## 2 Results
### Phylogenetic Tree Analysis of Finger Citron TPS  
The functions of the TPSs remained unknown, so we constructed a phylogenetic tree based on their amino acid sequences (Figure 9) together with the Citrus TPS reported by [PERSON] et al. In Figure 9, _TPS_ genes in the phylogenetic tree were highlighted by red dots. Finger citron _TPS_ genes were assigned to four subfamilies: 20 in TPS-a, 18 in TPS-b, 2 in TPS-e/f, and 4 in TPS-g. Genes in the TPS-a subfamily are predicted to catalyze the formation of sesquiterpenes [12]. There were 20 finger citron _TPS_ belong to this subfamily. Genes in TPS-b usually encode proteins that function as monoterpene synthases. TPS-g is a clade closely related to TPS-b and there is evidence that monoterpenes, sesquiterpenes and diterpenes can be formed by genes from the TPS-g clade [10; 51]. Despite their diverse functions, they share the common feature that all their products are acyclic. There are two finger citron TPSs that belong to the e/f clade. To get a more precise prediction of finger citron TPS function, sequence identities compared with characterized _TPS_ genes from other _Citrus_ species were calculated and are summarized in Figure S9. Since the correlated volatiles to Module Red and Module Green were monoterpenoids (Figure 6), attention was paid to genes in TPS-b and g subfamilies.  
The extracted Subnetwork of Module Red contains 4 _TPS_ genes. Cm269930 and Cm186730 shared 97.66% identity and they both belonged to TPS-b subfamily (Figure 9). Cm269930 was the hub gene, highly connected node, in Module Red. Sequence analysis showed that Cm269930 shared high amino acid sequence identity with _C. unshiiu_\(\gamma\)-terpinene synthase BAD27258 (72.78%) and _C. limon_\(\gamma\)-terpinene synthase AAM53943 (71.01%) (Figure S9). Low sequence identity (29.26%-40.00%) was observed between Cm105420 and _Citrus TPSs_ (Figure S9). Module Green contains 6 _TPSs_. TPS family member Cm310520 was ruled out for the phylogenetic analysis because of its inadequate length. Three members (Cm028750, Cm074160, and Cm257260) belong to TPS-b family. Sequence analysis showed that Cm257260 had 90.7% identity with _C. limon_ (+)-limonene synthase AAM53944 and _C. jambhiri_ limonene synthase BAF73932 (Figure S9). Cm116700 and Cm252580 belong to TPS-a family (Figure 9) and the Cm116700 sequence was 95.02% identical with _C. sinensis_ sesquiterpene synthases  
Figure 8: Gene co-expression subnetwork of Module Green. Network was reconstructed by edge weight cutoff = 0.35 and visualize by cytoscape. Gene IDs and annotations in Module Green subnetwork were listed in Table S5.  
Cs4g12350 (Figure S9). Cm028750 and Cm074160 sequence identities were less than 50% homolgous to _Citrus TPSs_ sequences. For three _TPS_ genes from Module Blue, Cm206970 and Cm279170 belong to TPS-a subfamily, while Cm107390 belong to TPS-g subfamily (Figure 9). Sequence analysis revealed that Cm206970 and Cm279170 had 96.17% and 97.76% identity with _C. unshiu_linal synthase BAP75561, respectively (Figure S9). For Cm107390, sequence identities to characterized _Citrus TPSs_ were less than 45%. These results indicated possible roles of finger citron TPSs from three Modules (Red, Green, and Blue) in biosynthesis of volatile terpenoids, although their functions need to be further investigated.  
Figure 9: Phylogeny tree analysis of _Citrus_ TPSs. Triangles represent finger citron TPSs, and filled colors indicate their location in modules shown in Figure 5. TPSs accession number of sweet orange and other _Citrus_ species were reported by [PERSON] et al. (2015). Sequence alignment was performed by ClustalX. Phylogeny tree was visualized by FigTree.