First report of strawberry crinivirus 3 and strawberry crinivirus 4 on strawberry in China
Notice bibliographique
Résumé
Strawberry (Fragaria × ananassa) is grown in almost all regions of China. As a result of the rapid expansion in cultivation in recent years, China has become the world's largest strawberry producer (Wu et al., 4). In the past several years, viral diseases have emerged as a serious threat to strawberry production in many countries. To monitor the viral pathogen(s) on strawberry in Fuzhou, Fujian province, China, strawberry plants showing virus-like symptoms were collected from commercial fields in April and May 2016. Small RNAs from 12 strawberry plant samples were isolated and mixed into two pools of sRNAs, each pool representing six plants each. The NEBNext Multiplex Small RNA Library Prep Set was used for sRNA library construction and next-generation sequencing (NGS) was done using a paired-end (2 times 150) configuration on an Illumina MiSeq. NGS reads were trimmed with Trimmomatic (Bolger et al., 2) and assembled with Velvet (EMBL-EBI) and SeqMan software (Lasergene). BlastN (Altschul et al., 1) was used to compare the resulting contigs against the NCBI database. Eleven contigs (ranging from 59 to 293nt) obtained by NGS were found to share 98-100% nucleotide sequence identity with the partial genomic sequence of the putative strawberry crinivirus 3 (SCrV-3) isolate M1 (GenBank Accession No. EU267168) from Maryland, USA. Another nine contigs (ranging from 53 to 115 nt) shared 97-100% nucleotide sequence identity with the partial genomic sequence of a putative strawberry crinivirus 4 (SCrV-4) isolate B1156-M3 (EU490423) also from Maryland, USA. Strawberry vein banding virus, which is already known to infect strawberry in China, was also identified by Blast searches. RT-PCR was used to verify the presence of SCrV-3 and SCrV-4 in the strawberry plants. RT-PCR primers, SCrV3f1 (5'-AGCTTCGTCGCGTTAACGTGGAC-3') and SCrV3r1 (5'-GATTTCGCCTTCACAACGTCATAGTG-3'), were designed from the sequence of a ScrV3 isolate (EU267168) and generated a 1775 bp amplicon from two samples. The cloned and sequenced amplicon shared 99% nucleotide identity with the US SCrV-3 isolate (EU267168), confirming that the virus discovered in this study is SCrV-3. The Chinese isolate was named SCrV-3 FZ (KX852314). RT-PCR primers, SCrV4f1 (5'-AATTCTGATCCTATCCTTAGT-3') and SCrV4r1(5'-TGGTGATTGTGCTACTTCTTTAGC-3'), were designed from the sequence of a ScrV4 isolate (EU490423) and generated a 1452 bp amplicon from three samples. The cloned and sequenced amplicons shared 99% nucleotide identity with the American SCrV-4 isolate, and an isolate (KU237245) recently found in Canada (Ding et al., 3). The Chinese isolate was named SCrV-4 FZ1 (KY488557). A further 90 strawberry plants with virus-like symptoms collected from other regions in Fujian province were tested by RT-PCR for both viruses. SCrV-3 and SCrV-4 were not detected in any sample, suggesting that these viral pathogens are not widespread in this province. To our knowledge, this is the first report of SCrV-3 and SCrV-4 on strawberry in China. Further work is needed to determine the occurrence and distribution of SCrV-3 and SCrV-4, and its impact on strawberry production in China.
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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 | 0,002 | 0,000 |
| Communication savante | 0,001 | 0,001 |
| Science ouverte | 0,001 | 0,001 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 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 ».