Institut für nationale und internationale Angelegenheiten der Pflanzengesundheit
Whole genome sequencing (WGS) and tools of comparative genomics are of increasing importance in plant pathology. Their combined use has in recent years enabled more efficient outbreak management (tracking strains and source identification) and informed selection of novel targets for rapid development of diagnostic tests.In recent years technologies e.g. Nanopore sequencing have made WGS more accessible to laboratories with smaller sample throughput needing occasional ability to sequence whole genomes.No EPPO standards exist specifically for WGS and there is little data on WGS approaches undertaken by different laboratories in the area of plant health.Laboratories use different pipelines for WGS which can affect the final results of sequencing. These differences are present in both wet and dry lab part of the pipeline. Crucial steps are DNA extraction, library preparation, sequencing technology and bioinformatic analysis. DNA extraction method have impact on the size of the extracted DNA and can contribute to contaminations which effect library preparation. The most prominent sequencing technologies currently in use are Illumina, Nanopore and PacBio sequencing. Illumina sequencing generates short reads with higher accuracy, Nanopore and PacBio sequencing on the other hand generate longer reads. Commonly used strategy to obtain whole genomes with good accuracy is to combine short end long reads sequencing.Due to the widespread use of WGS there is an increased need for EPPO guidelines for WGS and bioinformatic analysis pipeline for plant pathogenic bacteria. Such guidelines could increase quality of data obtained by WGS and ease the comparative genomics studies which could further facilitate the use of WGS in plant health.
Federal Ministry of Food and Agriculture
