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Open Access Research

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

James A Cotton1, Catherine J Lilley2, Laura M Jones2, Taisei Kikuchi45, Adam J Reid1, Peter Thorpe23, Isheng J Tsai156, Helen Beasley1, Vivian Blok3, Peter J A Cock3, Sebastian Eves-van den Akker23, Nancy Holroyd1, Martin Hunt1, Sophie Mantelin3, Hardeep Naghra17, Arnab Pain18, Juan E Palomares-Rius39, Magdalena Zarowiecki1, Matthew Berriman1*, John T Jones3* and Peter E Urwin2*

Author Affiliations

1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK

2 Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK

3 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK

4 Forestry and Forest Products Research Institute, Tsukuba, Japan

5 Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan

6 Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan

7 Present address: School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK

8 Present address: Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia

9 Present address: Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n Apdo 4084, 14080 Córdoba, Spain

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Genome Biology 2014, 15:R43  doi:10.1186/gb-2014-15-3-r43

Published: 3 March 2014

Abstract

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.