A domesticated phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria
Data files
Apr 17, 2024 version files 27.83 MB
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GC00000067_16_gaps_test.pal2nal
1.36 MB
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GC00000067_16_gaps.pal2nal
1.32 MB
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GC00000079_25.pal2nal
6.63 KB
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GC00000079_49.pal2nal
137.13 KB
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GC00000079_r1_3_gaps.pal2nal
1.57 MB
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GC00000079_r1_3_nogap.pal2nal
208.53 KB
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GC00000079_r1_gaps.pal2nal
2.41 MB
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GC00000108_16.pal2nal
357.57 KB
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GC00000190_12.pal2nal
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GC00000190_13_gaps.pal2nal
371.69 KB
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GC00000190_13_nogap.pal2nal
371.69 KB
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GC00000236_r1_2.pal2nal
114.78 KB
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GC00000236_r1_r1_1.pal2nal
177.79 KB
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GC00000236_r1_r1.pal2nal
177.79 KB
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GC00000236_r1.pal2nal
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GC00000514_13_gaps.pal2nal
3.60 MB
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GC00000514_13_nogap.pal2nal
429.08 KB
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GC00000617_8.pal2nal
3.62 KB
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GC00000719_6.pal2nal
722.74 KB
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GC00000887_2_gaps.pal2nal
619.10 KB
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GC00000887_2_nogap_test.pal2nal
243.23 KB
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GC00000887_2_nogap.pal2nal
227.01 KB
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GC00001065_6.pal2nal
2.34 KB
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GC00001065_9.pal2nal
13.38 KB
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GC00001207_5.pal2nal
268.92 KB
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GC00001306_5_gaps.pal2nal
2.11 MB
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GC00001534_6.pal2nal
347.89 KB
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GC00001535_5.pal2nal
311.95 KB
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GC00001752_3.pal2nal
735.16 KB
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GC00001829_2.pal2nal
257.68 KB
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GC00001957_r1_2.pal2nal
347.38 KB
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GC00001957_r1_gaps.pal2nal
726.14 KB
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GC00001957_r1_nogap.pal2nal
383.01 KB
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GC00001992_3.pal2nal
500.78 KB
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GC00002074_4.pal2nal
835.90 KB
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GC00002516_6_gaps.pal2nal
868.22 KB
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GC00002516_6_nogap.pal2nal
319.59 KB
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GC00002517_4_gaps.pal2nal
745.91 KB
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GC00002517_4_nogap.pal2nal
85.12 KB
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GC00002518_3_gaps.pal2nal
2.14 MB
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GC00002518_3_nogap.pal2nal
222.19 KB
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GC00002770_4.pal2nal
566.80 KB
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GC00003095_2.pal2nal
423.28 KB
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GC00003164_r1_1_p2.pal2nal
554.38 KB
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GC00003508_5.pal2nal
236.39 KB
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GC00007116_3.pal2nal
17 KB
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GC00009150.pal2nal
1.64 KB
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GC00009936.pal2nal
2.06 KB
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popgenstats.xlsx
12.25 KB
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ps_1524_uncollapsed_5_2018.nwk
83.31 KB
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README.md
1.08 KB
Abstract
Bacteria have repeatedly repurposed the machinery of their viruses (bacteriophage) to kill strains of neighboring bacteria. These bacteriophage (phage)-derived elements are strain-specific in their killing activity, and this specificity has been proposed to drive bacterial population dynamics. Direct evidence of the impact of phage-derived elements on natural populations over time is limited. Here we identified viral sequences in a metapopulation of wild plant-associated Pseudomonas spp. genomes. We discovered that the most abundant viral cluster does not encode an intact phage but instead encodes a tailocin: a phage-derived element that bacteria use to kill bacterial competitors. Each pathogenic Pseudomonas sp. strain carries one of a few distinct tailocin variants, which target variable polysaccharides in the outer membrane of co-occurring pathogenic strains. Analysis of historic herbarium samples from the past 170 years revealed that the same tailocin and receptor variants have persisted in the Pseudomonas populations for at least two centuries, suggesting the continued use of a defined set of tailocin haplotypes and receptors. These results indicate that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control.
https://doi.org/10.5061/dryad.hx3ffbgn9
Description of the data and file structure
ps_1524_uncollapsed_5_2018.nwk
1,524 Pseudomonas strain core genome phylogeny
popgenstats.xlsx
The first column includes panX gene file names (column= panX_ID) which can be used to associate alignment file names with VIBRANT annotation names (column= VIBRANT_ID) for each gene, the associated manuscript gene names (column= Simplified_ID), and the GenBank file locus tag for each gene (column= locus_tag_p25A12_gbk). Lastly, the population genetics statistics for each gene are included and were calculated with the R scripts on GitHub.
pal2nal files
Alignments of tailocin genes in pal2nal format
Sharing/Access information
Zenodo
Code/Software
Software and Algorithms: VIBRANT v1.2.1 (Kieft et al., 2020), Mash v2.2.2 (Ondov et al., 2016), panX (Ding et al., 2018), pankmer (Aylward et al., 2023)
Phylogeny is from Karasov TL, Almario J, Friedemann C, Ding W, Giolai M, Heavens D, Kersten S, Lundberg DS, Neumann M, Regalado J, Neher RA, Kemen E, Weigel D. Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host Microbe. 2018 Jul 11;24(1):168-179.e4. doi: 10.1016/j.chom.2018.06.011. PMID: 30001519; PMCID: PMC6054916.