Genomic Based Analysis of the Biocontrol Species Trichoderma harzianum: A Model Resource of Structurally Diverse Pharmaceuticals and Biopesticides
<p><span class="html-italic">Trichoderma</span> species SMs core enzymes and their associated BGCs.</p> "> Figure 2
<p>Maximum likelihood tree of five conserved genes (chitinase gene {chi18-5}, endochitinase1 {ech1}, β-tubulin, glyceraldehyde-3-phosphate dehydrogenase {gpdh}, and translation elongation factor {tef} of <span class="html-italic">T. harzianum</span> M10 v1.0, <span class="html-italic">T. harzianum</span> CBS226.95, <span class="html-italic">T. harzianum</span> TR274, <span class="html-italic">T. harzianum</span> T22, and <span class="html-italic">T. afroharzianum</span>. Nodes labels indicate species taxon-protein ID-gene function.</p> "> Figure 3
<p>Maximum likelihood tree of the core NRPS/NRPS-like protein sequences of <span class="html-italic">T. harzianum</span> M10 v1.0 and other experimentally described NRPSs of different microbial species. Nodes labels indicate species taxon-protein ID-chemical. <span class="html-italic">T. harzianum</span> M10 predicted proteins are in red.</p> "> Figure 4
<p>Organization of the genetic structure of the predicted non-ribosomal peptide BGCs of <span class="html-italic">Trichoderma harzianum</span> M10 v1.0 Sizes and directions of arrows represent different genes sizes and their 5′-3′ direction. Full description of gene function is provided in <a href="#app1-jof-09-00895" class="html-app">Tables S2–S20 in the supplementary information</a>.</p> "> Figure 5
<p>Maximum likelihood tree of the core PKS/PKS-like of <span class="html-italic">T. harzianum</span> M10 v1.0 and other experimentally described NRPS protein sequences of different microbial species Nodes labels indicate species taxon-protein ID-chemical. <span class="html-italic">T. harzianum</span> M10 predicted proteins are in red.</p> "> Figure 6
<p>Organization of the genetic structure of the predicted polyketide synthase (PKS/PKS-like) BGCs of <span class="html-italic">Trichoderma harzianum</span> M10 v1.0. Sizes and directions of arrows represent different gene sizes and their 5′-3′ direction. Full description of gene function is provided in <a href="#app1-jof-09-00895" class="html-app">Tables S21–S41 in the supplementary information</a>.</p> "> Figure 7
<p>Organization of the genetic structure of the predicted hybrid polyketide synthase (HrPKS) BGCs of <span class="html-italic">Trichoderma harzianum</span> M10 v1.0. Sizes and directions of arrows represent different genes sizes and their 5′-3′ direction. Full description of gene function is provided in <a href="#app1-jof-09-00895" class="html-app">Tables S42–S47 in the supplementary information</a>.</p> "> Figure 8
<p>Maximum likelihood tree of the core terpene cyclase (TC) of the <span class="html-italic">T. harzianum</span> M10 v1.0 and other experimentally described TC protein sequences of different microbial species. Nodes labels indicate Species taxon-protein ID-chemical. <span class="html-italic">T. harzianum</span> M10 predicted proteins are in red.</p> "> Figure 9
<p>Organization of the genetic structure of the predicted terpene cyclase (TC) BGCs of <span class="html-italic">Trichoderma harzianum</span> M10 v1.0. Sizes and directions of arrows represent different gene sizes and their 5′-3′ direction. Full description of gene function is provided in <a href="#app1-jof-09-00895" class="html-app">Tables S48–S52 in the supplementary information</a>.</p> "> Figure 10
<p>Organization of the genetic structure of the predicted dimethylallyltryptophan (DMAT) BGC of <span class="html-italic">Trichoderma harzianum</span> M10 v1.0. Sizes and directions of arrows represent different gene sizes and their 5′-3′ direction. Full description of gene function is provided in <a href="#app1-jof-09-00895" class="html-app">Table S53 in the supplementary information</a>.</p> "> Figure 11
<p>Cblaster analysis of three types of SMs enzymes that had high percentage matches with the <span class="html-italic">T. harzianum</span> M10 v1.0 SMs enzymes in our phylogenetic analysis. (<b>A</b>) Eight NRPS genes of <span class="html-italic">T. harzianum</span> were used as query, three of which had homologous sequence with <span class="html-italic">T. asperellum</span>. (<b>B</b>) Eight PKS genes of <span class="html-italic">T. harzianum</span> were used as query, five of which had homologous sequence with <span class="html-italic">T. gracile</span>. (<b>C</b>) Five TC genes of <span class="html-italic">T. harzianum</span> were used as query, none of which had sequences similarity with other organisms on NCBI database. A darker shade of blue denotes a higher percentage identity of the query in the output cluster, while the number within each box, resembles the counts of hits for a specific query sequence in the co-localized region. Orange and red borders indicate that similar genes found in multiple clusters.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Trichoderma Species Genome Scan
2.2. Validation of the M10 v1.0 Isolate and Annotation of the Core Enzymes of Its Secondary Metabolites (SMs)
2.3. Secondary Metabolites Phylogenetic Analysis
2.4. Annotation of the Predicted Biosynthetic Gene Clusters
3. Results
3.1. Genome Scan
3.2. Trichoderma Harzianum Genomes Comparison
3.2.1. NRPS and NRPS-Like Phylogenetic Analysis and Biosynthetic Gene Clusters Annotation
3.2.2. PKS and PKS-like Phylogenetic Analysis and Biosynthetic Gene Clusters Annotation
3.2.3. Terpene Cyclase Phylogenetic Analysis and Biosynthetic Gene Clusters Annotation
3.3. Clinker Investigation
3.3.1. Core Enzymes Cblaster
3.3.2. Biosynthetic Gene Clusters Cblaster
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Most Similar BGC on antiSMASH | BGC Type | Trichoderma harzianum CBS 226.95 v1.0 (Triha1) | Trichoderma harzianum T22 v1.0 (TriharT22) | Trichoderma harzianum TR274 v1.0 (Trihar1) | Trichoderma harzianum M10 v1.0 (TriharM10) |
---|---|---|---|---|---|
Metachelin A-C | NRPS | 62% | 75% | 62% | 62% |
Ochratoxin | NRPS-PKS | X | X | X | 100% |
Dichlorodiapothin | PKS | 50% | 50% | 50% | 33% |
Trichoxide | PKS | 75% | 83% | 75% | 83% |
Harzianopyridone | NRPS-PKS | 60% | 60% | 60% | 70% |
Clavaric acid | Terpene | 100% | X | 100% | 100% |
Harziphilone | PKS | 80% | 80% | 80% | 80% |
Squalestatin | Terpene | 40% | 40% | X | 40% |
Depudecin | PKS | 33% | 33% | 33% | 33% |
Trichobrasilenol | Terpene | 60% | 60% | 60% | X |
Tricholignan | PKS | 100% | 100% | 100% | 100% |
Choline | NRPS | 100% | 100% | 100% | 100% |
Peramine | NRPS | X | 100% | X | 100% |
Lucilactaene | PKS | X | X | X | 38% |
BGC of Interest | No. of Organisms Searched | No. of Genomic Scaffold Searched | No. of Scaffolds Identified with the BGC | No. of Trichoderma Species with Similar BGC |
---|---|---|---|---|
Ochratoxin | 416 | 566 | 573 | 18 |
Clavaric acid | 513 | 568 | 559 | None |
Harziphilon | 631 | 2971 | 735 | 9 |
Tricholignan | 93 | 390 | 96 | 7 |
Choline | 1088 | 1134 | 1133 | None |
Peramine | 346 | 628 | 512 | 8 |
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Al-Salihi, S.A.A.; Alberti, F. Genomic Based Analysis of the Biocontrol Species Trichoderma harzianum: A Model Resource of Structurally Diverse Pharmaceuticals and Biopesticides. J. Fungi 2023, 9, 895. https://doi.org/10.3390/jof9090895
Al-Salihi SAA, Alberti F. Genomic Based Analysis of the Biocontrol Species Trichoderma harzianum: A Model Resource of Structurally Diverse Pharmaceuticals and Biopesticides. Journal of Fungi. 2023; 9(9):895. https://doi.org/10.3390/jof9090895
Chicago/Turabian StyleAl-Salihi, Suhad A. A., and Fabrizio Alberti. 2023. "Genomic Based Analysis of the Biocontrol Species Trichoderma harzianum: A Model Resource of Structurally Diverse Pharmaceuticals and Biopesticides" Journal of Fungi 9, no. 9: 895. https://doi.org/10.3390/jof9090895