Next generation sequencing for rose viruses

6 years ago

There is a relatively new method for detecting rose viruses. It is called Next Generation Sequencing. A review has just appeared (Oct 24, 2017) that may be useful for those with science backgrounds:

Title: "Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice"

https://www.frontiersin.org/articles/10.3389/fpls.2017.01770/full

---------------------------------------------------------------------------

An example of its use is the recent report concerning a number of rose viruses found in a wild rose (Rosa multiflora Thunb) in China:

Title: "Deep sequencing reveals a novel closterovirus associated with wild rose leaf rosette disease"

The following quote from the abstract identifies the viruses found:

"The assembly of siRNAs led to the reconstruction of the complete genomes of three known viruses, namely Apple stem grooving virus (ASGV), Blackberry chlorotic ringspot virus (BCRV) and Prunus necrotic ringspot virus (PNRSV), and of a novel virus provisionally named 'rose leaf rosette-associated virus' (RLRaV). "

Please note that PNRSV (one of the common virus found in U.S. roses and thought by some not to spread by natural means) was found.

https://www.ncbi.nlm.nih.gov/pubmed/25187347

Sort by:Oldest

Comment (1)

henry_kuska
Original Author
6 years ago
last modified: 6 years ago
This paper was presented this summer at the VII International Symposium
on Rose Research and Cultivation, Angers, France, July 6, 2017.

"Session 7 Oral Presentation 3
Title: Testing EDNA-ROSE: a novel in silico approach for detection of rose
viruses combining next generation sequencing and bioinformatics.

Authors: Lizbeth Peña-Zuñigaa, Andrés Espíndolaa, Patricia Kleinb, Thomas Debenerc, Jasper Reesd, David Byrneb, and Francisco M. Ochoa-Coronaa.

Authors affiliations:
aOklahoma State University, Stillwater, OK, USA.
bTexas A&M University, College Station, TX, USA.
c Leibniz Universität Hannover, Institute of Plant Genetics, Hannover, Germany
dAgricultural Research Council, LNR, Onderstepoort, South Africa
*ochoaco@okstate.edu
Session: Rose genomics

The garden rose production is seriously affected by viral infections in USA. Twenty-four viruses have been reported to infect rose worldwide and numerous are reported in the USA and in Europe. Early viral infections in rose may not be diagnosed until symptoms develop. Currently single-virus assay methods are used in the diagnosis and detection for most of these pathogens.
Next-generation sequencing (NGS) can be used as a diagnostic tool because of its ability to amplify multiple unique DNA signatures of infecting viruses. Electronic probe Diagnostic Nucleic acid Analysis (EDNA) was used to detect rose viruses in simulated metagenomics runs (mock sequencing databases, MSDs) containing rose-virus reference sequences as positive controls and rose host genome sequences. MSDs were generated using MetaSim, and were configured simulating Illumina average read length and error rates. Electronic probes (e-probes) with lengths of 20-40 nucleotides were designed by comparing the target viral genome versus all potential co-infecting viral genomes. To avoid false positives, e-probes were curated by BLAST alignments of sequences from published public databases (nt NCBI). Positive MSDs containing only the intended target viral genome were considered positive controls. MSDs mimicking single and multiple infections were also generated. Generated E-probes were tested in silico and in vitro. If compared with other NGS procedures, EDNA is a relatively rapid response methodology that provides the framework for a new sequence-based diagnosis. EDNA-ROSE can also be combined with other diagnostics methods for virus monitoring in microbial forensics, biosecurity and epidemiological studies of rose plants."
Related Discussions
Shovel Pruned Virused Rose: Can I replant?
Q
Comments (14)
For someone in zone 10, there probably is very little chance of mosaic type virus spread as the rose's immune system is effective at high temperatures. ----------------------------------------- Concerning Davis's indexed roses. Davis has recently published a paper where they announced that they found an aphid spread virus in their indexed rose plantings (see page 511): "In this test, RSDaV was detected in many different rose species and cultivars from the Foundation Rose Collection at FPS. In all, 129 plants in this collection were tested, and 77 were positive for RSDaV. Some of the hybrid rose cultivars tested positive for RSDaV included Queen Elizabeth, China Doll, Heirloom, Lowell Thomas, Jack Frost, New Dawn, Uncle Joe, Bridal White, Butterscotch, and Cynthia. It is interesting that the virus was detected in more than 69 plants in two rows (total number of plants in these rows was 89) of the collection which were planted in the mid 1990s. In all, 162 samples of R. multiflora from the virusindexing rose blocks also were assayed in the spring and RSDaV was found in 94 plants. The majority of RT-PCR-positive R. multiflora plants were symptomatic. Another 40 additional plants from the same virus-indexing blocks were tested in the summer and 6 were positive." Here is a link that might be useful: link for above.
...See More
Should we give our virused roses an aspirin?
Q
Comments (10)
I am interested in research papers that investigate the temperature dependence to a plant's ability to fight off virus infections. The full paper accessed through the link below states: "Development of symptoms following inoculation of N. tabacum (Ã¯Â¿Â½Ã¯Â¿Â½Petite GerardÃ¯Â¿Â½Ã¯Â¿Â½) with ToRSV was influenced by temperature. At 34Ã¯Â¿Â½aC, visual symptoms did not develop on the inoculated leaves or on upper, noninoculated leaves and neither viral RNA nor viral-derived siRNAs were detected in samples collected randomly (data not shown). At lower temperatures, lesions developed on the inoculated leaves 2 to 3 days postinoculation (dpi). At 21Ã¯Â¿Â½aC, lesions were clearly defined and necrotic (Fig. 1A, panel 1)." This paper titled (Salicylic Acid-Dependent Restriction of Tomato ringspot virus Spread in Tobacco Is Accompanied by a Hypersensitive Response, Local RNA Silencing, and Moderate Systemic Resistance) ties together the "RNA silencing" type immune system response with the "Salicylic Acid" type immune response. The following is a key quote from the abstract: "Lesion size and viral systemic spread were reduced with SA pretreatment but enhanced in NahG transgenic lines deficient in SA accumulation, suggesting that SA-dependent mechanisms play a key role in limiting ToRSV spread in tobacco." In the full paper the following results should be of interest in this thread: "The percentage of plants that became systemically infected was also significantly reduced in SA-treated plants (9% Ã¯Â¿Â½b 6 in SAtreated plants versus 49% Ã¯Â¿Â½b 15 in control plants; three independent experiments; P Here is a link that might be useful: link for above, full paper is free
...See More
Vulcanicolas & viruses
Q
Comments (47)
As I stated before it is not a personal attack. I am hoping to get you to spread more useful, accurate information. I am very sorry that you feel so threatened. That is absolutely in no way my intentions. This is the type of content of your website I was referring to: "when any other variegated plant is placed in the same area, they die within a matter of a week." My 'Maya' is placed in full sun until 3 or 4 in the afternoon. As I'm sure you're aware, the temperatures here in Southern California are regularly over 90 degrees. 'Maya' is the strongest plant in my collection. It holds up to the heat, cold, and insects. I am in no way saying 'Shorty' might not be as good. ( and it sucks that I have to say that because you're being so defensive) 'Shorty' looks good! It looks like a 'Maya' with a little more Versicolor in it. But all I'm seeing is information that's seems pretty darn biased. Who grows a 'Maya' cutting that takes two years to flower? With proper technique it should flower at less than two feet tall in less than a year. As far as growing virused plants goes...... You know why I do it....... But I will spell it out for new growers. My collection contains virused plants because most plants these days are random multi-hybrids. If we continue along this path all of the Brugmansia hybrids will start to look the same. The true species plants have been propagated so long vegetatively that most if not all have acquired viruses. As stated I keep my seedlings far away from my collection and any known Brugs. My collection consists of mostly true species plants. I work toward hybridizing for pure species plants. This ensures we will have these species in the future and I will be able to return seeds of these species to their native habitats if needed. Especially with plants like vulcanicola. I know what's coming.......... What about 'Maya'??? It's not a pure species. Ahhh... But it is a x Candida, and with enough crossing back to Aurea can be almost 100% Aurea. Or the same thing with Versicolor. Thank you! Good night.
...See More
The History And Future Of Roses In Review (RIR)
Q
Comments (12)
Chris, you are welcome to send me the complete reorganization you have in mind. If you are concerned it might give Board members a coronary, then send it to me by email. My email address is available on this site. I promise you I won't have a coronary, even though I am on the Board. As to the three year terms of Board members, elections are expensive and time consuming. Holding them more often than every three years would mean we were spending an inordinate amount of time and effort on elections and less time on the business of the organization. I have to tell you I think such an approach would be counterproductive. However, I do agree the Board is too large and think we should have more effective limits on the number of consecutive years someone can serve on the Board. I am in my second term on the Board and it will be my last. If I can't get things done in six years, it's time for someone else to work on them. I'm not sure which big businesses you have dealt with, but I can tell you Boards of big businesses do not ask stockholders or anyone else for input before conducting the business of the company. I have seen them in action in their business meetings and they are less open than the ARS Board. Anyway, lay your suggestions on me and I will let you know what I think. The ARS is not perfect by any means and any ideas that will help will be welcomed.
...See More

Next generation sequencing for rose viruses

Comment (1)

henry_kuska
Original Author

Related Discussions

COMPANY

BUSINESS SERVICES

GET HELP

CONNECT WITH US

Next generation sequencing for rose viruses

Comment (1)

henry_kuskaOriginal Author

Related Discussions

COMPANY

BUSINESS SERVICES

GET HELP

CONNECT WITH US

henry_kuska
Original Author