Diverse and variable virus communities in wild plant populations revealed by metagenomic tools
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 Åland 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.
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Subjects: | H20 - Maladies des plantes, F40 - Écologie végétale, virus des végétaux, biodiversité, Plantago lanceolata, virologie, Caulimovirus, Enamovirus, Clostérovirus, http://aims.fao.org/aos/agrovoc/c_5985, http://aims.fao.org/aos/agrovoc/c_33949, http://aims.fao.org/aos/agrovoc/c_34743, http://aims.fao.org/aos/agrovoc/c_8259, http://aims.fao.org/aos/agrovoc/c_32853, http://aims.fao.org/aos/agrovoc/c_7b747a58, http://aims.fao.org/aos/agrovoc/c_32854, http://aims.fao.org/aos/agrovoc/c_2905, |
Online Access: | http://agritrop.cirad.fr/590576/ http://agritrop.cirad.fr/590576/1/Susi%20et%20al_viral%20metagenomics%20Aland%20Plantago_2019.pdf |
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dig-cirad-fr-5905762024-01-29T01:31:41Z http://agritrop.cirad.fr/590576/ http://agritrop.cirad.fr/590576/ Diverse and variable virus communities in wild plant populations revealed by metagenomic tools. Susi Hanna, Filloux Denis, Frilander Mikko J., Roumagnac Philippe, Laine Anna-Liisa. 2019. PeerJ, 7:e6140, 24 p.https://doi.org/10.7717/peerj.6140 <https://doi.org/10.7717/peerj.6140> Diverse and variable virus communities in wild plant populations revealed by metagenomic tools Susi, Hanna Filloux, Denis Frilander, Mikko J. Roumagnac, Philippe Laine, Anna-Liisa eng 2019 PeerJ H20 - Maladies des plantes F40 - Écologie végétale virus des végétaux biodiversité Plantago lanceolata virologie Caulimovirus Enamovirus Clostérovirus http://aims.fao.org/aos/agrovoc/c_5985 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_34743 http://aims.fao.org/aos/agrovoc/c_8259 http://aims.fao.org/aos/agrovoc/c_32853 http://aims.fao.org/aos/agrovoc/c_7b747a58 http://aims.fao.org/aos/agrovoc/c_32854 Finlande http://aims.fao.org/aos/agrovoc/c_2905 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 Åland 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/590576/1/Susi%20et%20al_viral%20metagenomics%20Aland%20Plantago_2019.pdf text cc_by info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ https://doi.org/10.7717/peerj.6140 10.7717/peerj.6140 info:eu-repo/semantics/altIdentifier/doi/10.7717/peerj.6140 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.7717/peerj.6140 |
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H20 - Maladies des plantes F40 - Écologie végétale virus des végétaux biodiversité Plantago lanceolata virologie Caulimovirus Enamovirus Clostérovirus http://aims.fao.org/aos/agrovoc/c_5985 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_34743 http://aims.fao.org/aos/agrovoc/c_8259 http://aims.fao.org/aos/agrovoc/c_32853 http://aims.fao.org/aos/agrovoc/c_7b747a58 http://aims.fao.org/aos/agrovoc/c_32854 http://aims.fao.org/aos/agrovoc/c_2905 H20 - Maladies des plantes F40 - Écologie végétale virus des végétaux biodiversité Plantago lanceolata virologie Caulimovirus Enamovirus Clostérovirus http://aims.fao.org/aos/agrovoc/c_5985 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_34743 http://aims.fao.org/aos/agrovoc/c_8259 http://aims.fao.org/aos/agrovoc/c_32853 http://aims.fao.org/aos/agrovoc/c_7b747a58 http://aims.fao.org/aos/agrovoc/c_32854 http://aims.fao.org/aos/agrovoc/c_2905 |
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H20 - Maladies des plantes F40 - Écologie végétale virus des végétaux biodiversité Plantago lanceolata virologie Caulimovirus Enamovirus Clostérovirus http://aims.fao.org/aos/agrovoc/c_5985 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_34743 http://aims.fao.org/aos/agrovoc/c_8259 http://aims.fao.org/aos/agrovoc/c_32853 http://aims.fao.org/aos/agrovoc/c_7b747a58 http://aims.fao.org/aos/agrovoc/c_32854 http://aims.fao.org/aos/agrovoc/c_2905 H20 - Maladies des plantes F40 - Écologie végétale virus des végétaux biodiversité Plantago lanceolata virologie Caulimovirus Enamovirus Clostérovirus http://aims.fao.org/aos/agrovoc/c_5985 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_34743 http://aims.fao.org/aos/agrovoc/c_8259 http://aims.fao.org/aos/agrovoc/c_32853 http://aims.fao.org/aos/agrovoc/c_7b747a58 http://aims.fao.org/aos/agrovoc/c_32854 http://aims.fao.org/aos/agrovoc/c_2905 Susi, Hanna Filloux, Denis Frilander, Mikko J. Roumagnac, Philippe Laine, Anna-Liisa Diverse and variable virus communities in wild plant populations revealed by metagenomic tools |
description |
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 Åland 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. |
format |
article |
topic_facet |
H20 - Maladies des plantes F40 - Écologie végétale virus des végétaux biodiversité Plantago lanceolata virologie Caulimovirus Enamovirus Clostérovirus http://aims.fao.org/aos/agrovoc/c_5985 http://aims.fao.org/aos/agrovoc/c_33949 http://aims.fao.org/aos/agrovoc/c_34743 http://aims.fao.org/aos/agrovoc/c_8259 http://aims.fao.org/aos/agrovoc/c_32853 http://aims.fao.org/aos/agrovoc/c_7b747a58 http://aims.fao.org/aos/agrovoc/c_32854 http://aims.fao.org/aos/agrovoc/c_2905 |
author |
Susi, Hanna Filloux, Denis Frilander, Mikko J. Roumagnac, Philippe Laine, Anna-Liisa |
author_facet |
Susi, Hanna Filloux, Denis Frilander, Mikko J. Roumagnac, Philippe Laine, Anna-Liisa |
author_sort |
Susi, Hanna |
title |
Diverse and variable virus communities in wild plant populations revealed by metagenomic tools |
title_short |
Diverse and variable virus communities in wild plant populations revealed by metagenomic tools |
title_full |
Diverse and variable virus communities in wild plant populations revealed by metagenomic tools |
title_fullStr |
Diverse and variable virus communities in wild plant populations revealed by metagenomic tools |
title_full_unstemmed |
Diverse and variable virus communities in wild plant populations revealed by metagenomic tools |
title_sort |
diverse and variable virus communities in wild plant populations revealed by metagenomic tools |
url |
http://agritrop.cirad.fr/590576/ http://agritrop.cirad.fr/590576/1/Susi%20et%20al_viral%20metagenomics%20Aland%20Plantago_2019.pdf |
work_keys_str_mv |
AT susihanna diverseandvariableviruscommunitiesinwildplantpopulationsrevealedbymetagenomictools AT fillouxdenis diverseandvariableviruscommunitiesinwildplantpopulationsrevealedbymetagenomictools AT frilandermikkoj diverseandvariableviruscommunitiesinwildplantpopulationsrevealedbymetagenomictools AT roumagnacphilippe diverseandvariableviruscommunitiesinwildplantpopulationsrevealedbymetagenomictools AT laineannaliisa diverseandvariableviruscommunitiesinwildplantpopulationsrevealedbymetagenomictools |
_version_ |
1792499620331388928 |