Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities
Abstract
:1. Introduction
2. Role of Weeds and Wild Plants in Virus Emergence
2.1. Mixed Infection in Wild Plants
2.2. Novel Viruses and Viral Diversity in Wild Plant Populations
2.3. Effect of Host Population, Climate Changes, and Land Use on Virus Emergence and Biodiversity
3. Problems to Be Solved and Future Directions
3.1. Challenges in Virus Enrichment and Nucleic Acid Extraction
3.2. Challenges in HTS and Bioinformatics
4. Concluding Remarks
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample Collection Year | Country | Host Plant | HTS Platform | HTS Template | Main Conclusions | Reference |
---|---|---|---|---|---|---|
2005–2008 | USA | Ambrosia psilostachya Vernonia baldwinii Asclepias viridis Ruellia humilis Panicum virgatum Sorghastrum nutans | 454 | VANA and dsRNA | •Many unknown viruses identified in asymptomatic plants. •More viruses detected by dsRNA than by VANA. •Plant virus composition is highly variable. Of the factors investigated, host plant explains most but only a small fraction of this variation. | [31] |
2010–2012 | South Africa, France | Cultivated and un-cultivated plants along the interface of natural and agricultural ecosystems. | 454 | VANA | •94 unknown viruses were identified, primarily from uncultivated plants. •Highest prevalence and identified diversity of plant viruses found in agricultural ecosystems. | [8] |
2012–2013 | South Africa, New Zealand | Arctopus echinatus Lolium perenne, Panicum ecklonii, Stipagrostis sp | 454, Illumina | VANA, and enrichment of circular DNA | •5 novel, circular DNA viruses were identified. | [32] |
2013 | Finland | Plantago lanceolata | Illumina | Small RNA of 20–30 nucleotides, mainly composed of small interfering RNAs. | •Virus prevalence and diversity varied among the sampled host populations. •Potentially novel virus species belonging to Caulimovirus, Betapartitivirus, Enamovirus, and Closterovirus genera were identified. •In a PCR-based follow-up study, viral prevalence and diversity were lower in natural ecosystems, suggesting spillover from agricultural to natural ecosystems. | [2] |
2017 | France | 200 plants (representing 80 species) collected for each of 4 sites, with 2 sites being managed and 2 being unmanaged sites. | Illumina | dsRNA on both leaves and leaf- associated, cultured fungi | •161 fungal families and 18 viral families were identified. •A large viral diversity dominated by novel dsRNA viruses was detected. •At the family level, more diversity in the managed plots, as some ssRNA viruses are only present there. •Leaf associated fungal communities were more diverse in unmanaged systems. | [33] |
2017–2018 | France | Solanum nigrum | Illumina | dsRNA | •A total of 20 viral families were discovered. •The novel ilarvirus, here named Solanum nigrum ilarvirus 1 (SnIV1), was detected in both tomato and nightshade samples. •Virome richness was highly variable. Tomato and nightshade shared only 17.9% OTUs, indicating different viromes for close relatives at the same location. | [6] |
2018–2019 | Poland | Verbena officinalis L., Silene latifolia Poir. Rorippa × prostrata Robinia pseudoaccacia L | Illumina | Total RNA | •Detection of two viruses that had not been previously found in Poland: Clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). | [34] |
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Hasiów-Jaroszewska, B.; Boezen, D.; Zwart, M.P. Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities. Viruses 2021, 13, 1939. https://doi.org/10.3390/v13101939
Hasiów-Jaroszewska B, Boezen D, Zwart MP. Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities. Viruses. 2021; 13(10):1939. https://doi.org/10.3390/v13101939
Chicago/Turabian StyleHasiów-Jaroszewska, Beata, Dieke Boezen, and Mark P. Zwart. 2021. "Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities" Viruses 13, no. 10: 1939. https://doi.org/10.3390/v13101939
APA StyleHasiów-Jaroszewska, B., Boezen, D., & Zwart, M. P. (2021). Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities. Viruses, 13(10), 1939. https://doi.org/10.3390/v13101939