Genomic Characterization of the Mycoparasite Pestalotiopsis sp. Strain cr013 from Cronartium ribicola
, , , und | 16. Dez. 2023
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Article Category: ORIGINAL PAPER
Online veröffentlicht: 16. Dez. 2023
Seitenbereich: 433 - 442
Eingereicht: 17. Juli 2023
Akzeptiert: 24. Okt. 2023
DOI: https://doi.org/10.33073/pjm-2023-041
Schlüsselwörter
© 2023 Jinde Yu et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
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Fig. 4.
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 |
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 |
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% |
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 |
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 | / |
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 |
| 10 | 11 | 16 | 24 | 1 | 4 | 4 | 2 | 2 | 1 | 75 | ||
| 10 | 12 | 14 | 18 | 1 | 3 | 5 | 1 | 1 | 2 | 67 | ||
| 8 | 10 | 10 | 12 | 4 | 44 | |||||||
| 10 | 16 | 11 | 14 | 6 | 1 | 1 | 59 | |||||
| 8 | 6 | 5 | 9 | 4 | 32 | |||||||
| 9 | 9 | 9 | 20 | 8 | 1 | 56 |