期刊
PLANTS-BASEL
卷 11, 期 15, 页码 -出版社
MDPI
DOI: 10.3390/plants11151939
关键词
CTV; hop stunt viroid (HSVd); citrus dwarfing viroid (CDVd); citrus exocortis viroid (CEVd); next-generation sequencing; repeatability; specificity
资金
- Citrus Research International (CRI)
- Research for Citrus Exports Fund of the Department of Science and Innovation (DSI), South African Government [1241]
The credibility of high-throughput sequencing (HTS) as a pathogen detection assay for citrus viruses was assessed in this study. The results showed that HTS has good reproducibility and sensitivity, and its detection capability is comparable or more sensitive than the standard RT-PCR assays.
The credibility of a pathogen detection assay is measured using specific parameters including repeatability, specificity, sensitivity, and reproducibility. The use of high-throughput sequencing (HTS) as a routine detection assay for viruses and viroids in citrus was previously evaluated and, in this study, the reproducibility and sensitivity of the HTS assay were assessed. To evaluate the reproducibility of HTS, the same plants assayed in a previous study were sampled again, one year later, and assessed in triplicate using the same analyses to construct the virome profile. The sensitivity of the HTS assay was compared to routinely used RT-PCR assays in a time course experiment, to compensate for natural pathogen accumulation in plants over time. The HTS pipeline applied in this study produced reproducible and comparable results to standard RT-PCR assays for the detection of CTV and three viroid species in citrus. Even though the limit of detection of HTS can be influenced by pathogen concentration, sample processing method and sequencing depth, detection with HTS was found to be either equivalent or more sensitive than RT-PCR in this study.
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