## 2 Results
### Full-Length Transcriptome Profiling and DEGs Identification
\begin{table}
\begin{tabular}{c c c} \hline \hline  & \multicolumn{2}{c}{**PacBio**} \\ \cline{2-3}  & **Before Correct** & **After Correct** \\ \hline Subreads base (G) & 23.92 & \\ Subreads number & 15,216,963 & \\ Average subreads length & 1572 & \\ N50 (subreads) & 1893 & \\ CCS\_number & 520,718 & \\ Full length & 446,770 & \\ FLNC & 416,262 & \\ Average FUNC read length & 1719 & \\ Consensus reads & 38,784 & \\ Total\_nucleotides & 72,040,170 & 72,013,662 \\ Total\_number & 38,784 & 38,784 \\ Mean\_length & 1858 & 1857 \\ Min\_length & 75 & 75 \\ Max\_length & 9057 & 9060 \\ N50 (consensus) & 2143 & 2142 \\ N90 (consensus) & 1139 & 1138 \\ Number of transcripts & & 38,784 \\ Number of Genes & & 17,266 \\ Number of genes annotated & & 98.30\% \\ Number of genes unannotated & & 1.70\% \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Summary of PacBio transcripts of masson pine needles in the high and common resin yield. To obtain a comprehensive gene functional annotation, a total of 17,266 genes were analyzed using Nr, Nt, Pfam, KOG, Swiss-Prot, KEGG, and GO. The results showed that 8200 genes were simultaneously annotated in all the databases (Nr, Nt, Pfam, GO, KEGG, KOG, and Swiss-Prot) (Figure S1A). There were 16,973 genes annotated in at least one database of which 16,678 (96.59%) genes were annotated by the Nr database. The alignment of sequence homology demonstrated that 8913 (51.62%) sequences were found against _Picea stichensis_, 1897 (10.99%) sequences had significant hits for _Amborella trichropoda_, then followed by _Nelumbo nucifera_ (1105, 6.40%), _Marchantia polymorpha_ (351, 2.03%), _Elais guinensis_ (282, 1.63%), and 23.57% of the sequences were homologous to other species (Figure S1B). A total of 12,187 (70.58%) genes were annotated in the GO database. The results of the GO enrichment analysis showed that genes were mainly enriched in metabolic process, cellular process, single-organism process, cell, cell part, organelle, binding, catalytic activity, transporter activity in biological process (BP), molecular function (MF), and cellular component (CC) (Figure S1C). A total of 16,284 genes were annotated in the KEGG database. The top three KEGG pathways were \"Metabolism, Carbohydrate Metabolism\" (771, 4.47%), \"Environmental Information Processing, Signal Transduction\" (858, 4.97%), and \"Genetic Information Processing, Translation\" (740, 4.29%) (Figure S1D). In total, 3811 DEGs were identified in needles. To reveal the metabolic pathways related to the resin yield, these DEGs were divided into two groups of up- and down-regulated, and then functional category enrichment analysis was performed for each group, respectively. There were 1840 up-regulated and 1971 down-regulated DEGs (Figure 4A). These up-regulated DEGs were significantly enriched in photosynthesis, photosynthesis-antenna proteins, glycerolipid metabolism, and metabolic pathways. In contrast, those down-regulated DEGs were significantly enriched in phenylpropanol biosynthesis, flavonoid biosynthesis, metabolic pathways, biosynthesis of secondary metabolites, glutathione metabolism, and fatty acid degradation (Figure 4B). To validate the RNA-Seq results, a total of 12 genes, which were involved in terpeniosynthesis, JA biosynthesis & signaling, photosynthesis, and carbohydrate metabolism, were tested by the qRT-PCR. The results of qRT-PCR showed that expression levels of all selected genes were consistent with RNA-Seq data, indicating that transcriptome data are reliable (Figure S2). Figure 4: Identification of DEGs/DEPs. **(A)** Number of DEGs/DEPs. **(B)** Functional category enrichment of DEGs/DEPs. DEGs/DEPs were classified into two groups of up-regulated or down-regulated, without DEGs and DEPs comparison. The degree of the pathway enrichment was indicated according to the value of \(-\)log(\(q\)-value), as shown in the color bar. Each group was indicated by expression level (“g” for gene and “p” for protein, respectively) and regulatory direction (“up” for up-regulated and “dn” for down-regulated, respectively).