Virus diversity and genome evolution in natural plant ecosystems

Plant virus genomes are highly diverse and can evolve rapidly, as highlighted by recent metagenomics advances. However, most research on plant viruses focuses on agricultural systems, and we therefore know little about virus diversity and evolution in natural ecosystems. Viruses can spill over from natural to agricultural systems; hence, it is highly relevant to know what virus diversity is present in wild plants and whether they act as viral reservoirs. Moreover, to know what role plant viruses play in shaping natural plant communities, we must first characterize their biodiversity and evolution. Initial analyses of natural plant virus communities revealed a high incidence of asymptomatic and mixed infections, suggesting that evolutionary dynamics in natural virus populations differ from those in agricultural systems. Here we propose to study virus diversity and genome evolution in natural plant communities, using state-of-the-art metagenomics and bioinformatics approaches. We have randomly sampled individual plants of various species at several sites over time, and we will use long- and short-read high-throughput sequencing to reconstruct high-quality virus genomes and to identify genetic variation within virus populations. These results will allow us to characterize virus biodiversity, determine realized virus host ranges and mixed infections, look for evidence of recombination and reassortment events, infer adaptation to different plant species and geographic sites, and identify virus genome regions under selection. Understanding these plant-virus evolutionary dynamics is interesting and highly relevant from a basic perspective, and it is important for knowing the evolutionary stability and adaptive potential of natural viral reservoirs.

This project is lead by Dr. Anne Kupczok (Wageningen University and Research), and carried out by PhD candidate Jan Baijens (Wageningen University and Research).