A previously unknown virus is found worldwide in the most studied plant species, the thale cress (Arabidopsis thaliana). The presence of the virus may have far-reaching implications for research projects. Researchers from Utrecht University and Wageningen University & Research tracked down the virus. In the journal New Phytologist, they call on plant scientists to test their thale cress plants for the presence of the virus.
Pollution of datasets
UU researcher Dr Ava Verhoeven, who worked in Wageningen a few years ago on an RNA dataset infected by the virus, discovered more or less by accident that similar problems arose in a dataset in Utrecht as in those from Wageningen. Verhoeven: “In both datasets it turned out that in some samples more than 90 percent of the RNA was not from thale cress, but from something else. In Wageningen, the unknown RNA had already been compared with RNA from a large database. It then became clear that the RNA must be from an as yet unknown virus. And when we compared the unknown RNA from the Utrecht dataset with the virus RNA from Wageningen, it turned out that it was the same unknown virus.”
Lots of work and money wasted
Verhoeven is therefore certain that the virus has not only resulted in unusable datasets in Utrecht and Wageningen. “Sand rocket is the model plant,” says Verhoeven. “Now that our publication is available, many fellow researchers indicate that they recognize the problems with the datasets. They just didn’t know before that it was because of this virus.”
“RNA data sets containing very little plant RNA are easily considered to have failed. The results are often not published and can therefore not be found online for other researchers. Thus, the virus remained hidden, despite being widespread. So the actual percentage of ‘contaminated’ data sets is probably much higher than 8.5 percent. Making those datasets has already cost a lot of time and money, while the virus does not help you much.”
Verhoeven and colleagues recommend that researchers from now on test their thale cress seeds for the presence of the virus before creating large data sets. Verhoeven: “Of course you want to prevent a virus from accidentally being present in the plants you use for research. Not only because it can yield unusable data sets, but also because the virus can affect the plants in unknown ways. We have therefore made a protocol available with which every researcher can easily test whether the virus is present in their plants.”
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