Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays
| Autor: | Maher Al Rwahnih, Vicki Klaassen, Min Sook Hwang, Alfredo Diaz-Lara, Kristian Stevens |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
0301 basic medicine viruses detection virus Genome Viral 01 natural sciences Microbiology Fragaria Virus Article high throughput sequencing 03 medical and health sciences Crinivirus diagnostic assay Virology RNA Viruses Viral Phylogeny Plant Diseases Apple mosaic virus virome Genome biology Strawberry mottle virus Reverse Transcriptase Polymerase Chain Reaction RT-qPCR Chromosome Mapping Genetic Variation High-Throughput Nucleotide Sequencing Reproducibility of Results germplasm biology.organism_classification QR1-502 030104 developmental biology Infectious Diseases Strawberry vein banding virus Strawberry crinkle virus Tomato ringspot virus Metagenomics strawberry Infection 010606 plant biology & botany Biotechnology |
| Zdroj: | Viruses Viruses, Vol 13, Iss 1442, p 1442 (2021) Volume 13 Issue 8 Viruses, vol 13, iss 8 |
| ISSN: | 1999-4915 |
| Popis: | Viruses are considered of major importance in strawberry (Fragaria × ananassa Duchesne) production given their negative impact on plant vigor and growth. Strawberry accessions from the National Clonal Germplasm Repository were screened for viruses using high throughput sequencing (HTS). Analyses of sequence information from 45 plants identified multiple variants of 14 known viruses, comprising strawberry mottle virus (SMoV), beet pseudo yellows virus (BPYV), strawberry pallidosis-associated virus (SPaV), tomato ringspot virus (ToRSV), strawberry mild yellow edge virus (SMYEV), strawberry vein banding virus (SVBV), strawberry crinkle virus (SCV), strawberry polerovirus 1 (SPV-1), apple mosaic virus (ApMV), strawberry chlorotic fleck virus (SCFaV), strawberry crinivirus 4 (SCrV-4), strawberry crinivirus 3 (SCrV-3), Fragaria chiloensis latent virus (FClLV) and Fragaria chiloensis cryptic virus (FCCV). Genetic diversity of sequenced virus isolates was investigated via sequence homology analysis, and partial-genome sequences were deposited into GenBank. To confirm the HTS results and expand the detection of strawberry viruses, new reverse transcription quantitative PCR (RT-qPCR) assays were designed for the above-listed viruses. Further in silico and in vitro validation of the new diagnostic assays indicated high efficiency and reliability. Thus, the occurrence of different viruses, including divergent variants, among the strawberries was verified. This is the first viral metagenomic survey in strawberry, additionally, this study describes the design and validation of multiple RT-qPCR assays for strawberry viruses, which represent important detection tools for clean plant programs. |
| Databáze: | OpenAIRE |
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