The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

Cotton, James A. et al.

[Background] Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security.

[Results] We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control.

[Conclusions] The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.

We thank the many people at the Wellcome Trust Sanger Insitute who contributed to this work: Mark Simmonds, Natalie Smerdon, Dave Willey, Michael Quail, Matthew Jones and Richard Rance provided technical support in generating sequencing libraries; Robert Davies and Quan Lin arranged for data release to the SRA; Martin Aslett and Jacqueline Keane provided informatics support; Christine Lloyd assisted with sequencing management; Karen Brooks, Richard Clark, Olivia Lambert, Sarah Nichol and Alan Tracey assisted with curation and annotation of gene models. We thank Jennie Hibbard and Beverley Merry at the University of Leeds who provided technical support in generating biological material.

Peer Reviewed