First detection of saffron dwarf virus, wheat dwarf virus, wheat dwarf virus‐associated alphasatellite and a new putative potyvirus species in saffron in Iran
Notice bibliographique
Résumé
Saffron (Crocus sativus, Iridaceae), the most valuable spice in the world, is propagated vegetatively through corms and cultivated widely in Iran (Moradi et al., 2021). Several viruses have been reported in saffron in Iran: saffron latent virus, saffron yellow mosaic virus and beet western yellows virus (Parizad et al., 2018; Tavoosi et al., 2024; Haseli et al., 2024). During 2022, a total of 100 leaf tissue samples were collected from diseased (leaf curling, mosaics and mottling) (Figure 1) and asymptomatic saffron plants growing in cultivated fields in Fars and Tehran provinces in Iran (an area of 8,385 and 1,650 ha, respectively). The diseased and asymptomatic samples were pooled together into two groups of 50. Viral particles were enriched from the pooled samples using the virion-associated nucleic acid extraction protocol (Maclot et al., 2021). Libraries were prepared with the Illumina TruSeq PCR-Free preparation kit, and sequencing was performed on the NovaSeq 6000 platform with paired-end reads (2 × 150 bp). A total of 2,305,263 raw reads were obtained by high-throughput sequencing (HTS) and trimmed to 1,609,204 high-quality reads (with a quality score above 32) using BBDuK (version 38.84) with default parameters within Geneious Prime 2020.2. After de novo contig assembly using the SPAdes assembler (version 3.13.0), 6,608 contigs were generated. The tblastx comparison was conducted with a local database created using the viral refseq database (downloaded from NCBI, November 2021). The tentative viral contigs were extended by iterative mapping using Geneious assembler (custom sensitivity mode, with mismatch set according to the demarcation criteria of each virus). This resulted in three sequences with high nucleotide identity with known species: a sequence of 2,538 nt with 98% identity to wheat dwarf virus (WDV; GenBank Accession No. KU877917); a sequence of 2,726 nt with 96% identity to saffron dwarf virus (SaDV, BK067261); and a sequence of 1,486 nt with 89% identity to wheat dwarf virus-associated alphasatellite (WDVaA, PP445014). In addition, a contig of 9,548 nt (PQ740911) had limited homology (<71%) with various potyviruses, and the putative polyprotein (3,113 aa) shared 62% identity with Narcissus yellow stripe virus (BBE01234), suggesting that this sequence might correspond to a new potyvirus based on the demarcation threshold for members of the genus (Inoue-Nagata et al., 2022). To confirm the presence of the viruses detected in the pooled samples, PCR/RT-PCR assays were developed using novel specific primer pairs (Table 1). Amplified cDNA fragments of the expected size were sequenced bi-directionally, and showed 93–100% identity with the corresponding genome sequences obtained by HTS. These detections correspond to the first report of the presence of WDV (PQ740908), WDVaA (PQ740910) and SaDV (PQ740909) in saffron plants in Iran. The discovery of a putative new potyvirus (PQ740911), tentatively named Potyvirus crociranense (saffron Iran virus, SaIRV) will be further investigated. HTS data is available under Bioproject PRJNA1187297. Additional research is necessary to determine the prevalence and effects of these viruses on saffron crop. A. Dizadji, A. Golnaraghi and S. Massart contributed equally to this report. The authors would like to acknowledge the financial supports of Iran National Science Foundation (INSF, Project No. 4000914), Fond National de la Recherche Scientifique (FNRS, Belgium; Grant J.0149.20) and University of Tehran (73148924/6/19).
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,000 |
| Méta-épidémiologie (sens large) | 0,001 | 0,001 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,001 | 0,000 |
| Communication savante | 0,001 | 0,000 |
| Science ouverte | 0,000 | 0,001 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».