Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Genomic Sequences and Quality Assessment
2.2. Identification of Prophage-like Sequences within Erwinia spp. Genomes
2.3. Taxonomic Classification of Putative ERWINIA Prophages
2.4. CRISPR-Cas Systems Identification
2.5. Protospacer Identification
2.6. In Silico Screening for DISARM System in Erwinia spp. Genomes
2.7. In Silico Screening for BREX Types 1–6 in Erwinia spp. Genomes
3. Results
3.1. Acquisition of Erwinia spp. Genome Assemblies and Quality Assessment
3.2. Prophage-like Sequences Are Pervasive in Erwinia spp. Genomes
3.3. Sequence Diversity and Taxonomic Classification of the Putative Erwinia Prophages
3.4. CRISPR-Cas Systems Are Unevenly Distributed across the Erwinia Genus and Have a High Proportion of Unknown Targets
3.5. BREX and DISARM Anti-Phage Defense Systems Are Rare in Erwinia spp. Genomes
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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Morgan, T.; Rezende, R.R.d.; Lima, T.T.M.; Souza, F.d.O.; Alfenas-Zerbini, P. Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species. Pathogens 2023, 12, 44. https://doi.org/10.3390/pathogens12010044
Morgan T, Rezende RRd, Lima TTM, Souza FdO, Alfenas-Zerbini P. Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species. Pathogens. 2023; 12(1):44. https://doi.org/10.3390/pathogens12010044
Chicago/Turabian StyleMorgan, Tulio, Rafael Reis de Rezende, Thamylles Thuany Mayrink Lima, Flávia de Oliveira Souza, and Poliane Alfenas-Zerbini. 2023. "Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species" Pathogens 12, no. 1: 44. https://doi.org/10.3390/pathogens12010044