Table 3.
Identification of genes involved in the KEGG limonene and pinene degradation pathway within the four mountain pine beetle metagenomes compared to a combined data set of publicly available metagenomesa
| Product annotation | EC no. | KEGG Orthology (KO) identifier | No. of genes |
||||
|---|---|---|---|---|---|---|---|
| Hybrid pine |
Lodgepole pine |
Plant biomass-degrading communities combined | |||||
| D. ponderosae | D. ponderosae gallery | D. ponderosae | D. ponderosae gallery | ||||
| Oxidoreductases | 1.1.-.- | K00120 | 0 | 0 | 0 | 0 | 62 |
| Aldehyde dehydrogenase | 1.2.1.3 | K00128 | 43 | 37 | 91 | 80 | 1,485 |
| Oxidoreductases | 1.2.1.- | K00155 | 0 | 0 | 1 | 1 | 23 |
| Oxidoreductases | 1.14.13.- | K00492 | 12 | 7 | 17 | 13 | 96 |
| Oxidoreductases | 1.14.-.- | K00517 | 4 | 2 | 6 | 5 | 378 |
| Acyltransferases with transferring groups other than amino-acyl groups | 2.3.1.- | K00680 | 1 | 0 | 3 | 0 | 271 |
| Hydrolases acting on ester bonds | 3.1.2.- | K01076 | 0 | 0 | 0 | 0 | 25 |
| Enoyl-CoA hydratase | 4.2.1.17 | K01692 | 32 | 19 | 51 | 34 | 768 |
| Carbon-oxygen lyases | 4.2.1.- | K01726 | 0 | 0 | 0 | 0 | 0 |
| 3-Hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase/3-hydroxybutyryl-CoA epimerase | 1.1.1.35; 4.2.1.17; 5.1.2.3 | K01782 | 10 | 16 | 15 | 15 | 182 |
| 3-Hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase/3-hydroxybutyryl-CoA epimerase/enoyl-CoA isomerase | 1.1.1.35; 4.2.1.17; 5.1.2.3; 5.3.3.8 | K01825 | 10 | 8 | 14 | 18 | 56 |
| Ligases forming carbon-sulfur bonds | 6.2.1.- | K01913 | 0 | 0 | 0 | 0 | 10 |
| (S)-Limonene 6-monooxygenase | 1.14.13.48 | K07381 | 0 | 0 | 0 | 0 | 0 |
| (S)-Limonene 7-monooxygenase | 1.14.13.49 | K07382 | 0 | 0 | 0 | 0 | 0 |
| Limonene 1,2-epoxide hydrolase | 3.3.2.8 | K10533 | 0 | 0 | 0 | 0 | 0 |
| trans-Carveol dehydrogenase | 1.1.1.275 | K12466 | 0 | 0 | 0 | 0 | 0 |
| trans-Carveol dehydrogenase | 1.1.1.243 | K14730 | 0 | 0 | 0 | 0 | 0 |
| Monoterpene epsilon-lactone hydrolase | 3.1.1.83 | K14731 | 0 | 0 | 0 | 0 | 0 |
| Limonene hydroxylase | 1.14.13.48; 1.14.13.49; 1.1.1.243; 1.1.1.144 | K14732 | 0 | 0 | 0 | 0 | 0 |
| Limonene 1,2-monooxygenase | 1.14.13.107 | K14733 | 1 | 1 | 0 | 0 | 49 |
| Total no. of proteins | 42,427 | 53,182 | 86,784 | 66,204 | 4,241,298 | ||
a
The publicly available metagenomes consist of plant biomass-degrading microbial communities associated with the termite hindgut, wallaby foregut, cow rumen, panda gut, leaf-cutter ant fungus garden, switchgrass compost community, and poplar biomass bioreactor (for details see Materials and Methods and Data Set S2 in the supplemental material). Results representing genes enriched relative to other plant biomass-degrading metagenomes are highlighted in boldface (P < 0.05, Fisher's exact test).