High-throughput sequencing (HTS) is a powerful tool that enables the simultaneous detection and potential identification of any organisms present in a sample. The growing interest in the application of HTS technologies for routine diagnostics in plant health laboratories is triggering the development of guidelines on how to prepare laboratories for performing HTS testing. This paper describes general and technical recommendations to guide laboratories through the complex process of
High-throughput sequencing (HTS) technologies have the potential to become one of the most significant advances in molecular diagnostics. Their use by researchers to detect and characterize plant pathogens and pests has been growing steadily for more than a decade and they are now envisioned as a routine diagnostic test to be deployed by plant pest diagnostics laboratories. Nevertheless, HTS technologies and downstream bioinformatics analysis of the generated datasets represent a complex process including many steps whose reliability must be ensured. The aim of the present guidelines is to provide recommendations for researchers and diagnosticians aiming to reliably use HTS technologies to detect plant pathogens and pests. These guidelines are generic and do not depend on the sequencing technology or platform. They cover all the adoption processes of HTS technologies from test selection to test validation as well as their routine implementation. A special emphasis is given to key elements to be considered: undertaking a risk analysis, designing sample panels for validation, using proper controls, evaluating performance criteria, confirming and interpreting results. These guidelines cover any HTS test used for the detection and identification of any plant pest (viroid, virus, bacteria, phytoplasma, fungi and fungus-like protists, nematodes, arthropods, plants) from any type of matrix. Overall, their adoption by diagnosticians and researchers should greatly improve the reliability of pathogens and pest diagnostics and foster the use of HTS technologies in plant health.
Anthropogenic activities contribute to changes in the range and distribution of species. Globalization is resulting in human‐mediated dispersal that is causing a breakdown in normal biogeographic barriers. But the impact of anthropogenic activities on plant pathogen communities is still poorly understood. We conducted an eDNA metabarcoding study to compare communities of oomycetes, a group of eukaryotic microorganisms that comprises important crop and tree pathogens, in urban, natural, and interface environments. Oomycete diversity and abundance were highest in human impacted urban environments and lowest in natural environments, while the interface environments were intermediate. Urban environments had the highest proportion of sites where species of the plant pathogenic genus Phytophthora were found, as well as the largest number of unknown or undescribed Phytophthora species. The taxa overlap between urban and interface environments was one order of magnitude larger than the overlap between urban and natural environments. Our analyses show that urban/natural interface areas likely act as a bridge for invasion into natural environments. This could impact both the natural biota and natural ecosystem processes. Our study serves as a warning that some Phytophthora species introduced from nurseries or spread by human movement could pose a threat to natural ecosystems. Shifting patterns in oomycete communities could interfere with natural ecosystem processes and result in increases in disease and ecosystem declines.
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