Fig. 1.
Detection of the strain cr013 genome by electrophoresis.
The concentration of agarose: 1%; voltage: 180 V; time: 36 min.; molecular weight standard name: M1: λ-Hind III digest (TaKaRa Bio, Inc., Japan), M2: D2000 (Tiangen Biotech(Beijing)Co., Ltd., China); sample volume: M1: 2.5 μl, M2: 5 μl.
Table I
Main features of genome of the strain cr013 and four isolates of Trichoderma species.
| Feature | Strain cr013 | Trichoderma atroviride | Trichoderma virens | Trichoderma reesei | Trichoderma harzianum |
|---|---|---|---|---|---|
| Genome size (Mb) | 46.69 | 36.1 | 38.8 | 34.1 | 38.8 |
| Number of scaffolds | 13 | 50 | 135 | 89 | 498 |
| Scaffold N50 (Mb) | 6.39 | 2 | 1.8 | 1.2 | 6.2 |
| GC content (%) | 52.1 | 49.5 | 49 | 52.5 | 49.5 |
| Protein-coding genes | 14,893 | 11,865 | 12,518 | 9,143 | 11,264 |
| Exons per gene | 2.95 | 2.93 | 2.98 | 3.06 | / |
| Exon length (bp) | 498.14 | 528.17 | 506.13 | 507.81 | / |
| Intron length (bp) | 113.76 | 104.20 | 104.95 | 119.64 | / |
Table II
Statistics of the annotation results of different database functions.
| Strain cr013 | Total | NR | Swissport | KEGG | COG | GO | CAZy | PHI | ARDB | Overall |
|---|---|---|---|---|---|---|---|---|---|---|
| Number | 14893 | 14003 | 8869 | 9768 | 2812 | 8924 | 710 | 20 | 1735 | 14,014 |
| Percentage | 100% | 94.02% | 59.55% | 65.59% | 18.88% | 59.92% | 4.77% | 0.13% | 11.65% | 94.10% |
Fig. 2.
Classification of the KEGG pathways of the cr013 strain.
Table III
Gene annotation of the KEGG pathways of the strain cr013.
| Pathway | Genes with pathway annotation | Pathway ID |
|---|---|---|
| Metabolic pathways | 3,279 | ko01100 |
| Biosynthesis of secondary metabolites | 1,153 | ko01110 |
| Biosynthesis of antibiotics | 816 | ko01130 |
| MAPK signaling pathway – yeast | 404 | ko04011 |
| Glycine, serine and threonine metabolism | 356 | ko00260 |
| RNA transport | 304 | ko03013 |
| Biosynthesis of amino acids | 288 | ko01230 |
| Carbon metabolism | 280 | ko01200 |
| Glycerophospholipid metabolism | 231 | ko00564 |
| Meiosis – yeast | 230 | ko04113 |
Fig. 3.
COG functional classification of the cr013 strain.
Fig. 4.
GO functional annotation of the cr013 strain.
Table IV
Numbers of glycoside hydrolases related to mycoparasitism between the strain cr013 and four Trichoderma species.
| Species | GH18 | GH17 | GH55 | GH64 | GH81 | GH75 | Total |
|---|---|---|---|---|---|---|---|
| Strain cr013 | 3 | 7 | 9 | 3 | 1 | 5 | 28 |
| Trichoderma atroviride | 29 | 5 | 8 | 3 | 2 | 5 | 52 |
| Trichoderma virens | 36 | 4 | 10 | 3 | 1 | 5 | 59 |
| Trichoderma reesei | 20 | 4 | 10 | 3 | 1 | 5 | 43 |
| Trichoderma harzianum | 20 | 4 | 5 | 3 | 2 | 4 | 38 |
Table V
Numbers of BGCs in the strain cr013 and selected fungi.
| Species | Ter- pene | NRPS | NRPS- like | T1 PKS | T3 PKS | Indole | NRPS-PKS | Bata- lactone | NRPS- terpene | RiPP | Indole- PKS | Total |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Strain cr013 | 6 | 9 | 15 | 19 | 1 | 2 | 6 | 1 | 2 | 1 | 2 | 64 |
| Pestalotiopsis fici | 10 | 11 | 16 | 24 | 1 | 4 | 4 | 2 | 2 | 1 | 75 | |
| Pestalotiopsis sp. JCM | 10 | 12 | 14 | 18 | 1 | 3 | 5 | 1 | 1 | 2 | 67 | |
| Trichoderma atroviride | 8 | 10 | 10 | 12 | 4 | 44 | ||||||
| Trichoderma virens | 10 | 16 | 11 | 14 | 6 | 1 | 1 | 59 | ||||
| Trichoderma reesei | 8 | 6 | 5 | 9 | 4 | 32 | ||||||
| Trichoderma harzianum | 9 | 9 | 9 | 20 | 8 | 1 | 56 |
Table VI
Numbers of P450 enzymes, proteases and Zn2Cys6 transcription factors in the strain cr013 and four Trichoderma species.
| Other genes | Strain cr013 | Trichoderma atroviride | Trichoderma virens | Trichoderma reesei | Trichoderma harzianum |
|---|---|---|---|---|---|
| Cytochrome P450 | 234 | 69 | 120 | 73 | 120 |
| Protease | 74 | 24 | 28 | 14 | 53 |
| Zn2Cys6 transcription factor | 3 | 69 | 95 | 9 | 7 |