Diverse and variable virus communities in wild plant populations revealed by metagenomic tools

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Susi , H , Filloux , D , Frilander , M J , Roumagnac , P & Laine , A-L 2019 , ' Diverse and variable virus communities in wild plant populations revealed by metagenomic tools ' , PeerJ , vol. 7 , 6140 . https://doi.org/10.7717/peerj.6140

Title: Diverse and variable virus communities in wild plant populations revealed by metagenomic tools
Author: Susi, Hanna; Filloux, Denis; Frilander, Mildco J.; Roumagnac, Philippe; Laine, Anna-Liisa
Other contributor: University of Helsinki, Research Centre for Ecological Change
University of Helsinki, Institute of Biotechnology
University of Helsinki, Ecology and Evolutionary Biology

Date: 2019-01-11
Language: eng
Number of pages: 24
Belongs to series: PeerJ
ISSN: 2167-8359
DOI: https://doi.org/10.7717/peerj.6140
URI: http://hdl.handle.net/10138/300038
Abstract: Wild plant populations may harbour a myriad of unknown viruses. As the majority of research efforts have targeted economically important plant species, the diversity and prevalence of viruses in the wild has remained largely unknown. However, the recent shift towards metagenomics-based sequencing methodologies, especially those targeting small RNAs, is finally enabling virus discovery from wild hosts. Understanding this diversity of potentially pathogenic microbes in the wild can offer insights into the components of natural biodiversity that promotes long-term coexistence between hosts and parasites in nature, and help predict when and where risks of disease emergence are highest. Here, we used small RNA deep sequencing to identify viruses in Plantago lanceolata populations, and to understand the variation in their prevalence and distribution across the Aland Islands, South-West Finland. By subsequent design of PCR primers, we screened the five most common viruses from two sets of P. lanceolata plants: 164 plants collected from 12 populations irrespective of symptoms, and 90 plants collected from five populations showing conspicuous viral symptoms. In addition to the previously reported species Plantago lanceolata latent virus (PlLV), we found four potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera. Our results show that virus prevalence and diversity varied among the sampled host populations. In six of the virus infected populations only a single virus species was detected, while five of the populations supported between two to five of the studied virus species. In 20% of the infected plants, viruses occurred as coinfections. When the relationship between conspicuous viral symptoms and virus infection was investigated, we found that plants showing symptoms were usually infected (84%), but virus infections were also detected from asymptomatic plants (44%). Jointly, these results reveal a diverse virus community with newly developed tools and protocols that offer exciting opportunities for future studies on the eco-evolutionary dynamics of viruses infecting plants in the wild.
Subject: Betapartitivirus
Plantago lanceolata latent virus
Small RNA
1181 Ecology, evolutionary biology
1183 Plant biology, microbiology, virology

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