Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum
Abstract
:1. Introduction
2. Materials and Methods
2.1. Isolates and Phenotyping
2.2. DNA Extraction and Libraries
2.3. Microsatellite Analyses
2.4. SNP Calling
2.5. Structural Variant Calling
2.6. Test of Asexual Evolution
2.7. Phylogenetic Reconstruction and Ancestral State Reconstruction
2.8. Environmental Sampling and Modelling
2.9. Association with Genomic Features
3. Results
3.1. SNP Markers Confidently Reconstruct the Phylogeny of P. ramorum NA1
3.2. SNPs and SVs Support Asexual Evolution
3.3. Persistence of SVs in the Population is Associated with Host and Mutation Load
3.4. Stress-Related Environmental Conditions Drive SV Parallelism
3.5. SVs are Associated with Genes Involved in Pathogenesis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Host/Source | Common | Uncommon | |
---|---|---|---|
Cluster | |||
1 | 16 | 4 | |
2 | 1 | 4 |
Count by SV Type | Monterey Co.: Coef. Est. | Monterey Co.: 5% | Monterey Co.: 95% | Sonoma Co.: Coef. Est. | Sonoma Co.: 5% | Sonoma Co.: 95% | Bayes Factor Relative to Model/ AMPno. | Bayes Factor Relative to Model/ BNDno. | Bayes Factor Relative To Model/ DELno. | Bayes Factor Relative to Model/ SVno. | Bayes Factor Relative to Model/ Parallel SIG_SV |
---|---|---|---|---|---|---|---|---|---|---|---|
AMPno | 0.08 | −0.01 | 0.22 | 0.10 | 0.03 | 0.21 | ⏤ | 27.86 | 0.06 | 0.82 | 9.19 × 1014 |
BNDno | −0.39 | −1.97 | 0.80 | 0.31 | −0.48 | 1.47 | 0.04 | ⏤ | 0.00 | 0.03 | 3.10 × 1013 |
DELno | 2.89 | 0.35 | 5.72 | 1.55 | 0.37 | 3.02 | 15.51 | 489.51 | ⏤ | 13.05 | 1.47 × 1016 |
SVno | 0.07 | −0.01 | 0.21 | 0.10 | 0.03 | 0.21 | 1.19 | 35.03 | 0.08 | ⏤ | 1.21 × 1015 |
Parallel SIG_SV | 0.35 | −0.25 | 1.08 | 0.35 | −0.25 | 1.07 | 0.00 | 0.00 | 0.00 | 0.00 | ⏤ |
Genomic Feature | Intersect SV and Genomic Feature | Unique to Genomic Feature | Unique to SV | Neither SV Nor Genomic Feature | Odds Ratio | p-Value |
---|---|---|---|---|---|---|
N. densiflorus RNAseq | 58534 | 1095221 | 2635487 | 56523374 | 1.15 | <2.2 × 10−16 |
RXLR | 12691 | 243686 | 2681330 | 57374909 | 1.11 | <2.2 × 10−16 |
CRN | 1850 | 20319 | 2692171 | 57598276 | 1.95 | <2.2 × 10−16 |
Genes | 2200663 | 46065733 | 493358 | 11552862 | 1.12 | <2.2 × 10−16 |
Repeats | 459449 | 14743843 | 2234572 | 42874752 | 0.60 | <2.2 × 10−16 |
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Yuzon, J.D.; Travadon, R.; Malar C, M.; Tripathy, S.; Rank, N.; Mehl, H.K.; Rizzo, D.M.; Cobb, R.; Small, C.; Tang, T.; et al. Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum. Microorganisms 2020, 8, 940. https://doi.org/10.3390/microorganisms8060940
Yuzon JD, Travadon R, Malar C M, Tripathy S, Rank N, Mehl HK, Rizzo DM, Cobb R, Small C, Tang T, et al. Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum. Microorganisms. 2020; 8(6):940. https://doi.org/10.3390/microorganisms8060940
Chicago/Turabian StyleYuzon, Jennifer David, Renaud Travadon, Mathu Malar C, Sucheta Tripathy, Nathan Rank, Heather K. Mehl, David M. Rizzo, Richard Cobb, Corinn Small, Tiffany Tang, and et al. 2020. "Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum" Microorganisms 8, no. 6: 940. https://doi.org/10.3390/microorganisms8060940