New reference genome sequences for genotyping virulence in continental European field populations of cyst nematodes

Holterman, M. H. M. (Speaker), T. Blokhina (Contributor), van den Elsen, S. J. J. (Contributor), Lozano Torres, J. L. (Contributor), Smant, G. (Contributor), Helder, J. (Contributor)

Activity: Talk or presentationOral presentation

Description

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, G. pallida and Heterodera schachtii), 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 improve understanding of the genetic mechanisms underlying selection for virulence in cyst nematodes in The Netherlands, we preferred to generate reference genomes from nematode populations with either minimal or well-defined exposure to host plant resistances. For G. pallida, we deliberately chose an old isolate that had not been exposed to potato cultivars harbouring the resistance genes that were most widely used over the past thirty years. For G. rostochiensis, two near isogenic inbred lines were used that differ in their susceptibility towards the H1 resistance gene in potato. PacBio sequencing technology allowed us to generate new reference genomes for G. pallida, two G. rostochiensis lines and H. schachtii. By comparing these reference genomes with re-sequenced field isolates, we can study the effect of continuous exposure of nematode populations to a limited set of resistance genes on virulence characteristics. The newly generated genome sequences consist of significantly fewer and longer contigs than the publicly available ones from the two potato cyst nematode 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, these genome sequences will serve as a reference for the elucidation of virulence characteristics in cyst nematode populations from The Netherlands and surrounding countries.
Period11 Sep 2018
Held atESN Conference 2018
Event typeConference
LocationGhent, Belgium
Degree of RecognitionInternational