A new reference genome sequence for genotyping virulence in continental European field populations of Globodera pallida

Plant-parasitic nematodes form an increasingly important problem in agriculture, causing significant crop losses worldwide. The majority of these losses are caused by a small number of species, such as cyst nematodes (e.g., Globodera rostochiensis and G. pallida), root-knot nematodes (Meloidogyne spp.) and stem nematodes (Ditylenchus spp.). With a regulatory ban on most nematicidal agrochemicals, the main method of control at the moment is the use of resistant crop cultivars. However, the current spectrum of nematode resistance genes used in major crops is extremely narrow. Prolonged exposure of field populations to a narrow range of resistance genes can result in the appearance of nematode genotypes with modified virulence characteristics.
To better understand the genetic mechanisms underlying selection for virulence in the potato cyst nematode G. pallida in the Netherlands, we needed to generate a new reference genome. For this, we deliberately chose an old isolate; a population that had not been exposed to potato cultivars harbouring the resistance genes that were most widely used over the past thirty years. We generated a new genome sequence of this G. pallida isolate with PacBio sequencing technology. This resulted in a new genome sequence which consists of significantly fewer and longer contigs than the publicly available genome sequence of this species. An automated procedure was used to create an initial annotation. After a further manual refinement of the annotation with a particular focus on effector families, this genome sequence will serve as a reference for the elucidation of virulence characteristics in G. pallida populations from The Netherlands and surrounding countries.