First Report of <i>Mexican papita viroid</i> Infecting Greenhouse Tomato in Canada
Bibliographic record
Abstract
In the summer of 2008, tomato (Solanum lycopersicum) plants in a large greenhouse tomato facility located in Delta, British Columbia, Canada exhibited general stunting, chlorosis, and purple-leaf symptoms that were distinct from those of Pepino mosaic virus (PepMV) (1). Diseased plants were localized mainly in two rows in a section of the greenhouse and produced no fruits or only fruits with reduced size. Leaf samples were collected from four individuals among numerous diseased plants in this greenhouse. Screening samples by ELISA, PCR, or reverse transcription (RT)-PCR for PepMV, Tomato spotted wilt virus, Tomato yellow leaf curl virus, Tomato torrado virus, Tomato apex necrosis virus, and Begomovirus, Tobamovirus, and Pospiviroid species showed that all four plants had a mixed infection of both PepMV and a pospiviroid. RT-PCR with the pospiviroid-specific primers Pospil-RE and Pospil-FW (3) amplified the expected 196-bp products from these four samples. Each amplicon was cloned into the pCR4-TOPO vector (Invitrogen, Carlsbad, CA) and one individual cDNA clone from each isolate was sequenced. BLASTN analyses of nucleotide sequences of these clones showed 97 to 99% identity to Mexican papita viroid (MPVd) isolates currently in the NCBI Genbank. These four newly identified MPVd isolates were not identical; seven nucleotide substitutions or indels were identified in this region. The full viroid genome was obtained by RT-PCR in isolate VF2 with a new reverse primer MPVd-RE (5' GATCCCTGAAGCGCTCCT 3') in combination with the forward primer Pospil-FW (3). Using the same approach as stated above, this amplicon was cloned and sequenced. The nucleotide sequence of the 196-nt amplicon previously amplified and cloned from the isolate VF2 genome was identical to this region in the genomic clone. BLASTN analysis showed that the VF2 genome (GenBank Accession No. FJ824844) had >98% sequence identity to each of nine MPVd isolates (GenBank Accession Nos. L78454 and L78456-L78463), 94% identity to Tomato planta macho viroid (TPMVd) (GenBank Accession No. K00817) and ~80% identity to Tomato chlorotic dwarf viroid (GenBank Accession Nos. EF582392-EF582393). Prior to this find, MPVd had been identified only in papita (Solanum cardiophyllum) in Mexico and is considered a possible ancestor of TPMVd, Potato spindle tuber viroid (PSTVd), and possibly of other PSTVd-group viroids now infecting crop plants (2). The origin of MPVd in this greenhouse facility in Delta, British Columbia is unknown. The infected plants were destroyed by the grower. The pathogenicity of MPVd isolates characterized in this study was not evaluated on tomato because of quarantine regulations governing this viroid in the United States. The identification of MPVd infecting an important agricultural crop (tomato) outside its center of origin in Mexico indicates a potentially important major shift in the epidemiology of MPVd. To our knowledge this is the first report of MPVd from tomato in Canada. References: (1). K.-S. Ling et al. Plant Dis. 92:1683, 2008. (2) J. P. Martinez-Soriano et al. Proc. Natl. Acad. Sci. U.S.A. 93:9397, 1996. (3) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 110:823, 2004.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".