Characterization of the partial RNA1 and RNA2 3′ untranslated region of Tomato ringspot virus isolates from North America
Bibliographic record
Abstract
Abstract The 3′ untranslated regions (UTRs) of RNA1 and RNA2 of Tomato ringspot virus (ToRSV) are 1.3 kb in size and virtually identical. In this study, sequences containing most of the 3′ UTRs (1168–1265 bp) were determined from 18 ToRSV isolates collected from fruit trees, small fruits and grapevines in North America. Pairwise nucleotide sequence comparisons with sequences of two isolates available in GenBank showed identities ranging from 95.1 to 100% for the majority of ToRSV isolates. Most genetic variation occurs as point mutations and single insertions and/or deletions. Phylogenetic analysis showed that 17 of the 20 isolates grouped together into a major cluster and three isolates grouped into two minor clusters, with genetic divergence rates among the three clusters of 11.8% to 23.8%. No correlation was found between the 3′ UTR sequences and symptom expression on Nicotiana benthamiana, host plant or geographic origin of ToRSV isolates. RT-PCR using primers designed within the highly conserved 3′ UTR regions detected all 18 ToRSV isolates as well as two isolates from a vineyard. This assay can serve as a practical methodology for the sensitive detection of varied ToRSV isolates as it is more sensitive than a RT-PCR assay based on previously reported U1/D1 primers. Résumé Les séquences non traduites (3′ UTR) de l'ARN1 et de l'ARN2 du virus des taches annulaires de la tomate (ToRSV) mesurent 1,3 kb et sont essentiellement identiques. Dans cette étude, les séquences contenant la majorité des 3′ UTR (1168–1265 bp) ont été déterminées á partir de 18 isolats de ToRSV collectés en Amérique du Nord sur des arbres fruitiers, des petits fruits et des vignes. Les comparaisons binaires de séquences de nucléotides avec les séquences de deux isolats de la GenBank ont montré des similarités variant de 95.1% á 100% en ce qui a trait á la majorité des isolats de ToRSV. La plupart des variations génétiques se produisent en tant que mutations ponctuelles et qu'insertions/délétions uniques. L'analyse phylogénétique a montré que 17 des 20 isolats étaient groupés en super-famille et que trois isolats l'étaient en deux familles mineures, dont les taux de divergence génétique, chez les trois familles, variaient de 11.8% á 23.8%. Nous n'avons trouvé aucune corrélation entre les séquences 3′ UTR et l'expression des symptômes sur Nicotiana benthamiana, plante hôte ou origine géographique des isolats de ToRSV. Des amorces RT-PCR conçues dans les régions 3′ UTR hautement conservées ont permis de détecter les 18 isolats de ToRSV ainsi que deux isolats provenant d'un vignoble. Ce test peut être utilisé comme méthode pratique pour la détection précise d'isolats de ToRSV puisqu'il est plus sensible qu'un test RT-PCR basé sur les amorces U1/D1 utilisées précédemment. Keywords: ToRSV3′ UTRgenetic variationphylogenetic relationshipsRT-PCR detectionMots clés: 3′ UTRdétection par RT-PCRrelations phylogénétiquesToRSVvariation génétique Acknowledgements The authors would like to thank Dennis Bennett, Whitney Hymes, Anthony Rugh and Rachael Kime for their technical assistance and Michael Bernardy, Bob Martin and Joseph Postman for sharing ToRSV isolates.
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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".