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Genome Biol. 2016 Jun 10;17(1):124. doi: 10.1186/s13059-016-0985-1.

The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

Author information

1
Division of Plant Sciences, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. s.evesvandenakker@dundee.ac.uk.
2
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK.
3
Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK.
4
Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK.
5
INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France.
6
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK.
7
School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, HU6 7RX, UK.
8
INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France.
9
Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada.
10
Sidney Laboratory, Canadian Food Inspection Agency (CFIA), 8801 East Saanich Rd, Sidney, BC, V8L 1H3, Canada.
11
Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
12
Information and Computational Sciences Group, James Hutton Institute, Dundee, UK.
13
USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA.
14
CNRS UMR 7257, INRA, USC 1408, Aix-Marseille University, AFMB, 13288, Marseille, France.
15
Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
16
School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK.

Abstract

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 (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.

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.

KEYWORDS:

Effectors; Genome sequence; Horizontal gene transfer; Plant-parasitic nematode; Virulence

PMID:
27286965
PMCID:
PMC4901422
DOI:
10.1186/s13059-016-0985-1
[Indexed for MEDLINE]
Free PMC Article

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