A next-generation sequencing approach for the simultaneous detection of plant viruses for plant quarantine testing
Notice bibliographique
Résumé
<p>Potato (Solanum tuberosum L.) is one of the most important vegetable crops in the world and plays a vital role in human nutrition and food security. However, potato crops have been known to be infected by at least 40 viruses and 2 viroids contributing to reduced yields. The detection of viruses and viroids is limited from a diagnostic perspective as there are very few validated procedures that exist. Globalization of agriculture has meant that crop plants are now grown further from their centres of origin and far from the pathogens that had co-evolved with them. Crops introduced to a new area may be poorly equipped to resists pathogenic organisms that are already resident. Similarly, increased trade leads to the potential of introducing pathogenic organisms that may not be endemic to a particular region leading to outbreaks having the potential for extreme economic consequences.</p>\n<p>The Potato Post-Entry Quarantine (PPEQ) program implemented by the Canadian Food Inspection Agency (CFIA) was established under the Plant Protection Act to prevent the introduction of economically devastating foreign plant diseases into Canada. The PPEQ program allows the Canadian potato industry to obtain disease-free germplasm from other countries to meet international demands for the production of seed, table, or processing potatoes. The diagnostic methods employed in the current PPEQ program are time-consuming and rely on both traditional and modern techniques. Many of these techniques are only specific for single viral targets having weak specificity and sensitivity. Recently, next-generation sequencing (NGS) platforms have been widely accepted as high-throughput, unbiased technologies that have attractive features in the field of plant diagnostics. NGS has opened the door to very sensitive and specific testing with the opportunity to detect multiple pathogens in a single sample.</p>\n<p>In this study, various RNA extraction methods were evaluated to acquire high quality non-fragmented RNA. Integrity values ranging from 7-9 were obtained using the PureLink Total RNA Mini kit and lysis buffer (Thermo Scientific, Waltham, USA). Using this method for RNA extraction, the application of NGS was explored to determine if plant pathogenic viral genomes could be generated de novo via a bioinformatic pathway when mapped to the whole host genome without a priori knowledge of their presence. Intended potato tuber imports intercepted from Bangladesh showed that viral contigs from multiple mixed infections of Potato aucuba mosaic virus (PAMV), Potato virus Y (PVY), Potato virus X (PVX), Potato virus S (PVS), Potato virus M (PVM), Potato leaf roll virus (PLRV), and Tomato chlorosis virus (ToCV) could be detected simultaneously with high specificity. Similarly, NGS was successfully applied to determine the causal agents of unknown etiology in tomato (S. lycopersicum) without a priori knowledge of their existence in the sample and confirmed the first report of Southern tomato virus (STV) in Canada. This NGS protocol will aid in the diagnosis of pathogens that were otherwise unable to be tested for within the current PPEQ program as well as identify unknown agents from other samples allowing for the development of new routine diagnostic assays and timely epidemiological and eradication strategies to be performed.</p>\n<p></p>
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 distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,001 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| 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 tête enseignante, 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 ».