Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae
Abstract
:1. Introduction
2. Materials and Methods
2.1. Biological Material
2.2. Chemicals
2.3. Phage PEG-Precipitation
2.4. Transmission Electron Microscopy (TEM) Analyses
2.5. Phage Virion Whole Genome Sequencing
2.6. Phage Virion Genome Assembly, Taxonomic Evaluation, Annotation, and Phylogeny
2.7. Mechanical Properties of the PsgM02F and PsgM04F Phage Genomes
2.8. Viral Proteomic Trees
2.9. Statistical Analyses
3. Results
3.1. Phage Plaque Morphologies and Virion Morphotypes and Physical Features
3.2. Genomic Characterization
3.3. DNA Structural Features of Phages PsgM02F and PsgM04F
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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Structural Feature | Phage Virion Dimensions | |
---|---|---|
Phage PsgM02F | Phage PsgM04F | |
Capsid length (nm) | 101.3 ± 4.0 | 77.5 ± 3.5 |
Capsid width (nm) | 81.5 ± 2.8 | 73.0 ± 2.2 |
Tail length (nm) | 108.7 ± 0.8 | 102.5 ± 4.3 |
Tail thickness (nm) | 21.9 ± 3.0 | 15.6 ± 3.8 |
Feature | Phage PsgM02F | Phage PsgM04F |
---|---|---|
NCBI/Genbank accession number | OR584013 | OR584014 |
Genome size | 165,282 bp | 151,205 bp |
Number of PE reads mapping in the final assembly | 47,224,300 (91.64%) | 25,251,477 (99.48%) |
Average sequencing coverage (calculated as (length of reads × number of reads mapping)/genome size) | 171,636× | 33,443× |
GC content | 35.37% | 42.30% |
tRNA genes | 11 | 11 |
Protein-coding genes (CDS) predicted | 278 | 324 |
• With function assigned | 136 (48.9%) | 73 (22.5%) |
• Hypothetical/unknown function | 142 (51.1%) | 251 (77.5%) |
Similar phage genome sequences NCBI/RefSeq accession number of similar phage | Escherichia phage HP3/Shigella phage Sf21 GCF_002619885.1/GCF_002955385.1 | Escherichia phage phiWec190 LC739539.1 |
Morphotype | Myovirus | Myovirus |
Family/Genus | Straboviridae/Tequatrovirus | Stephanstirmvirinae/Phapecoctavirus |
Source of Variation | SS | df | MS | F-Ratio | p-Value | F-Critical |
---|---|---|---|---|---|---|
Between Groups | 17.288 | 1.000 | 17.288 | 428.585 | 9.105 × 10−95 | 3.842 |
Within Groups | 1823.138 | 45,197 | 0.040 | |||
Total | 1840.426 | 45,198 |
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Silva, E.C.; Quinde, C.A.; Cieza, B.; Basu, A.; Vila, M.M.D.C.; Balcão, V.M. Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes 2024, 15, 113. https://doi.org/10.3390/genes15010113
Silva EC, Quinde CA, Cieza B, Basu A, Vila MMDC, Balcão VM. Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes. 2024; 15(1):113. https://doi.org/10.3390/genes15010113
Chicago/Turabian StyleSilva, Erica C., Carlos A. Quinde, Basilio Cieza, Aakash Basu, Marta M. D. C. Vila, and Victor M. Balcão. 2024. "Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae" Genes 15, no. 1: 113. https://doi.org/10.3390/genes15010113
APA StyleSilva, E. C., Quinde, C. A., Cieza, B., Basu, A., Vila, M. M. D. C., & Balcão, V. M. (2024). Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae. Genes, 15(1), 113. https://doi.org/10.3390/genes15010113