Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities
High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection – often in the absence of disease symptoms – and tend to discover many novel...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-09-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/10/1939 |
| _version_ | 1827678470831865856 |
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| author | Beata Hasiów-Jaroszewska Dieke Boezen Mark P. Zwart |
| author_facet | Beata Hasiów-Jaroszewska Dieke Boezen Mark P. Zwart |
| author_sort | Beata Hasiów-Jaroszewska |
| collection | DOAJ |
| description | High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection – often in the absence of disease symptoms – and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach. |
| first_indexed | 2024-03-10T06:08:41Z |
| format | Article |
| id | doaj.art-a357ce41f34d46a29d2630a94defbf9b |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T06:08:41Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-a357ce41f34d46a29d2630a94defbf9b2023-11-22T20:18:21ZengMDPI AGViruses1999-49152021-09-011310193910.3390/v13101939Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus CommunitiesBeata Hasiów-Jaroszewska0Dieke Boezen1Mark P. Zwart2Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Węgorka 20, 60-318 Poznań, PolandDepartment of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The NetherlandsDepartment of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The NetherlandsHigh throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection – often in the absence of disease symptoms – and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.https://www.mdpi.com/1999-4915/13/10/1939HTSviromesweedswild plantsplant virus |
| spellingShingle | Beata Hasiów-Jaroszewska Dieke Boezen Mark P. Zwart Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities Viruses HTS viromes weeds wild plants plant virus |
| title | Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities |
| title_full | Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities |
| title_fullStr | Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities |
| title_full_unstemmed | Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities |
| title_short | Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities |
| title_sort | metagenomic studies of viruses in weeds and wild plants a powerful approach to characterise variable virus communities |
| topic | HTS viromes weeds wild plants plant virus |
| url | https://www.mdpi.com/1999-4915/13/10/1939 |
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