Table 2. A total of 54 predicted cytochrome P450 genes were identified in the Hypothenemus hampei draft genome.
| H. hampei protein | FPKM | HMMERe-value | CYPclade | CUFFLINKStranscript |
|---|---|---|---|---|
| evmmodelscaffold6481.6 | 1004190 | 1.70E-98 | CYP4 | CUFF.12736.1 |
| evmmodelscaffold2770.7 | 375522 | 5.90E-80 | CYP4 | C125194 |
| evmmodelscaffold865.28 | 240521 | 1.20E-69 | CYP3 | CUFF.14635.1 |
| evmmodelscaffold2197.7 | 183475 | 2.70E-84 | CUFF.4464.1 | |
| evmmodelscaffold1456.32 | 174361 | 1.50E-172 | CYP4 | CUFF.3616 |
| evmmodelscaffold4033.5 | 147147 | 4.10E-54 | Mito | CUFF.9032.1 |
| evmmodelscaffold1325.7 | 101273 | 2.10E-33 | Mito | CUFF.2068.1 |
| evmmodelscaffold2653.5 | 99649 | 2.40E-71 | CYP3 | CUFF.5808.1 |
| evmmodelscaffold1456.33 | 65672 | 4.00E-108 | CYP4 | CUFF.3617 |
| evmmodelscaffold4525.3 | 65455 | 4.10E-83 | CYP3 | CUFF.9829 |
| evmmodelscaffold10450.1 | 60925 | 1.20E-64 | CYP4 | CUTT.985.2 |
| evmmodelscaffold571.12 | 53606 | 1.70E-104 | CYP4 | CUFF.11699.1 |
| evmmodelscaffold1307.2 | 49167 | 5.70E-45 | Mito | — |
| evmmodelscaffold844.4 | 46252 | 6.90E-60 | CUFF.14420.1 | |
| evmmodelscaffold3349.1 | 45619 | 2.50E-64 | Mito | CUFF.7694.1 |
| evmmodelscaffold4576.1 | 40606 | 5.20E-65 | CYP3 | CUFF.9942.1 |
| evmmodelscaffold1506.2 | 40106 | 3.50E-79 | Mito | CUFF.2636.1 |
| evmmodelscaffold4576.2 | 37291 | 1.30E-66 | CYP3 | CUFF.9937.1 |
| evmmodelscaffold247.1 | 36092 | 1.50E-88 | CYP4 | CUFF.5327.1 |
| evmmodelscaffold10728.2 | 35742 | 6.00E-102 | CYP3 | CUFF.1158.1 |
| evmmodelscaffold916.2 | 27657 | 1.50E-100 | CYP3 | CUFF15114.1 |
| evmmodelscaffold4428.1 | 20286 | 2.00E-98 | CYP3 | CUFF.9689.1 |
| evmmodelscaffold8984.1 | 20186 | 5.50E-46 | CYP4 | CUFF.14931.1 |
| evmmodelscaffold4198.1 | 19820 | 4.30E-65 | CYP2 | CUFF.9256.1 |
| evmmodelscaffold4292.3 | 18337 | 2.70E-107 | CYP4 | CUFF.10885 |
| evmmodelscaffold1142.1 | 16123 | 2.30E-66 | C132918 | |
| evmmodelscaffold240.1 | 14007 | 5.20E-92 | CYP2 | CUFF.5111.1 |
| evmmodelscaffold3776.2 | 12574 | 9.00E-101 | CYP4 | CUFF.8596 |
| evmmodelscaffold5922.1 | 11959 | 4.80E-98 | CYP4 | CUFF.11953.1 |
| evmmodelscaffold2612.8 | 11249 | 3.60E-68 | CYP2 | — |
| evmmodelscaffold5063.4 | 10986 | 3.30E-39 | CUFF.10760.1 | |
| evmmodelscaffold10090.1 | 10659 | 1.40E-82 | CYP3 | CUFF.708.1 |
| evmmodelscaffold240.2 | 10581 | 1.00E-110 | CYP2 | CUFF.5112.1 |
| evmmodelscaffold559.1 | 10526 | 2.10E-10 | CUFF.11505 | |
| evmmodelscaffold865.30 | 10475 | 5.30E-85 | CYP3 | CUFF.14635.2 |
| evmmodelscaffold10367.1 | 10240 | 3.40E-61 | CYP3 | CUFF.952.1 |
| evmmodelscaffold2770.6 | 7772 | 8.10E-87 | CYP4 | CUFF.6104.2 |
| evmmodelscaffold9450.1 | 6295 | 4.00E-50 | CUFF.15342.1 | |
| evmmodelscaffold3315.4 | 5399 | 6.40E-76 | CYP3 | CUFF.7475.1 |
| evmmodelscaffold5648.6 | 4430 | 5.50E-79 | CYP4 | CUFF.1157.1 |
| evmmodelscaffold1619.2 | 3247 | 2.40E-64 | CYP2 | CUFF.2900.1 |
| evmmodelscaffold6508.1 | 3198 | 4.40E-87 | CUFF.12657 | |
| evmmodelscaffold2545.3 | 3128 | 6.50E-32 | CUFF.5506.1 | |
| evmmodelscaffold116.1 | 2531 | 4.30E-82 | CYP3 | CUFF.1594.1 |
| evmmodelC2699611.1 | 2099 | 4.90E-14 | CYP3 | CUFF.639.1 |
| evmmodelC2699611.2 | 2099 | 4.40E-68 | CYP2 | — |
| evmmodelscaffold5011.2 | 2098 | 1.20E-54 | CUFF10656.1 | |
| evmmodelscaffold444.1 | 1850 | 1.90E-77 | CYP3 | CUFF.9710.1 |
| evmmodelscaffold10728.1 | 1532 | 3.30E-106 | CYP3 | CUFF.1152.1 |
| evmmodelscaffold2600.2 | 1327 | 4.00E-150 | Mito | CUFF.5658.1 |
| evmmodelscaffold5648.5 | 100 | 2.20E-99 | CYP4 | — |
| evmmodel10351.1 | 20 | 4.10E-13 | Mito | — |
| evmmodelscaffold5666.2 | 10 | 4.70E-95 | CYP4 | — |
| evmmodelscaffold601.3 | 2 | 5.40E-80 | CYP3 | — |
Gene expression is shown as FPKM values generated by Cufflinks. Cytochrome protein function is inferred by motif analysis of translated PASA/EVM predicted gene coding regions with HMMER hmmsearch (v.3.0) using the consensus cytochrome HMM model from PFAM (PF00067.17). Cytochrome clade was inferred by phylogenetic clustering with reference genes from D. melanogaster by minimum evolution with MEGA6.