## 2 Results
### Integrated Analysis of Transcriptome and Proteome  
By comparing the DEGs with the DEPs, there were 156 up-regulated and 205 down-regulated genes changed with the same trend both at the mRNA and protein levels (Figure S4). These up-regulated genes were significantly enriched in the biosynthesis of secondary metabolites, carbon metabolism, carbon fixation in photosynthetic organism/Calvin cycle, metabolic pathways, and glycolysis/glucoseogenesis (Figure 6). It is noteworthy that one monoterpene synthase-like alpha-terpineol synthase (_MonoTPS1_), together with two sesquiterpene synthase-like cyanophyllene/humulene synthase (_SesquiTPS1_) and 5-germacradien-4-ol synthase (_SesquiTPS2_) were dramatically up-regulated, indicating their crucial roles in the resin yield in masson pine. Consistently, photosystem II protein _PsbR_ and ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (_rbcS_), together with F-type H+-transporting ATPase subunit delta (_ATPD_) involved in photosynthesis and chlorophyll synthase (_chlG_) involved in chlorophyll biosynthesis were significantly up-regulated. Besides, five genes, hexokinase (_HXK_), sucrose synthase (_SUS_), phosphoglycerate kinase (_PGK_), dihydroploamide dehydrogenase (_PDH_), and dihydroploamide succinyltransferase (_DLST_) involved in carbohydrate metabolism, were also obviously up-regulated (Table S3). In contrast, these down-regulated genes were significantly enriched in metabolic pathways, biosynthesis of secondary metabolites, glutathione metabolism, alpha-Linoleic acid metabolism/JA biosynthesis, flavonoid biosynthesis, phenylpropanol biosynthesis, and fatty acid degradation (Figure 6). Notably, sesquiterpenoid biosynthesis-related genes like (E)-alpha-bisabolene synthase (_SesquiTPS3_) and MVA pathway-related genes like phosphomevalonate kinase (_PMK_) and diphosphonate decarboxylase (_MVD_) were significantly down-regulated. Consistently, flavanone 3-hydroxylase (_F3H_), bifunctional dihydroplavonol 4-reductase (_DFR_), anthocyanin synthase (_ANS_), and anthocyanin reductase (_ANR_) participated in flavonoid biosynthesis, together with caffeoyl-CoA O-methyltransferase (_CCoAOMT_) and caffe acid 3-O-methyltransferasease (_COMT_) participated in phenylpropanol biosynthesis were also obviously down-regulated. Totally three JA biosynthesis genes, of which 12-oxophylle acid reductase (_OPR_) and two jasmonate O-methyltransferaseases (_JMTs_), were significantly down-regulated. In addition, glutathione reductase (_GSR_) and glutathione S-transferases (_GST_) referred to as glutathione metabolism were also notably down-regulated (Table S3). Since only a few genes were significantly altered both at the transcriptomic and proteomic levels, similar functional enrichment results were obtained for the up-and down-regulated genes with or without removing those genes that were significantly altered at the proteomic level and also for the up- and down-regulated proteins with or without removing those proteins that were significantly altered at the transcriptomic level (Figures 4B and 6). Next, we primarily focused on the genes/proteins regulated only at the transcriptomic or proteomic level in specific pathways. There were 1666 up-regulated and 1734 down-regulated DEGs whose corresponding proteins were not differentially expressed (Figure S4). Consistent with the results of functional enrichment, the expression levels of genes involved in photosynthesis were significantly elevated, including photosystem I subunit _PsaE_, _PsaF_, _PsaG_, _PsaL_, and _PsaO_, photosystem II protein _PsbP_, _PsbS_, and _PsbY_, chlorophyll a/b binding protein _Lhca1_, _Lhca3_, _Lhcb1_, _Lhcb2_, and _Lhcb4_, and Calvin cycle-related genes like _rbcS_, glyceraldehyde 3-phosphate dehydrogenase (_GAPDH_) and fructose-1,6-bisphosphatase I (_FBP1_).