Table 3.
Subgenus- and species-level primers used to determine the transcriptional levels of fungal cellulolytic genes in biomass compost
| Enzyme type/core species | Target gene/enzyme | Genbank accession No. or reference | Primer sequences [I] | Amplicon size (bp) |
|---|---|---|---|---|
| Trichoderma spp. | ITS | - | F: TACCAAHCTGTTGCCTCGGCGG | ~200 |
| R: GATGAAGAAGGCAGCGAAATGCGATA | ||||
| Cellulase/Trichoderma spp. | cbh1/Cel7 A | [II] | F: GATGATTACTACGCCAACATGCTG | 77 |
| R: ACGGCACCGGGTGTGG | ||||
| egl1/Cel7 B | [III] | F: CTGCAACGAGATGGATATCCTG | 250 | |
| R: GTGATGATGGTGAAGGTCTTGGAG | ||||
| bgl1/Cel3 A | [IV] | F: ATCAAGGTAGCTCAACATCGGG | 124 | |
| R: ACCTTATCTTGGAGATTGAGCTTTGCC | ||||
| Hemicellulase/Trichoderma spp. | xyn1 and xyn2 | [V] | F: CCGAGAAGTTGATGACCTTGTTC | 87 |
| R: GGTCCAACTCGGGCAACTTT | ||||
| Ligninase/Phanerochaete chrysosporium | LipA/B | M37701 | F: ATCTCTGCCCACCCTGTCCT | 256 |
| R: CTGAGCCAGCGAATGAGAGTC | ||||
| LipD | M18743 | F: CCCGGTCCTCGATGATATCC | 201 | |
| R: ATGTTCGGGTGGTACGTGGT | ||||
| LipH | M24082 | F: CGTCCACGGATATCGCTCTCT | 102 | |
| R: GCGAGGGAGACGCAAATTC | ||||
| LipJ | AF140062 | F: GCCGAGGCACATGAGTCTCTC | 252 | |
| R: TGTTCGGGTGGAAATTGGTC | ||||
Note: the group primers targeting specific functional protein-encoding genes:
[I]. Orpinomyces spp. endo-1,4-glucanase gene: O. sp. PC-2, U97153; O. joyonii, AF015248.
[II]. Trichoderma spp. cellobiohydrolase I gene (cbh1): T. koningii, X69976; T. reesei, DD393553-DD393571; T. sp. FJ026620; T. viride, AY368686.
[III]. Trichoderma spp. endo-β-1,4-glucanase I gene (egl1): T. longibrachiatum, X60652; T. reesei, AY928809; T. viride, AY343986
[IV]. Trichoderma spp. β-glucosidase 1 gene (bgl1): T. reesei, U09580; T. sp. SSL, FJ040193; T. viride, AY368687
[V]. Trichoderma spp. xyn1 and xyn2: T.reesei, X69573 (xyn1), U24191 (xyn2); T. harzianum, EU821597 (xyn2); T. pseudokoningii, EU360941 (xyn2).