Characterization and Genome Analysis of Fusarium oxysporum Provides Insights into the Pathogenic Mechanisms of the Pokkah Boeng Disease in China
Abstract
:1. Introduction
2. Materials and Methods
2.1. Strain Culture and Morphological Observation
2.2. Pathogenicity Assay
2.3. Ultrastructure Analysis Using Scanning Electron Microscopy (SEM)
2.4. Reponses to Chemical Compounds In Vitro
2.5. Genome Sequencing, Assembly, and Evaluation
2.6. Gene Prediction
2.7. Gene Annotation
2.8. Phylogenetic Tree Construction
2.9. Comparative Genome Analysis
2.10. Transcriptome Analysis
3. Results
3.1. Colony Morphology and Determination of Pathogenicity
3.2. Effect of F. oxysporum BS2-6 on the Ultrastructure of Sugarcane Leaves
3.3. Physiological Response of F. oxysporum BS2-6 In Vitro
3.4. Sequencing, Assembly, and Evaluation
3.5. Genome Annotation
3.6. Phylogenetic Evolution
3.7. Comparative Genome Analysis
3.8. Identification of Secondary Metabolite Gene Families
3.9. Broad Spectrum Secondary Metabolite Production
3.10. Virulence Assay on Sugarcane
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Summary | BS2-6 |
---|---|
Genome size (bp) | 51,731,010 |
Contig number | 31 |
Contig N50 (bp) | 2,803,775 |
Contig N90 (bp) | 1,130,085 |
Contig max (bp) | 5,230,794 |
GC content | 47.37% |
Accession No. | JALBXV000000000 |
Complete BUSCOs (C) | 289 (99.66%) |
Complete and single-copy BUSCOs (S) | 288 (99.31%) |
Complete and duplicated BUSCOs (D) | 1 (0.34%) |
Fragmented BUSCOs (F) | 1 (0.34%) |
Missing BUSCOs (M) | 0 |
Total BUSCO groups searched | 290 |
Method | Software | BS2-6 | |
---|---|---|---|
Ab initio | Augustus | - | 12,255 |
Glimmer HMM | - | 14,455 | |
SNAP | - | 14,877 | |
Homolog-based | GeMoMa | F. fujikuroi IMI58289 | 14,581 |
F. fujikuroi KSU3368 | 14,907 | ||
F. fujikuroi FGSC8932 | 14,544 | ||
Unigene | PASA | - | 17,684 |
Integration | EVM | - | 15,794 |
Gene density (number of genes per Mb) | 305 | ||
Average gene length (Kb) | 1.6 | ||
Total exon length (Mb) | 22.91 | ||
Total intron length (Mb) | 2.5 | ||
Exons | 45,417 | ||
Average exon length (bp) | 504.4 | ||
Introns | 29,623 | ||
Average intron length (bp) | 84.29 |
Database | F. oxysporum BS2-6 |
---|---|
GO | 8898 (56.34%) |
KOG | 7339 (46.47%) |
KEGG | 3774 (23.90%) |
Pfam | 11,329 (71.73%) |
Swiss-Prot | 8929 (56.53%) |
TrEMBL | 15,729 (99.59%) |
Nr | 15,729 (99.59%) |
CAZyme | 917 (5.81%) |
PHI | 5088 (32.21%) |
TCDB | 154 (0.98%) |
SP | 1243 (7.87%) |
EP | 250 (1.58%) |
tRNA | 338 (2.14%) |
rRNA | 96 (0.61%) |
Other ncRNA | 42 (0.27%) |
Pseudogene | 27 (0.17%) |
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Lin, W.; Zhang, C.; Akbar, S.; Wu, S.; Yue, Y.; Wang, G.; Zhou, Y.; Powell, C.A.; Yao, W.; Xu, J.; et al. Characterization and Genome Analysis of Fusarium oxysporum Provides Insights into the Pathogenic Mechanisms of the Pokkah Boeng Disease in China. Microorganisms 2025, 13, 573. https://doi.org/10.3390/microorganisms13030573
Lin W, Zhang C, Akbar S, Wu S, Yue Y, Wang G, Zhou Y, Powell CA, Yao W, Xu J, et al. Characterization and Genome Analysis of Fusarium oxysporum Provides Insights into the Pathogenic Mechanisms of the Pokkah Boeng Disease in China. Microorganisms. 2025; 13(3):573. https://doi.org/10.3390/microorganisms13030573
Chicago/Turabian StyleLin, Wenfeng, Chi Zhang, Sehrish Akbar, Suyan Wu, Yabing Yue, Gege Wang, Yu Zhou, Charles A. Powell, Wei Yao, Jianlong Xu, and et al. 2025. "Characterization and Genome Analysis of Fusarium oxysporum Provides Insights into the Pathogenic Mechanisms of the Pokkah Boeng Disease in China" Microorganisms 13, no. 3: 573. https://doi.org/10.3390/microorganisms13030573
APA StyleLin, W., Zhang, C., Akbar, S., Wu, S., Yue, Y., Wang, G., Zhou, Y., Powell, C. A., Yao, W., Xu, J., Chen, B., Zhang, M., & Bao, Y. (2025). Characterization and Genome Analysis of Fusarium oxysporum Provides Insights into the Pathogenic Mechanisms of the Pokkah Boeng Disease in China. Microorganisms, 13(3), 573. https://doi.org/10.3390/microorganisms13030573