Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence

Background: The yellow potato cyst nematode Globodera rostochiensis is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. Results: We generate a high-quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression through the life cycle focusing on key parasitic transitions, and sequence the genomes of eight populations including four additional pathotypes to identify variation. Horizontal gene transfer contributes 3.5% of the predicted genes, of which approximately 8.5% are deployed as effectors. Over one-third of all effector genes are clustered in 21 putative "effector islands" in the genome. We identify a dorsal gland promoter element motif present upstream of 26 out of 28 representative dorsal gland effector families, and predict a putative effector superset associated with this motif. We validate gland cell expression in two novel genes by in situ hybridisation, and catalogue dorsal gland promoter element-containing effectors from available cyst nematode genomes. Comparison of effector diversity between pathotypes highlights correlation with plant resistance-breaking. Conclusions: These G. rostochiensis genome resources will facilitate major advances in understanding nematode plant-parasitism. Dorsal gland promoter element-containing effectors are at the front line of the evolutionary arms race between plant and parasite, and the ability to predict gland cell expression a priori promises rapid advances in understanding their roles and mechanisms of action.

Usage notes;
Clusters and normalized expression tables
For each gene, lists the normalized expression data for each life stage, and (if significantly differentially expressed) which expression super cluster it is grouped into.
nGr.v1.0.annotation+TE
GFF file with locations of all gene calls in the G. rostochiensis genome and all transposable element predictions.
nGr.v1.0.blast2go
blast2go annotation as gff3 file
nGr.v1.0.blast2go.txt
blast2go annotation as gzipped text file
nGr.v1.0.iprscan.xml
inter pro scan as gzipped xml
nGr.v1.0.iprscan.xml
interproscan as tsv
Gr_pops.new.vs.nGr.v1.1.GQ.vcf.norm.filtered.vcf.snpeff.vcf.gz.data.txt
snpeff parsed vcf for G. rostochiensis pathotypes Ro1, 2, 3, 4, 5.
Gr_pops.new.vs.nGr.v1.1.GQ.vcf.norm.filtered.vcf.snpeff.vcf
Raw VCF for G. rostochiensis pathotypes Ro1, 2, 3, 4, 5.

Eves-van den Akker, Sebastian; Laetsch, Dominik; Thorpe, Peter et al. (2017). Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence [Dataset]. Dryad. https://doi.org/10.5061/dryad.4s5r6