Pathogenomic Insights into Piscirickettsia salmonis with a Focus on Virulence Factors, Single-Nucleotide Polymorphism Identification, and Resistance Dynamics
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Genomic Dataset Selection
2.2. Species Validation Using Average Nucleotide Identity
2.3. Pan-Genome Analysis
2.4. Phylogenetic Analysis and SNP Identification
2.5. Functional Annotation and Identification of Gene Encoders
3. Results
3.1. Genomic Features and ANI
3.2. Pan-Genome Characteristics
3.3. Phylogenetic Relationship and SNP Identification
3.4. Functional Annotation and Gene Encoding Factor Identification
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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Genes | Annotation | Position, SNPs Unique for P. salmonis |
---|---|---|
dnaK | Chaperone protein | 5 C > T/A, 408 A > T/-/G, 717 A > T/C, 724 G > T/A, 807 A > T/-/C, 1325 G > T/A, 1327 G > A/C, 1445 T > G/C, 1452 T > G/C, 1546 A > T/G, 1555 G > A/C, 1560 T > A/G, 1565 C > T/A, 1596 T > -/G/C, 1608 C > T/A/G, 1617 G > A/C, 1627 C > A/G, 1630 G > T/A,1690 A > T/G, 1697 A > T/G, 1717 G > A/C, 1761 T > -/A/G, |
ftsZ | Filamenting temperature-sensitive mutant Z | 297 T > G/C, 423 T > A/C, 459 A > G/T, 537 A > T/C, 612 C > CA/CG, 633 T > A/G, 634 G > T/C, 864 T > A/G, 876 C > G/T, 906 A > G/T, 975 T > A/C, 993 G > T/C, 1050 G > T/C, 1077 G > A/T, 1116 G > T/C, |
gyrA | DNA gyrase A | 36 A > /AT, 57 G > C/A/-, 192 T > G/C/-, 216 C > G/A/-, 373 A > G/C, 376 G > T/C, 380 T > G/C, 381 A > T/C, 382 T > G/C, 388 C > G/T, 390 G > T/C, 392 T > C/A, 397 C > G/T, 399 A > T/C, 402 G > T/C, 404 T > G/A, 406 T > C/A, 416 G > T/C, 419 A > G/C, 422 T > C/A, 428 A > G/C, 429 A > T/C, 431 A > G/T, 432 A > G/T, 433 A > T/C, 437 A > G/C, 440 T > G/C, 441 G > C/A, 443 T > C/A, 459 A > T/C, 461 C > G/T, 463 C > T/A, 468 T > G/A, 479 A > G/C, 480 G > C/A, 486 A > G/T, 493 G > T/A, 494 G > C/A, 495 A > G/T, 498 G > T/C, 501 G > C/A, 502 A > G/C, 505 C > T/A, 514 C > G/A/CAA, 518 G > T/A, 2106 A > G/T/-, 2343 C > G/A/-, |
rpoB | RNA polymerase, beta subunit | 1887 G > T/C, 2655 G > A/C, |
Gene Functional Category | Virulence Gene | Product | Replicon |
---|---|---|---|
Nutritional/Metabolic factor | ggt | gamma-glutamyltranspeptidase | Chromosome |
Adherence | htpB | Hsp60, 60K heat shock protein | Chromosome |
Adherence | tufA | Elongation factor Tu | Chromosome |
Effector delivery system | icmO/dotL | Dot/Icm type IV secretion system coupling protein | Chromosome |
Motility | flrA | sigma-54 dependent transcriptional activator | Chromosome I |
Adherence | rpoS | RNA polymerase sigma factor | Chromosome |
Regulation | csrA | carbon storage regulator | Chromosome |
Regulation | rpoS | RNA polymerase sigma factor | Chromosome |
Motility | fliA | flagellar biosynthesis sigma factor | Chromosome I |
Motility | flhA | flagellar biosynthesis protein | Chromosome I |
Nutritional/Metabolic factor | feoB | ferrous iron transporter B | Chromosome |
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Islam, S.I.; Shahed, K.; Ahamed, M.I.; Khang, L.T.P.; Jung, W.-K.; Sangsawad, P.; Dinh-Hung, N.; Permpoonpattana, P.; Linh, N.V. Pathogenomic Insights into Piscirickettsia salmonis with a Focus on Virulence Factors, Single-Nucleotide Polymorphism Identification, and Resistance Dynamics. Animals 2025, 15, 1176. https://doi.org/10.3390/ani15081176
Islam SI, Shahed K, Ahamed MI, Khang LTP, Jung W-K, Sangsawad P, Dinh-Hung N, Permpoonpattana P, Linh NV. Pathogenomic Insights into Piscirickettsia salmonis with a Focus on Virulence Factors, Single-Nucleotide Polymorphism Identification, and Resistance Dynamics. Animals. 2025; 15(8):1176. https://doi.org/10.3390/ani15081176
Chicago/Turabian StyleIslam, Sk Injamamul, Khandker Shahed, Md Imtiaz Ahamed, Luu Tang Phuc Khang, Won-Kyo Jung, Papungkorn Sangsawad, Nguyen Dinh-Hung, Patima Permpoonpattana, and Nguyen Vu Linh. 2025. "Pathogenomic Insights into Piscirickettsia salmonis with a Focus on Virulence Factors, Single-Nucleotide Polymorphism Identification, and Resistance Dynamics" Animals 15, no. 8: 1176. https://doi.org/10.3390/ani15081176
APA StyleIslam, S. I., Shahed, K., Ahamed, M. I., Khang, L. T. P., Jung, W.-K., Sangsawad, P., Dinh-Hung, N., Permpoonpattana, P., & Linh, N. V. (2025). Pathogenomic Insights into Piscirickettsia salmonis with a Focus on Virulence Factors, Single-Nucleotide Polymorphism Identification, and Resistance Dynamics. Animals, 15(8), 1176. https://doi.org/10.3390/ani15081176