Dear Colleagues,

Healthy plants are essential for life on Earth. They produce the oxygen we breathe and make up over 80% of the food we eat. Plant pathogens and pest species threaten food security and cause great economic losses, and when engaging with international trade, regulations have to be implemented restricting the introduction and spread of plant pests. These regulations rely heavily on accurate plant disease diagnostics, which can be challenging for organisms that are difficult to isolate and/or to differentiate from closely-related, non-regulated species. With the introduction of molecular tools, fast and reliable detection and identification tests for regulated pests became available. The early detection of non-indigenous plant pathogens is the key to managing regulated and invasive species.

With the introduction of whole genome shotgun sequencing techniques, new powerful tools have become available in diagnostic laboratories for regulatory plant health. No longer do diagnosticians have to rely on a single genetic locus, but now they have the power of an entire (meta)genome at their disposal. Genome sequencing with high throughput sequencing (HTS) technologies are capable of processing large numbers of samples and producing even larger volumes of genomics data. By mining the genome sequences of closely-related pests and comparing them to one another, it is possible to design molecular markers that can be used by diagnostics labs to distinguish them from one another. Moreover in virology, this is a way to identify (novel) plant pathogenic viruses from metagenomic samples. These approaches rely on exploiting the genetic differences between species for identification or population-level analyses in order to respond to questions in regulatory research. With the increasing use of HTS, more specific guidelines are developed for applications in regulatory plant health.

In this Special Issue, the following topics can be presented: the development and validation of generic and specific bioinformatic pipelines for regulated plant pests; the use of comparative genomics for novel assay design; genome-wide phylogenomic analyses to distinguish regulated from non-regulated organisms; and population-level studies for track-and-trace purposes. In addition, we invite authors to reflect on possible implications for the use of HTS in regulatory plant health for phytosanitary policies.

Dr. Guillaume J. Bilodeau
Dr. Bart T. L. H. Van De Vossenberg
Guest Editors

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• molecular detection and identification
• regulated plant pathogens
• HTS detection
• genomics
• metagenomics
• comparative genomics
• population dynamics