Table 5.
Unigenes in the sesquiterpenoid and triterpenoid pathway and DGE analysis
| Biosynthetic pathways | EC codes | Description | Unigenes | Size (bp) | DGE (RPKM)a | ERb | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| Domari | Imari | Myrna | Confiance | Flester | ||||||
| Farnesyl and squalene | 2.5.1.21 | Squalene synthase (FDFT) | Ce_contig46083 | 1940 | 111.3 ± 4.0 | 78.6 ± 7.8 | 124.4 ± 0.5 | 120.9 ± 6.7 | 134.5 ± 7.1 | H |
| 1.14.14.17 | Squalene monooxygenase (SQLE) | Ce_contig50302 | 2164 | 61.9 ± 4.1 | 66.3 ± 7.5 | 38.0 ± 6.8 | 59.7 ± 1.7 | 49.8 ± 0.1 | H | |
| Ce_contig83179 | 1808 | 0.8 ± 0.2 | 2.7 ± 1.3 | 0.3 ± 0.4 | 1.0 ± 0.0 | 0.7 ± 0.1 | M | |||
| Ce_contig85466 | 2036 | 5.0 ± 1.2 | 10.9 ± 2.5 | 6.9 ± 1.3 | 7.1 ± 2.5 | 6.4 ± 0.8 | M | |||
| Costunolide | 4.2.3.23 | Germacrene A synthase (GAS) | Ce_contig16955 | 2898 | 251.3 ± 15.3 | 260.4 ± 26.7 | 355.6 ± 35.9 | 207.8 ± 67.4 | 293.1 ± 15.3 | H |
| Ce_contig41447 | 1874 | 24.2 ± 6 | 13.3 ± 4.2 | 61.9 ± 3.9 | 17.8 ± 10.4 | 9.7 ± 3.1 | H | |||
| Ce_contig52991 | 1903 | 19.3 ± 3.6 | 8.9 ± 1.1 | 56.0 ± 5.7 | 5.3 ± 3.1 | 11.4 ± 4.5 | H | |||
| Ce_contig81731 | 1079 | 1.2 ± 0.2 | 0.6 ± 0.3 | 5.3 ± 2.5 | 0.9 ± 0.3 | 0.5 ± 0.1 | M | |||
| Ce_contig83192 | 1901 | 4.2 ± 1.5 | 11.1 ± 3.8 | 3.8 ± 0.9 | 1.3 ± 0.3 | 0.2 ± 0.1 | M | |||
| 1.1.1.314 1.14.13.123 | Germacrene A oxidase (GAO) | Ce_contig46043 | 2064 | 343.4 ± 40.4 | 231.1 ± 24.4 | 433.4 ± 50.9 | 253 ± 120.6 | 324.2 ± 26.8 | H | |
| 1.14.13.120 | Costunolide synthase (COS) | Ce_contig84591 | 1984 | 187.5 ± 29.8 | 95.3 ± 14.5 | 275.6 ± 32.4 | 147.3 ± 47.7 | 198.6 ± 19.4 | H | |
| Other sesquiterpenoids | 1.1.1.216 | NADP+-farnesol dehydrogenase (FLDH) | Ce_contig25141 | 1385 | 30.7 ± 0.8 | 28.73 ± 3.8 | 24.7 ± 0.4 | 26.6 ± 1.0 | 26.9 ± 0.2 | H |
| Ce_contig25142 | 2085 | 3.7 ± 0.2 | 3.79 ± 3.6 | 3.6 ± 0.5 | 2.6 ± 0.7 | 3.1 ± 0.6 | M | |||
| Ce_contig57512 | 952 | 3.4 ± 0.9 | 1.96 ± 0.1 | 2.6 ± 0.3 | 2.4 ± 0.8 | 2.6 ± 0.3 | M | |||
| Ce_contig64598 | 597 | 15.7 ± 1.0 | 7.03 ± 1.9 | 15.6 ± 2.0 | 11.7 ± 1.7 | 13.0 ± 1.8 | H | |||
| 4.2.3.75 4.2.3.22 | Germacrene D synthase (GERD) | Ce_contig9237 | 974 | 0.0 ± 0.0 | 0.0 ± 0.0 | 0.0 ± 0.0 | 0.0 ± 0.0 | 0.0 ± 0.0 | N | |
| 1.14.13.121 | Premnaspirodiene oxygenase (HPO) | Ce_contig34331 | 1267 | 3.8 ± 0.6 | 1.64 ± 0.1 | 9.6 ± 2.2 | 3.0 ± 0.3 | 3.6 ± 0.6 | M | |
| Ce_contig54036 | 783 | 0.2 ± 0.1 | 0.16 ± 0.1 | 9.2 ± 0.3 | 4.3 ± 1.2 | 6.9 ± 0.7 | M | |||
| Ce_contig69070 | 1693 | 5.2 ± 0.1 | 2.33 ± 0.3 | 13.4 ± 1.5 | 3.4 ± 0.2 | 4.7 ± 0.3 | M | |||
| 4.2.3.57 | β-Caryophyllene synthase (QHS1) | Ce_contig82792 | 1984 | 1.1 ± 0.1 | 1.14 ± 0.2 | 0.5 ± 0.1 | 3.0 ± 0.8 | 3.5 ± 0.4 | M | |
| Triterpenoids | 5.4.99.39 | β-Amyrin synthase (LUP4) | Ce_contig4595 | 523 | 0.0 ± 0.0 | 0.0 ± 0.0 | 0.0 ± 0.0 | 0.0 ± 0.0 | 0.0 ± 0.0 | N |
| Ce_contig16172 | 2965 | 100.3 ± 2.7 | 86.16 ± 13.1 | 133.6 ± 27.5 | 107.3 ± 10.7 | 93.4 ± 13.9 | H | |||
| Ce_contig72369 | 1602 | 1.8 ± 0.4 | 2.07 ± 0.9 | 1.8 ± 0.4 | 1.44 ± 0.5 | 1.3 ± 0.3 | M | |||
| Ce_contig73522 | 2434 | 13.9 ± 3.2 | 6.13 ± 0.2 | 13.8 ± 2.3 | 12.0 ± 0.4 | 9.7 ± 1.9 | H | |||
| Ce_contig86255 | 2633 | 0.1 ± 0.1 | 0.20 ± 0.2 | 0.1 ± 0.0 | 0.2 ± 0.0 | 0.1 ± 0.1 | L | |||
| 5.4.99.41 | Lupeol synthase (LUP1) | Ce_contig2965 | 2602 | 2.8 ± 0.3 | 2.99 ± 0.1 | 1.3 ± 0.2 | 1.9 ± 0.3 | 1.5 ± 0.4 | M | |
1DGE, digital gene expression (mean ± standard deviation). Bolded values indicate differentially expressed unigenes (FDR = 0.05; |log2 fold change| = 1) in each curly vs smooth comparison
bER, unigene mean expression range across all samples. H, high (RPKM > 8); M, moderate (RPKM 1–8); L, low (RPKM 0.1–1) expression. N, below the expression threshold (RPKM 0–0.1)