Malvaviscus yellow mosaic virus, a divergent begomovirus carrying a nanovirus‐like nonanucleotide and a modified stem‐loop structure
Bibliographic record
Abstract
Abstract Begomoviruses (family Geminiviridae ) have a circular, ssDNA genome encapsidated in twinned icosahedral particles. Numerous begomoviruses infecting noncultivated malvaceous plants have been described, and evidence suggests that they may have given rise to some of the viruses currently found in crop plants. Here we describe an atypical begomovirus infecting ornamental Turk's hat plants ( Malvaviscus arboreus , Malvaceae). Total DNA was extracted, and the viral genome was amplified by rolling‐circle amplification (RCA), cloned and sequenced. Sequence and phylogenetic analyses indicated that the virus corresponds to a new begomovirus phylogenetically related to other malvaceous‐infecting begomoviruses from Brazil, and for which the name malvaviscus yellow mosaic virus (MvYMV) is proposed. M. arboreus plants inoculated with MvYMV infectious clones showed bright yellow mosaic and the virus progeny was identical to the isolate inoculated, thus fulfilling Koch's postulates. Strikingly, MvYMV has a nanovirus/alphasatellite‐like nonanucleotide sequence (5′‐TAGTATTAC‐3′). Moreover, a short sequence located 5′ of the nonanucleotide potentially forms a minor hairpin structure embedded in the major hairpin. Intramolecular interactions involving the sequence of the atypical hairpin structure were predicted and functional analyses were conducted to assess its biological relevance, revealing that the MvYMV Rep protein recognises this unique replication origin but not the typical begomovirus origin. Thus, MvYMV is a begomovirus with an atypical origin of replication and naturally found in noncultivated malvaceous plants.
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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) | 0.001 | 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 | 0.001 |
| 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".