## Results
### Analysis of DGE Libraries and Mapping  
Five libraries were constructed, and sequence analyses were conducted. Approximately 34.19 million raw reads were generated. Date evaluation of the GC percentage of the clean reads in the five DGE libraries was performed (Table 1). The GC percentages of five libraries range from 46.38 % to 47.57 %. The clean data sets are available at the NCBI SRA with the accession number: SRP073696.  
Subsequently, to elucidate the molecular events underlying the DGE profiles, all clean reads were aligned to the reference transcriptome of _L. cubeba_. The average percentage of reads mapped to the reference transcriptome was 89.16% for the five development periods, including mismatching and empty position. Furthermore, after excluding mismatching and empty position, the average percentage of reads mapped to the reference transcriptome was 63.85%. Using the number of reads per kilobase transcriptome per million mapped reads (RPKM) approach, the expression level of each gene was measured by reading the sequencing depth and gene length. The results showed that mRNAs  
\begin{table}
\begin{tabular}{c c c c c} \hline \hline \multirow{2}{*}{**Samples**} & **Read** & **GC Percentage** & **Total Mapped Reads 1** & **Uniquely Mapped Reads 2** \\  & **Number** & **(\%)** & **(Mapped Ratio \%)** & **(Mapped Ratio \%)** \\ \hline
60 DAF & 8,971, 349 & 46.38 & 7,845,525 (87.45) & 5,707,386 (63.62) \\
75 DAF & 8,196,825 & 47.57 & 7,349,267 (89.66) & 5,410,062 (66.00) \\
90 DAF & 8,531,708 & 47.26 & 7,557,873 (88.58) & 5,483,701 (64.27) \\
105 DAF & 9,268,559 & 47.50 & 8,387,997 (90.50) & 5,827,196 (62.87) \\
130 DAF & 8,194,664 & 47.31 & 7,346,494 (89.64) & 5,122,138 (62.50) \\ \hline \hline \end{tabular}  
* Total mapped reads: reads mapped to the reference transcriptome, including mismatching and empty positions; 2 Uniquely mapped reads: reads mapped to the reference transcriptome, excluding mismatching and empty positions.  
\end{table}
Table 1: Summary of DGE sequencing data and mapping results during different fruit development stages of _L. cubeba_.  
Figure 1: Changes in the concentration of citral and oil content at different developmental stages in _L. cubeba_. Citral concentration (**A**) and oil content (**B**) were measured during the fruit development. The means \(\pm\) SE are given. The different lower case letters (a–f) indicate significant differences \(p<\) 0.05). Identical letters indicate the absence of a significant difference and different letters indicate a significant difference.  
transcribed from the major types of genes were represented by low RPKM values, and only a small proportion of genes was highly expressed (Figure S1). For example, in the 60 DAF stage, the number high expression genes (RPKM > 100) accounted for approximately 1% of the total number of genes (Figure S1-A(1)), whereas the total RPKM values of these genes accounted for 50% of the RPKM values of all the genes (Figure S1-A(2)). In contrast, the number of genes with a lower expression level (RPKM was 0-5) accounted for approximately 60% of the total number of genes, whereas the total RPKM values of these genes accounted for approximately 8% of the RPKM values of all the genes. This expression pattern indicated the non-uniformity and redundancy of mRNA.  
To confirm whether the number of detected genes (RPKM \(\geq\) 1) increased proportionally to the total number of clean reads, sequencing data saturation analysis was performed. Figure 2 shows that the relative number of genes identified increased as the total tag number of tags for all the five libraries. The number of detected genes plateaued when it approached eight million.  
Figure 2: Saturation curve analysis of the digital gene expression tag libraries. (**A**)–(**E**) represents 60 DAF, 75 DAF, 90 DAF, 105 DAF and 135 DAF, respectively. Data are shown as the reads number (X-axis, M represents million) and number of expressed genes (Y-axis, K stands for 1000) obtained using sequencing.