10 research outputs found
Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale
Disease emergence events regularly result from human activities such as agriculture, which
frequently brings large populations of genetically uniform hosts into contact with potential
pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic
information about virus distribution across agro-ecological interfaces and large gaps in understanding
of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics
approach to examine relationships between agricultural land use and distributions of plantassociated
viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of
South Africa and RhĂŽne river delta region of France). In total, we analysed 1725 geo-referenced plant
samples collected over two years from 4.5 Ă 4.5 km2 grids spanning farmlands and adjacent
uncultivated vegetation. We found substantial virus prevalence (25.8â35.7%) in all ecosystems, but
prevalence and identified family-level virus diversity were greatest in cultivated areas, with some
virus families displaying strong agricultural associations. Our survey revealed 94 previously
unknown virus species, primarily from uncultivated plants. This is the first effort to systematically
evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that
agriculture substantially influences plant virus distributions and highlight the extent of current
ignorance about the diversity and roles of viruses in nature
Virion-associated nucleic acid-based metagenomics: a decade of advances in molecular characterization of plant viruses
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010-2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsid-less RNA viruses that replicate in fungi, oomycetes and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring and ecology of plant viruses are provided
Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities
Viral metagenomic approaches have become essential for culture-independent and sequence-independent viral detection and characterization. This chapter describes an accurate and efficient approach to (1) concentrate viral particles from arthropods and plants, (2) remove contaminating non-encapsidated nucleic acids, (3) extract and amplify both viral DNA and RNA, and (4) analyze high-throughput sequencing (HTS) data by bioinformatics. Using this approach, up to 96 arthropod or plant samples can be multiplexed in a single HTS library
Two novel Alphaflexiviridae members revealed by deep sequencing of the Vanilla (Orchidaceae) virome.
The genomes of two novel viruses were assembled from 454 pyrosequencing data obtained from vanilla leaves from La RĂ©union. Based on genome organization and homologies, one agent was unambiguously classified as a member of the genus Potexvirus and named vanilla virus X (VVX). The second one, vanilla latent virus (VLV), is phylogenetically close to three unclassified members of the family Alphaflexiviridae with similarity to allexiviruses, and despite the presence of an additional 8-kDa open reading frame, we propose to include VLV as a new member of the genus Allexivirus. Both VVX and VLV were mechanically transmitted to vanilla plants, resulting in asymptomatic infections