Recurrent evolution of high virulence in isolated populations of a DNA virus
- The Department of Molecular Biosciences, University of Kansas, United States
Figures
Figure 1 with 3 supplements
Viral genome-wide association study for DiNV titer in wild D. innubila.
(A) Manhattan plot for each DiNV SNP and the significance of its association with DiNV titer. SNP point, shape and color denotes if they are upstream (black upward arrow), downstream (black downward …
Figure 1—figure supplement 1
Frequency of each significantly associated SNP within each individual, with individuals ranked by viral titer (left = lowest, right = highest), to show the strong linkage of SNPs and little evidence of co-infection among the high and low haplotype SNPs.
Also shown is the bell-shaped relationship between viral titer rank and the significantly associated SNP in Helicase-2, samples here are colored by the assigned haplotype, if the strain is High type …
Figure 1—figure supplement 2
Permutation test for association test for viral virulence.
(A) Distribution of mean differences between artificial High type and Low type titers generated by permuting the titer across strains. We binned the Titer of strains by the allele of most …
Figure 1—figure supplement 3
Linkage disequilibrium between SNPs in DiNV as a heatmap generated in LDheatplot.
The labelled SNPs (significantly associated SNPs found in the association study) are strongly linked, shown by the high r2 between these SNPs. Points are colored by the estimated linkage between …
Figure 2 with 2 supplements
DIfferential expression between two viral haplotypes.
(A) Differential expression of D. innubila and DiNV genes between D. innubila infected with either the Low type or High type DiNV multilocus genotypes. For host genes, the log-fold change of mRNA …
Figure 2—figure supplement 1
Volcano plot of changes in gene expression between D. innubila infected with DiNV and uninfected controls.
(A) Gene categories of interest, such as enriched categories, are highlighted in color. The FDR-correct significance cut-off of 0.01 (10,320 tests) is shown as a dashed line. (B) Comparison of gene …
Figure 2—figure supplement 2
Expression changes (shown as transcript fragments per 1 million reads per 1kbp of exon) of antimicrobial peptides between strains infected with High type DiNV, Low type DiNV or not infected.
Black stars above low samples show significant differential expression between DiNV-infected strains and uninfected strains (multiple testing corrected p-value<0.05). Red stars above high samples …
Figure 3 with 2 supplements
Effect of viral type in experimental infections.
(A) Survival curves of D. innubila infected with high and low viral types compared to control flies pricked with sterile media, for 15 days post-infection. Survival 5 days post-infection separated …
Figure 3—figure supplement 1
Effect of differences in viral type and titer in experimental infections.
(A) Survival curves of D. innubila infected with DiNV filtrate of different dilutions compared to control flies pricked with sterile media, for 15 days post infection. Each dilution was used to …
Figure 3—figure supplement 2
Survival of flies following infection with different titers and types of DiNV.
(A) Survival of D. innubila reference strain 5 days post infection, using filtrate from different samples versus uninfected control, colored by High type virus or Low type virus. (B) Survival of D. …
Figure 4 with 3 supplements
Genes implicated in host/virus interaction are rapidly evolving by positive selection in the Chiricahua population.
Difference in selection effect for viral and host gene categories of interest from nearby background genes (average shown as 0, the dashed line), as indicated by the proportion of substitutions …
Figure 4—figure supplement 1
McDonald-Kreitman based statistics for each gene in population of Drosophila innubila Nudivirus, with viral envelope and GrBNV potential virulence factors shown separately.
DoS = direction of selection, Selection Effect = SnIPRE estimated weighted DoS. Boxplots marked with a * are significantly higher than background/other viral genes (GLM p-value<0.05). In both cases, …
Figure 4—figure supplement 2
The ratio of nonsynonymous to synonymous polymorphisms and substitutions for both DiNV and D. innubila, used to generate Figure 4.
(A) The ratio of nonsynonymous polymorphism (Pn) to synonymous polymorphism (Ps) for DiNV functional categories, the ratio of nonsynonymous substitutions (Dn) to synonymous substitutions (Ds) for …
Figure 4—figure supplement 3
Host genome-wide association study for DiNV titer in wild D.innubila.
(A) Manhattan plot of significance of SNP on viral titer after factoring in interaction with the viral haplotype. The significance cut offs are labelled (p-value<0.05 after multiple testing …
Figure 5 with 4 supplements
The evolution and maintenance of two viral types.
(A) Phylogeographic reconstruction of the spread of DiNV through D. innubila, rooted on the Kallithea virus reference sequence, including a reconstruction of the High type evolution (with strains …
Figure 5—figure supplement 1
SNP association in the viral haplotype and principle component analysis of viral samples.
(A) Frequency of samples with different numbers of SNPs in the viral haplotype, there are very few intermediate types. (B) Frequency of each SNP in samples infected with the virus, showing there is …
Figure 5—figure supplement 2
Linkage (r2) between different types of SNPs in each population of DiNV, and across all samples.
Other = SNPs which are not significantly associated with DiNV titer and do not form the viral haplotype. Sig = SNPs which are significantly associated with DiNV titer and do not form the viral …
Figure 5—figure supplement 3
Associations of significantly associated SNPs and their neighboring SNPs, to attempt to determine if gene conversion is the cause of the recurrent evolution of the viral haplotype.
The significantly associated SNPs are shown at position 0, with the 5 SNPs upstream (−5 to −1) and downstream (1 to 5) plotted around them for each strain. Derived allele strains are shown in black, …
Figure 5—figure supplement 4
Effective population size backwards for each population of DiNV going backwards in time, estimated using StairwayPlot.
Dotted lines indicate the error windows for Ne at a given time point. Lines are colored by population.
Figure 6
Titer and frequency of different DiNV types infecting different species.
(A) Viral titer for CH samples of D. azteca, D. falleni and D. innubila infected with High and Low type DiNV. The D.innubila data presented here is a reconstruction of Figure 1B. (B) Proportion of D.…
Tables
Table 1
Candidate viral SNPs associated with viral titer with associated genes and the functional category of that gene.
| SNP locus | Nearest gene | SNP functional annotation | Nearest gene functional annotation | p-value (FDR-corrected) |
|---|---|---|---|---|
| G14249T | 19K/PIF-4 | Non-synonymous | Per OS Infectivity factor envelope protein, required for oral infection | 3.49e-15 (4.89e-12) |
| C41210T | LEF-4 | Non-synonymous | RNA polymerase subunit for RNA modification | 7.99e-12 (1.12e-09) |
| G42389T | gp83 | Upstream | Suspected virulence factor which suppresses Toll activity | 6.73–14 (9.44e-11) |
| A59194G | gp51 | Intergenic | Suspected virulence factor | 2.96e-12 (4.15e-09) |
| C59275A | PIF-6 | Upstream | Per OS Infectivity factor envelope protein, required for oral infection | 1.65e-18 (2.31e-15) |
| T59276C | PIF-6 | Upstream | Per OS Infectivity factor envelope protein, required for oral infection | 1.65e-18 (2.31e-15) |
| G66615A | gp19 | Non-synonymous | Suspected virulence factor | 3.49e-15 (4.89e-12) |
| C78978T | gp94 | Intergenic | Suspected virulence factor | 5.93e-17 (8.32e-14) |
| G78991A | gp94 | Intergenic | Suspected virulence factor | 1.12e-16 (1.57e-13) |
| C126118A | ODV-E56-2 | Upstream | Occlusion-derived virus envelope protein required for particle formation | 1.43e-18 (2.01e-15) |
| A132593C | Helicase-2 | Non-synonymous | Unwinds DNA and is critical for DNA replication | 1.11e-09 (1.56e-06) |
| T140117C | PIF-3 | Upstream | Per OS Infectivity factor envelope protein, required for oral infection | 2.96e-15 (4.15e-12) |
Additional files
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Supplementary file 1
Next-generation sequencing information of Drosophila infected with DiNV used in this survey.
Table 1: Summary of Drosophila innubila and D. azteca fly samples collected and sequenced for this study, table includes summary of coverage for X chromosome,, Muller B, other autosomes, virus and Wolbachia. Also contains SRA accessions for each strain. Table 2: Summary of Drosophila innubila fly RNA and DNA collected and sequenced for this study, including if infected with DiNV.
- https://cdn.elifesciences.org/articles/58931/elife-58931-supp1-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/58931/elife-58931-transrepform-v2.docx
