Broad detection strategies for multiple targets of rose virome using next generation sequencing and bioinformatics (Lizbeth Peña-Zúñiga)
The rose rosette task force compiled the rose virome in 2016 and twenty-four viruses have been reported worldwide to infect roses. These viruses can reduce yields of garden roses because they cause damage to roses even before visible symptoms develop. Therefore, early viral infections may not be diagnosed until symptoms break out or fully develop in the plant. Common and frequently used detection of viral diseases affecting roses are serologically based, such as ELISA, or alternatively, lateral flow devices. Numerous molecular methods, RT-PCR based, are also available for individual pathosystems. Next-generation sequencing (NGS) has recently demonstrated applicability as a detection and diagnostic method because of the amplification and quality of data generated from a single sample. Massive parallel sequencing has the ability to amplify multiple unique DNA signatures of viruses during the infection of plants. Traditional studies and analysis of metagenomics outputs uses sequence similarities with a reference database. Furthermore, current detection techniques, unless reliable, sensitive, specific, accurate, and reproducible, target a limited number of viruses per assay. Electronic diagnostic nucleic acid analysis (EDNA) is a computational tool that combines NGS and bioinformatics and detects multiple pathogens in a single run. EDNA databases targeting the rose virome were built to prove this concept through simulated metagenomics runs mimicking single and multiple viral infections. Specific electronic probes (e-probes) with a length of 20-40 nucleotides were designed and tested in a series of sensitivity assays in silico. The EDNA 2 server was used, uploading metagenomic infected databases to find the limit of detection of this detection methodology. EDNA is able to detect either single or multiple viral pathogens, generating results in a few minutes. NGS and bioinformatics can be used as procedures that provide the framework for a new sequence-based type of diagnosis. EDNA can be applied and combined with other pathogen recognition methods for virus monitoring in microbial forensics and biosecurity, epidemiological studies and foundation stock of breeding in rose plants.
Lizbeth Peña-Zúñiga won an ISHS student award for the best oral presentation at the VII International Symposium on Rose Research and Cultivation in France in July 2017.
The full article is available in Chronica Horticulturae