Abstract
Rubus yellow net virus (RYNV) infects Rubus spp., causing a severe decline when present in mixed infections with other viruses. RYNV belongs to the family Caulimoviridae, also known as plant pararetroviruses, which can exist as episomal or integrated elements (endogenous). Most of integrated pararetroviruses are noninfectious; however, a few cases have been reported where they excised from the plant genome and formed infectious particles. Graft transmission onto indicator plants R. occidentalis "Munger" has been the standard test method for RYNV detection in certification programs. Previously, it was noticed that some RYNV PCR-positive plants did not induce symptoms on "Munger", suggesting an integration event. In this study, bio-indexing and different molecular techniques were employed to differentiate between integrated and episomal RYNV sequences. Reverse transcription-PCR using RYNV-specific oligonucleotides after DNase treatment generated positive results for the virus in graft transmissible isolates (episomal) only. To confirm these results, rolling circle amplification on DNA preparations from the same samples resulted in amplicons identified as RYNV only from plants with graft transmissible RYNV. High-throughput sequencing was used to identify the RYNV-like sequences present in the host DNA. These results indicate the integration of RYNV into the red raspberry genome and highlight the necessity to recognize this phenomenon (integration) in future Rubus quarantine and certification programs.
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Claims 4
Claim · model-written summary
RT-PCR detected RYNV only in graft transmissible isolates.
- Taxon
- red raspberry
_Rubus_idaeus_-_Feuillage.jpg?width=60)
Rubus idaeuse1 - Interactor
- RYNVe0pathogen
- Outcome
- positive results for the viruse2
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
_Rubus_idaeus_-_Feuillage.jpg?width=500)
Verbatim
e0“Rubus yellow net virus (RYNV) infects Rubus spp.”
e1“the integration of RYNV into the red raspberry genome”
e2“Reverse transcription-PCR using RYNV-specific oligonucleotides after DNase treatment generated positive results for the virus in graft transmissible isolates (episomal) only”
Claim · model-written summary
Rolling circle amplification identified RYNV amplicons only from plants with graft transmissible RYNV.
- Taxon
- red raspberryRubus idaeuse1
- Interactor
- RYNVe0pathogen
- Outcome
- amplicons identified as RYNVe3
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Rubus yellow net virus (RYNV) infects Rubus spp.”
e1“the integration of RYNV into the red raspberry genome”
e3“rolling circle amplification on DNA preparations from the same samples resulted in amplicons identified as RYNV only from plants with graft transmissible RYNV”
Claim · model-written summary
High-throughput sequencing identified RYNV-like sequences present in the host DNA.
- Taxon
- red raspberryRubus idaeuse1
- Interactor
- RYNVe0pathogen
- Outcome
- RYNV-like sequences present in the host DNAe4
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Rubus yellow net virus (RYNV) infects Rubus spp.”
e1“the integration of RYNV into the red raspberry genome”
e4“High-throughput sequencing was used to identify the RYNV-like sequences present in the host DNA”
Claim · model-written summary
RYNV is integrated into the red raspberry genome.
- Taxon
- red raspberryRubus idaeuse1
- Interactor
- RYNVe0pathogen
- Outcome
- the integration of RYNV into the red raspberry genomee1
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Rubus yellow net virus (RYNV) infects Rubus spp.”
e1“the integration of RYNV into the red raspberry genome”