Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage
Abstract
:1. Introduction
2. Results
2.1. Population Structure and Geographical Distribution of CTV Isolates in Uruguay
2.2. Genetic Divergence Analysis
Region | NC average | RB | T3 | T30 | T36 | VT | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
nt | aa | nt | aa | nt | aa | nt | aa | nt | aa | nt | aa | |
p25 | 98.8 ± 0.1 | 98.8 ± 0.2 | 90.6 ± 1.3 | 95.2 ± 1.2 | 89.4 ± 1.5 | 96.4 ± 1.2 | 89.1 ± 1.5 | 94.4 ± 1.5 | 89.1 ± 1.5 | 93.6 ± 1.6 | 90.2 ± 1.4 | 95.4 ± 1.2 |
p20 | 98.9 ± 0.2 | 99.1 ± 0.3 | 84.4 ± 2.5 | 93.9 ± 2.1 | 82.1 ± 2.7 | 92.6 ± 2.2 | 81.8 ± 2.9 | 92.2 ± 2.4 | 88.6± 1.8 | 95.3 ± 1.8 | 84.1 ± 2.4 | 93.1 ± 2.2 |
p20 | 97.5 ± 0.3 | 96.9 ± 0.7 | 87.3 ± 1.5 | 88.2 ± 2.2 | 90.5 ± 1.2 | 89.9 ± 2.0 | 89.9 ± 1.2 | 90.9 ± 2.0 | 89.3 ± 1.3 | 88.5 ± 2.3 | 89.3 ± 1.3 | 88.7 ± 2.1 |
2.3. Recombination Analysis
3. Discussion
3.1. Composition of Viral Populations and Geographical Information
3.2. Phylogenetic Relationships among the Isolates
3.3. Genetic Divergence of CTV Populations in Uruguay
3.4. Evidence of Recombination
4. Materials and Methods
4.1. Virus Isolates
Isolate | Host | Origin | Collection date | Aspect of the tree in the field | Stem Pitting | ELISA | Number of clones | ||
---|---|---|---|---|---|---|---|---|---|
p25 | p20 | p23 | |||||||
119 | Lemon | San José | 1993 | Stunted | NA | + | 12 | 9 | 11 |
120 | Washington Navel sweet orange | Paysandú | 2006 | Stunted | NA | + | 8 | 4 | 14 |
121 | Star Ruby grapefruit | Salto | 1997 | Stunted | + | - | 3 | 6 | NC |
122 | Star Ruby grapefruit | Salto | 1997 | Stunted | + | + | 8 | 12 | 12 |
123 | Lemon | San José | 1998 | Normal | ++ | + | 12 | 5 | 10 |
124 | Lemon | San José | 1998 | Normal | ++ | UND | 11 | 11 | 12 |
125 | Lemon | San José | 1998 | Stunted | +++ | - | 1 | 14 | 8 |
164 | Lemon | San José | 1998 | Stunted | +++ | + | 8 | 12 | 11 |
165 | Valencia sweet orange | San José | 1998 | Stunted | - | + | 3 | 13 | 8 |
166 | Lemon | Canelones | 1998 | Stunted | +++ | - | 9 | 9 | 10 |
167 | Lemon | Canelones | 1998 | Normal | ++ | + | 11 | 11 | 10 |
168 | Star Ruby grapefruit | Salto | 1998 | Stunted | - | UND | NC | 12 | NC |
MIL | Satsuma Owari mandarin | Salto | 2012 | Normal | NA | NA | NC | 12 | 9 |
4.2. RNA Extraction, cDNA Synthesis, and PCR Amplification
Name | Sequence | Genome Position* | Expected Size (bp) | Reference |
---|---|---|---|---|
p20F | 5' ACAATATGCGAGCTTACTTTA 3' | 17691–17710 | 555 | [18] |
p20R | 5' AACCTACACGCAAGATGGA 3' | 18229–18246 | ||
p23F | 5' GTCTCTCCATCTTGCGGTGTAG 3' | 18224–18244 | 733 | [30] |
p23R | 5' CAATCAGATGAAGTGGTG3' | 18941–18957 | ||
p25F | 5' TGAATTATGGACGACGAAAC 3' | 16079–16097 | 676 | |
p25R | 5' TCAACGTGTGTTGAATTTCCC 3' | 16736–16755 |
4.3. Cloning
4.4. Nucleotide Sequences and Phylogenetic Analysis
4.5. Recombination Analysis
4.6. Nucleotide Sequence Accession Number
5. Conclusions
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interests
References
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Benítez-Galeano, M.J.; Rubio, L.; Bertalmío, A.; Maeso, D.; Rivas, F.; Colina, R. Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage. Viruses 2015, 7, 4152-4168. https://doi.org/10.3390/v7072814
Benítez-Galeano MJ, Rubio L, Bertalmío A, Maeso D, Rivas F, Colina R. Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage. Viruses. 2015; 7(7):4152-4168. https://doi.org/10.3390/v7072814
Chicago/Turabian StyleBenítez-Galeano, María José, Leticia Rubio, Ana Bertalmío, Diego Maeso, Fernando Rivas, and Rodney Colina. 2015. "Phylogenetic Studies of the Three RNA Silencing Suppressor Genes of South American CTV Isolates Reveal the Circulation of a Novel Genetic Lineage" Viruses 7, no. 7: 4152-4168. https://doi.org/10.3390/v7072814