Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability
Abstract
:1. Introduction
2. Materials and Methods
2.1. The Plant Samples
2.2. Total RNA Isolation and RT-PCR Diagnostics
2.3. Determination of CLRDV Genomes
2.4. Sequencing of CLRDV 5′- and 3′-Untranslated Ends
2.5. Sequence Comparisons
2.6. Phylogenetic Analysis
2.7. Recombination Analysis
2.8. Genetic Variability and Selection
3. Results
3.1. CLRDV Complete Genome Sequences
3.2. Pairwise Sequence Comparisons
3.3. Phylogenetic Relationship
3.4. Population Genetics
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Isolate | Location | Symptoms | PCR-ORF0 | # of Reads | Coverage | Reference |
---|---|---|---|---|---|---|
CLRDV-USA-AL-MC2 1 | Alabama | Severe | Positive | 33,141 | 850 | This study |
CLRDV-USA-AL-SC4 1 | Alabama | Mild | Positive | 16,964 | 435 | This study |
CLRDV-USA-TX-CT2 | Texas | Severe | Positive | 13,043 | 336 | This study |
CLRDV-USA-TX-CT3 1 | Texas | Severe | Positive | 147,639 | 3,780 | This study |
CLRDV-USA-TXa | Texas | Severe | Positive | Sanger-derived | This study | |
CLRDV-USA-TXb | Texas | Severe | Positive | Sanger-derived | This study | |
CLRDV-USA-TXc | Texas | Severe | Positive | Sanger-derived | This study | |
CLRDV-USA-TXd | Texas | Severe | Positive | Sanger-derived | This study | |
CLRDV-USA-AL 1 | Alabama | Severe | Positive | - | - | Avelar et al., 2020 |
Genomes—Nucleotide/Amino Acid | ORF0—Nucleotide/Amino Acid | ||||
---|---|---|---|---|---|
CLRDV-SA | CLRDV-US | CLRDV-SA | CLRDV-US | ||
CLRDV-SA | 95.9–99.5/- 1 | CLRDV-SA | 91.1–99.5/87.0–98.1 | ||
CLRDV-US | 94.0–96.2/- | 94.5–100.0/- | CLRDV-US | 89.4–94.3/81.6–90.4 | 92.1–100.0/90.8–100.0 |
ORF1—Nucleotide/Amino Acid | ORF1-ORF2—Nucleotide/Amino Acid | ||||
CLRDV-SA | CLRDV-US | CLRDV-SA | CLRDV-US | ||
CLRDV-SA | 94.3–99.5/93.8–99.5 | CLRDV-SA | 95.5–99.4/93.3–99.1 | ||
CLRDV-US | 92.4–95.5/90.3–95.0 | 93.8–100.0/91.6–100.0 | CLRDV-US | 92.9–96.2/87.8–94.7 | 92.5–100.0/87.5–100.0 |
ORF3—Nucleotide/Amino Acid | ORF3a—nucleotide/amino acid | ||||
CLRDV-SA | CLRDV-US | CLRDV-SA | CLRDV-US | ||
CLRDV-SA | 97.9–100.0/98.5–100.0 | CLRDV-SA | 97.8–100.0/100.0 | ||
CLRDV-US | 95.0–98.3/95.5–100.0 | 96.2–100.0/95.5–100.0 | CLRDV-US | 97.1–100.0/100.0 | 97.8–100.0/100.0 |
ORF4—Nucleotide/Amino Acid | ORF5—Nucleotide/Amino Acid | ||||
CLRDV-SA | CLRDV-US | CLRDV-SA | CLRDV-US | ||
CLRDV-SA | 98.1–100.0/95.4–100.0 | CLRDV-SA | 96.7–99.7/96.8–100.0 | ||
CLRDV-US | 94.9–98.9/89.7–97.1 | 96.0–100.0/92.5–100.0 | CLRDV-US | 94.8–96.8/94.1–98.3 | 96.5–100.0/95.7–100.0 |
Subpopulations | Nst 1 | Fst 1 | |
---|---|---|---|
subclade 1-US | subclade 2-US | 0.52 | 0.51 |
subclade 1-US | Subclade 3-US | 0.31 | 0.31 |
subclade 1-US | US | 0.07 | 0.07 |
subclade 1-US | typical-SA | 0.72 | 0.72 |
subclade 1-US | atypical-SA | 0.67 | 0.67 |
subclade 1-US | SA | 0.56 | 0.56 |
subclade 2-US | subclade 3-US | 0.51 | 0.50 |
subclade 2-US | US | 0.27 | 0.27 |
subclade 2-US | typical-SA | 0.71 | 0.71 |
subclade 2-US | atypical-SA | 0.66 | 0.66 |
subclade 2-US | SA | 0.56 | 0.55 |
subclade 3-US | US | 0.06 | 0.06 |
subclade 3-US | typical-SA | 0.62 | 0.62 |
subclade 3-US | atypical-SA | 0.56 | 0.55 |
subclade 3-US | SA | 0.45 | 0.45 |
US | typical-SA | 0.58 | 0.57 |
US | atypical-SA | 0.53 | 0.52 |
US | SA | 0.42 | 0.41 |
typical-SA | atypical-SA | 0.60 | 0.60 |
typical-SA | SA | 0.26 | 0.26 |
atypical-SA | SA | − 0.07 | − 0.07 |
Dataset | Gene | SLAC (dN/dS) | FEL (# of Sites) | |
---|---|---|---|---|
Negative | Positive | |||
CLRDV-subclade1-US | ORF0 | 0.52 | 2 | 0 |
ORF1 | 0.36 | 3 | 0 | |
ORF2 | 0.15 | 33 | 0 | |
ORF3 | 0.16 | 3 | 0 | |
ORF4 | 1.19 | 1 | 0 | |
ORF5 | 0.19 | 30 | 0 | |
CLRDV-subclade2-US | ORF0 | 0.36 | 8 | 0 |
ORF1 | 0.28 | 27 | 0 | |
ORF2 | 0.19 | 54 | 1 | |
ORF3 | − 1 | − | − | |
ORF4 | − | − | − | |
ORF5 | 0.24 | 20 | 0 | |
CLRDV-subclade3-US | ORF0 | 0.67 | 3 | 0 |
ORF1 | 0.55 | 17 | 0 | |
ORF2 | 0.47 | 54 | 3 | |
ORF3 | 0.50 | 6 | 0 | |
ORF4 | 0.98 | 1 | 1 | |
ORF5 | 0.38 | 29 | 0 | |
CLRDV-atypical-SA 2 | ORF0 | 1.63 | 1 | 0 |
ORF1 | 0.33 | 13 | 0 | |
ORF2 | 0.25 | 32 | 0 | |
ORF3 | 0.16 | 5 | 1 | |
ORF4 | 1.26 | 1 | 0 | |
ORF5 | 0.15 | 16 | 1 |
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Ramos-Sobrinho, R.; Adegbola, R.O.; Lawrence, K.; Schrimsher, D.W.; Isakeit, T.; Alabi, O.J.; Brown, J.K. Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability. Viruses 2021, 13, 2230. https://doi.org/10.3390/v13112230
Ramos-Sobrinho R, Adegbola RO, Lawrence K, Schrimsher DW, Isakeit T, Alabi OJ, Brown JK. Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability. Viruses. 2021; 13(11):2230. https://doi.org/10.3390/v13112230
Chicago/Turabian StyleRamos-Sobrinho, Roberto, Raphael O. Adegbola, Kathy Lawrence, Drew W. Schrimsher, Thomas Isakeit, Olufemi J. Alabi, and Judith K. Brown. 2021. "Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability" Viruses 13, no. 11: 2230. https://doi.org/10.3390/v13112230
APA StyleRamos-Sobrinho, R., Adegbola, R. O., Lawrence, K., Schrimsher, D. W., Isakeit, T., Alabi, O. J., & Brown, J. K. (2021). Cotton Leafroll Dwarf Virus US Genomes Comprise Divergent Subpopulations and Harbor Extensive Variability. Viruses, 13(11), 2230. https://doi.org/10.3390/v13112230