Table 1.
The cloning efficiencies of target BGCs from different actinomycetal genomic DNA samples
| Cloning performance | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Genome features | Target BGC features | Route 1 (simple and fast) | Route 2 (high efficiency)a | |||||||
| Strains and target NPs | Size | (G + C)% | Type | Length | (G + C)% | Correct/ checkedb | Efficiency | Correct/ checkedc | Efficiency | BGC integrityd |
| K. aureofaciens DM-1 | 7.1 Mb | 73% | ||||||||
| Demeclocycline | PKS | 41 kb | 73% | 11/20 | ∼55% | NA | NA | 100% | ||
| Sa. spinosa NHF132 | 8.9 Mb | 69% | ||||||||
| Spinosad | PKS | 80 kb | 67% | 6/20 | ∼30% | NA | NA | 100% | ||
| Sa. pogona NRRL 30141 | 9.6 Mb | 68% | ||||||||
| Butenyl-spinosyn | PKS | 79 kb | 66% | 5/20 | ∼25% | NA | NA | 100% | ||
| S. avermitilis ATCC 31267 | 10.5 Mb | 71% | ||||||||
| Avermectin | PKS | 80 kb | 69% | 5/20 | ∼25% | NA | NA | 100% | ||
| S. albus J1074 | 6.8 Mb | 73% | ||||||||
| Paulomycin | Quinone glycoside | 49 kb | 71% | 8/20, 5/20, 7/20 | 32 ± 7% | 7/10 | ∼70% | 100% | ||
| Surugamide | NRPS | 87 kb | 76% | 4/20, 4/20, 5/20 | 21 ± 3% | 7/10 | ∼70% | 100% | ||
| Candicidin | PKS | 145 kb | 75% | 2/20, 1/20, 2/24 | 8 ± 2% | 5/10 | ∼50% | 100% | ||
| Micromonospora sp. 181 | 7.6 Mb | 73% | ||||||||
| Marinolactam A | PKS | 110 kb | 72% | 5/20 | ∼25% | NA | NA | 100% | ||
aRoute 2: target DNA fragment isolation and purification with PFGE (Supplementary Figure S10).
bA total of 20 or 24 clones were randomly selected from each agar plate for PCR screening.
cA total of 10 clones were randomly selected from agar plate for PCR screening.
dConfirmed by digestion or PFGE of three to five PCR-validated clones.