Population Genomic Analysis of Mycoplasma bovis Elucidates Geographical Variations and Genes associated with Host-Types
Abstract
:1. Introduction
2. Materials and methods
2.1. Genomes Included in the Comparative Analysis
2.2. Genome Assembly and Validation
2.3. Genome Annotation, Core and Pangenome Analysis
2.4. Phylogeny Reconstruction and Functional Analysis
2.5. Identification of Host-Associated Genes
2.6. Identification of vsp Genes and Insertion Sequences (IS)
3. Results
3.1. Genome Sequencing and General Genomic Attributes of Geographically Diverse M. bovis Isolates
3.2. Phylogenetic Structure of M. bovis Isolates
3.3. Core and Pangenome Analysis
3.4. Function-Based Clustering and its Implication for Vaccine Development
3.5. Vsp Dynamics and IS Elements
3.6. Gene Level Prediction of Host-Associated Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Data Availability
References
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Gene | Odds Ratio | p | Pairwise-p | Sensitivity | NCBI_Reference_Sequence |
---|---|---|---|---|---|
Hypothetical protein | 8.351351 | 1.49E-10 | 0.0039–0.5078 | 58.1920904 | WP_014829940.1 |
Lipoprotein | 0.178279 | 1.48E-05 | 0.0117–0.2265 | 65.53672316 | AEI90200.1 |
variable surface lipoprotein-4 (vspI) | 3.564176 | 0.0005 | 0.0063–0.3876 | 34.46327684 | WP_013456472.1 |
5-formyltetrahydrofolate cyclo-ligase | 0.332237 | 0.0007 | 0.0390–0.5078 | 57.06214689 | WP_013954957.1 |
hypothetical protein (ICEB-2 encoded) | 4.974265 | 0.0008 | 0.0390–0.5078 | 23.16384181 | WP_075271017.1 |
hypothetical protein | 4.663043 | 0.0014 | 0.0019–0.1093 | 22.03389831 | WP_075271089.1 |
putative transmembrane protein | 0.403674 | 0.0019 | 0.0117–0.2265 | 29.94350282 | WP_075271035.1 |
Lipoprotein | 3.553957 | 0.0083 | 0.0019–0.3437 | 21.46892655 | SBO46265.1 |
putative transmembrane protein | 2.02886 | 0.0147 | 0.0390–0.507 | 64.40677966 | AIA33704.1 |
lipoprotein | 1.949627 | 0.0223 | 0.0224–0.2668 | 62.14689266 | WP_075271416.1 |
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Kumar, R.; Register, K.; Christopher-Hennings, J.; Moroni, P.; Gioia, G.; Garcia-Fernandez, N.; Nelson, J.; Jelinski, M.D.; Lysnyansky, I.; Bayles, D.; et al. Population Genomic Analysis of Mycoplasma bovis Elucidates Geographical Variations and Genes associated with Host-Types. Microorganisms 2020, 8, 1561. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101561
Kumar R, Register K, Christopher-Hennings J, Moroni P, Gioia G, Garcia-Fernandez N, Nelson J, Jelinski MD, Lysnyansky I, Bayles D, et al. Population Genomic Analysis of Mycoplasma bovis Elucidates Geographical Variations and Genes associated with Host-Types. Microorganisms. 2020; 8(10):1561. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101561
Chicago/Turabian StyleKumar, Roshan, Karen Register, Jane Christopher-Hennings, Paolo Moroni, Gloria Gioia, Nuria Garcia-Fernandez, Julia Nelson, Murray D. Jelinski, Inna Lysnyansky, Darrell Bayles, and et al. 2020. "Population Genomic Analysis of Mycoplasma bovis Elucidates Geographical Variations and Genes associated with Host-Types" Microorganisms 8, no. 10: 1561. https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8101561