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Sequencing viral siRNAs to identify previously undescribed viruses and viroids in a panel of ornamental plant samples structured as a matrix of pools
- Source :
- Virus Research, Virus Research, Elsevier, 2017, 241, pp.19-28. ⟨10.1016/j.virusres.2017.05.019⟩, Virus Research, Elsevier, 2017, Accepted manuscript, 31 May 2017, ⟨10.1016/j.virusres.2017.05.019⟩, Virus Research (241), 19-28. (2017)
- Publication Year :
- 2017
- Publisher :
- HAL CCSD, 2017.
-
Abstract
- paper originating from a presentation made at the 13th International Plant Virus Epidemiology Symposium held at Avignon, France June 6-10, 2016; Ornamental plants constitute a largely unknown and potentially important source of pathogens affecting not only ornamental plants, but also major crop species. We have carried out studies using high-throughput sequencing of 21-24 nt RNAs from potentially virus-infected ornamental plants, followed by assembly of sequence scaffolds, to identify the virus and viroid genomes present in a panel of 67 plant samples representing 46 species belonging to the main sectors of the ornamental plant industry (cut flowers, pot plants, bulbs). A pilot study demonstrated that samples could be pooled (5 samples per pool), and the overall process simplified without loss of detection of important known pathogens. In a full-scale study, pools of 5 samples were organized in a 5 × 5 matrix to facilitate attribution of a sequence to a precise sample directly from analysis of the matrix. In the total of 67 samples analyzed in the two studies, partial sequences suggesting the presence of 25 previously unknown viruses and viroids were detected, including all types of virus and viroid genomes, and also showed four cases of known viruses infecting previously undescribed hosts. Furthermore, two types of potential mis-assembly were analyzed, and were shown to not affect the conclusions regarding the presence of the pathogens identified, but show that mis-assembly can affect the results when the objective is determining complete bona fide viral genome sequences. These results clearly confirm that ornamental plants constitute a potential source of unknown viruses and viroids that could have a major impact on agriculture, and that sequencing siRNAs of potentially virus- or viroid-infected ornamental plants is an effective means for screening for the presence of potentially important pathogens.
- Subjects :
- 0301 basic medicine
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences
Cancer Research
Small interfering RNA
Viroid
Virologie
viruses
next-generation sequencing
siRNA
virus
viroid
ornamental plant
Genome
Plant Viruses
Potential source
RNA, Small Interfering
pathologie végétale
virus à arn
Genetics
High-Throughput Nucleotide Sequencing
food and beverages
Plants
Viroids
Agricultural sciences
Infectious Diseases
[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
séquençage de gènes
Phytopathology and phytopharmacy
Genome, Viral
Biology
Crop species
Virus
DNA sequencing
plante ornementale
03 medical and health sciences
phytopathogenic virus
viroide phytopathogène
Virology
Ornamental plant
emergence de maladies
Plant Diseases
virus phytopathogène
Base Sequence
Sequence Analysis, RNA
biology.organism_classification
Phytopathologie et phytopharmacie
rna virus
030104 developmental biology
Sciences agricoles
Subjects
Details
- Language :
- English
- ISSN :
- 01681702
- Database :
- OpenAIRE
- Journal :
- Virus Research, Virus Research, Elsevier, 2017, 241, pp.19-28. ⟨10.1016/j.virusres.2017.05.019⟩, Virus Research, Elsevier, 2017, Accepted manuscript, 31 May 2017, ⟨10.1016/j.virusres.2017.05.019⟩, Virus Research (241), 19-28. (2017)
- Accession number :
- edsair.doi.dedup.....ccc321cbaeb8dbafba1610dbf126d2a9