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Researchers Characterize Genetics Accompanying Plant Virus Host Shift

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – In a paper scheduled to appear in the March issue of the Journal of General Virology, Japanese and Australian researchers report that they have successfully tracked the genetic changes that occur when a plant virus called the turnip mosaic virus makes the leap from its usual turnip host to the radish plant.

To do this, the team converted a turnip mosaic virus that would not infect radish plants to one that would. They then used an RT-PCR-based method to compare the genetics of groups of viruses grown in different hosts, showing that the radish-adapted viruses had more genetic diversity than viruses infecting the original plant host but seemed to be less infectious.

"We are trying to understand how novel viruses emerge — particularly how viruses are able to cross the species barrier," lead author Kazusato Ohshima, a plant virology researcher at Saga University in Japan, said in a statement. "This in turn gives us a better idea of how pandemics are generated and how best to stem their spread."

Turnip mosaic virus is an RNA virus that infects plants in the Brassicaceae family, such as turnips, cabbage, cauliflower, and radishes. The virus, which can cause discoloration to patches of plants' leaves, is carried from one plant to the next by aphids. But not every turnip mosaic virus has the same host preference. Researchers have identified at least four different subtypes of the virus, each with a distinct set of host and infection patterns.

For the current study, Ohshima and his co-workers focused on a turnip mosaic virus-derived clone called p35Tunos, which usually infects turnip plants but only rarely infects radishes.

After growing p35Tunos in an herb plant called Nicotiana benthamiana, they isolated viruses from the plants' leaves, sequencing some of the viral isolates with an RT-PCR-based approach and using other isolates to infect Brassica rapa (turnip) and Raphanus sativus (radish) seedlings.

The team then passaged the viruses in each group of plants for many times over several years, eventually using an RT-PCR-based approach to track genetic changes in viruses affecting the original B. rapa host with those that they were able to coax into infecting radishes.

The researchers also used targeted sequencing of a 3,264-nucleotide region to look at the genetic diversity in 269 p35Tunos clones from more than two dozen viral populations infecting N. benthamiana, B. rapa, or radish plants, evaluating everything from viral mutation rates to nucleotide diversity in the viruses.

In total, the researchers identified nearly 2,300 mutations in 16 populations of radish-adapted viruses — an average of 142 per virus.

Looking at protein-coding regions specifically, they found 722 coding mutations in the radish viruses compared with just 26 mutations affecting coding genes in the viruses grown in B. rapa plants.

The B. rapa-grown viruses also had far more silent mutations that did not affect amino acid sequence than the radish grown viruses: 81 percent of changes in turnip plants were silent compared with 56 percent in viruses from radish plants.

Many of the mutations in radish-grown viruses occurred in or near genes coding for proteins called P3 and CI, which are known to interact with plant resistance genes.

And based on their calculations, researchers say the new radish-adapted virus has roughly five times the nucleotide diversity found in the viruses infecting the original host.

Still, they noted, on their way to being able to infect radish plants, the turnip mosaic viruses apparently went through successive genetic bottlenecks. And even after about six years of moving through radish plants, the team reported, these new host-adapted viruses didn't seem to be as infectious as those in the original B. rapa host.

Those involved say the current study sets the stage for further exploration of the viral evolution, both for other plant viruses as well as viruses infecting animals. In addition, understanding the ways that viruses shift to move into new hosts is expected to offer insights that could help in combating viruses that cause damage and disease.

"Revealing the subtleties of the interaction between viruses and plant resistance mechanisms could help breeders produce better crops, for example by selecting strains that block changes to [turnip mosaic virus]," Ohshima said.

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