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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. rostochiensisis classified into pathotypes with different plant resistance-breaking phenotypes. We generate a high quality genome assembly for G. rostochiensispathotype 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 (termed DOG Box) present upstream in representatives from 26 out of 28 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. These G. rostochiensisgenome 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.

In order to expand our understanding of the genetics of root-knot nematodes, variation in nuclear DNA and mitochondrial DNA in Meloidogyne incognita, M. arenariaand M. javanicawas investigated. Despite the obligate mitotic parthenogenetic mode of reproduction, a large number of AFLP polymorphisms were observed among all 16 populations studied. Both UPGMA and principle coordinate analyses revealed three distinct groups that corresponded with the respective species identities of the 16 populations. M. incognitawas genetically most distinct. Amplification of 63-bp tandem repeats (TR) in mtDNA from single individuals enabled the calculation of diversity measures at three hierarchical levels: within individuals, among individuals of a single population and among populations. For all three species, the highest diversity was observed within individuals explaining 43–65% of the total diversity. Many individuals contained more than one mtDNA size variant. M. incognitaharboured the most heteroplasmic individuals and was the most homogenous at the population level. Only 13% of the total diversity was observed among populations, while this figure was 35% for M. arenaria. Both TR and AFLP data showed that M. arenariais the most heterogeneous species. The comparison of the genetic distances based on AFLPs and mtDNA size variants revealed a significant correlation for the six M. arenariapopulations, whereas no consistent correlation was observed for the populations of the other two species.