \end{tabular}  
* Genes whose log2(FC) \(\geq\) 1 and \(p\)\(<\) 0.05 were considered as differentially expressed genes (DEGs). AACT, Acetoacetyl-CoA thiolase; HMGS, HMG, HMG-CoA reductase; MVK, mexulonate kinase; PMK, phosphomevalonate kinase; MVD, mexulonate diphosphate decarboxylase; FPPS, farnesyl diphosphate synthase; DXS, 1-deoxy-D-xylulose 5-phosphate synthase; DXR, 1-deoxy-D-xylulose 5-phosphate reductio isomerase; MCT, 4-diphosphocytidyl-2 C-methyl-D-erythitol synthase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythitol kinase; MDS, 2-C-methyl-D-erythitol 2.4-cyclodextrinphosphate synthase; HDS, 4-hydroxy-3-methylbut-2-enyl diphosphate synthase; HDR, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase.  
\end{table}