Beets beat hidden viruses within in their genomes

Sugar beets (Beta vulgaris) contribute 14-20% of raw sucrose produced worldwide, whilst the rest of sugar production mainly comes from sugarcanes. Whilst sugarcanes are the “thirstiest crop” in the world, beets require around five times less water than sugarcane. Beets were domesticated from its wild relative, Beta maritime around 8,500 BC for medicinal, ornamental, fodder uses and in 1804, for its sugar content properties. 

Endogenous pararetroviruses (EPRVs) have been called the “two-faced travelers in the plant genome”. They are double-stranded DNA viruses that do not require integration into the host genome for multiplication. In comparison, most plant viruses have single-stranded RNA genomes (much like SARS-CoV-2). Plant EPRVs belong to the family Caulimoviridae that might have emerged during the Devonian era (320 MYA) and contains several common viruses (e.g., cauliflower mosaic virus, dahlia common mosaic virus, banana streak virus, rice tungro bacilliform virus). Almost every vascular plant and more primitive taxa (clubmosses, ferns and gymnosperms) genome contains fragments of this virus. EPRVs can be silent within plants, lead to viral infection or provide its host with viral resistance. There are many questions about their functioning but scientists can use fragments of EPRVs in plant genomes as a genomic fossil records of past viral sequences and invasion events.

In the latest study, Nicola Schmidt and colleagues from the Technische Universität Dresden, University of Leicester and South China Botanical Gardens wanted to test sugar beet’s genome for buried, disassembled and inactivated EPRVs.

Schmidt and colleagues first needed to identify beet-specific EPRVs (beetEPRVs) and estimate how much they contribute to the beet’s genome. They compiled 16 publicly available EPRV sequences from eight genera belonging to Caulimoviridae focusing on two genomic regions (movement protein and reverse transcriptase) and searched them in a recently constructed sugar beet genome assembly.

Secondly, the researchers investigated whether beetEPRVs are transcribed in another publicly available database and looked for potential epigenetic gene silencing by the host. 

Thirdly, a sugar beet and seven other closely related plant species (e.g., B. maritima, spinach and quinoa) were grown in greenhouses for further analyses. Researchers looked for one group of beetEPRVs within the DNA of the eight plants, and then hybridised beetEPRV-specific probes to the sugar beet’s 18 chromosomes and visualised it with fluorescent microscopy.

Schmidt and colleagues discovered that beetEPRVs make up approximately 0.3% of the B. vulgaris genome based on the two genomic regions. The phylogenetic analysis of 119 beetEPRVs identified three distinct genetic groups (beetEPRV1, beetEPRV2, and beetEPRV3). Whilst the groups differed in their structure, they all belonged to florendoviruses. 

The group beetEPRV3 was found in all B. vulgaris genomes and in related Beta species but not in other closely related species (quinoa, spinach). 

“[T]ogether, this may point to an initial beetEPRV3 integration into the beet genome after the split of the sections Corollinae/Nanae from Beta approx. 13.4 to 7.2 million years ago and before speciation within the section Beta”, Schmidt and colleagues write.

It might seem puzzling how the plant prevents the virus from causing disease in the host. Closer experimental study revealed that beet uses a few methods. The team found that small RNAs are involved in the epigenetic silencing of the beetEPRVs by the host plants. 

“[T]he sugar beet host employs three strategies to shut down the beetEPRV copies,” write the authors, “thus preventing re-infection: heterochromatic burial, epigenetic silencing, and structural disassembly. As a result, EPRVs in beet provide an example for the complete assimilation and inactivation of a plant virus in the host genome.”

This study tells the complicated story of how a cultivated crop is “managing” ancestral virus fragments within its genome today, using publicly available data and lab experiments. The manuscript is dedicated to Prof Thomas Schmidt, who passed away in 2019. 

“The identification of beetEPRVs have been on the mind of Thomas, his group, and his collaborators for a long time, dating back 20 years. A number of people have helped us to get to this point and we thank them for their initial work,” Schmidt and colleagues write in the acknowledgements. 

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