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Sabeh M, Lord E, Grenier É, St-Arnaud M, Mimee B. What determines host specificity in hyperspecialized plant parasitic nematodes? BMC Genomics 2019; 20:457. [PMID: 31170914 PMCID: PMC6555003 DOI: 10.1186/s12864-019-5853-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/28/2019] [Indexed: 12/21/2022] Open
Abstract
Background In hyperspecialized parasites, the ability to grow on a particular host relies on specific virulence factors called effectors. These excreted proteins are involved in the molecular mechanisms of parasitism and distinguish virulent pathogens from non-virulent related species. The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida are major plant-parasitic nematodes developing on numerous solanaceous species including potato. Their close relatives, G. tabacum and G. mexicana are stimulated by potato root diffusate but unable to establish a feeding site on this plant host. Results RNA sequencing was used to characterize transcriptomic differences among these four Globodera species and to identify genes associated with host specificity. We identified seven transcripts that were unique to PCN species, including a protein involved in ubiquitination. We also found 545 genes that were differentially expressed between PCN and non-PCN species, including 78 genes coding for effector proteins, which represent more than a 6-fold enrichment compared to the whole transcriptome. Gene polymorphism analysis identified 359 homozygous non-synonymous variants showing a strong evidence for selection in PCN species. Conclusions Overall, we demonstrated that the determinant of host specificity resides in the regulation of essential effector gene expression that could be under the control of a single or of very few regulatory genes. Such genes are therefore promising targets for the development of novel and more sustainable resistances against potato cyst nematodes. Electronic supplementary material The online version of this article (10.1186/s12864-019-5853-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Sabeh
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada.,Biodiversity Center, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Etienne Lord
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada
| | - Éric Grenier
- INRA, UMR1349 IGEPP (Institute of Genetics, Environment and Plant Protection), F-35653, Le Rheu, France
| | - Marc St-Arnaud
- Biodiversity Center, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Benjamin Mimee
- St-Jean-sur-Richelieu Research and Development Center, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada.
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Sabeh M, Duceppe MO, St-Arnaud M, Mimee B. Transcriptome-wide selection of a reliable set of reference genes for gene expression studies in potato cyst nematodes (Globodera spp.). PLoS One 2018; 13:e0193840. [PMID: 29499068 PMCID: PMC5834164 DOI: 10.1371/journal.pone.0193840] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/19/2018] [Indexed: 12/31/2022] Open
Abstract
Relative gene expression analyses by qRT-PCR (quantitative reverse transcription PCR) require an internal control to normalize the expression data of genes of interest and eliminate the unwanted variation introduced by sample preparation. A perfect reference gene should have a constant expression level under all the experimental conditions. However, the same few housekeeping genes selected from the literature or successfully used in previous unrelated experiments are often routinely used in new conditions without proper validation of their stability across treatments. The advent of RNA-Seq and the availability of public datasets for numerous organisms are opening the way to finding better reference genes for expression studies. Globodera rostochiensis is a plant-parasitic nematode that is particularly yield-limiting for potato. The aim of our study was to identify a reliable set of reference genes to study G. rostochiensis gene expression. Gene expression levels from an RNA-Seq database were used to identify putative reference genes and were validated with qRT-PCR analysis. Three genes, GR, PMP-3, and aaRS, were found to be very stable within the experimental conditions of this study and are proposed as reference genes for future work.
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Affiliation(s)
- Michael Sabeh
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada
- Biodiversity Centre, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Marc-Olivier Duceppe
- Ottawa Laboratory Fallowfield, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Marc St-Arnaud
- Biodiversity Centre, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Benjamin Mimee
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, St-Jean-sur-Richelieu, Quebec, Canada
- * E-mail:
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Eves-van den Akker S, Laetsch DR, Thorpe P, Lilley CJ, Danchin EGJ, Da Rocha M, Rancurel C, Holroyd NE, Cotton JA, Szitenberg A, Grenier E, Montarry J, Mimee B, Duceppe MO, Boyes I, Marvin JMC, Jones LM, Yusup HB, Lafond-Lapalme J, Esquibet M, Sabeh M, Rott M, Overmars H, Finkers-Tomczak A, Smant G, Koutsovoulos G, Blok V, Mantelin S, Cock PJA, Phillips W, Henrissat B, Urwin PE, Blaxter M, Jones JT. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biol 2016; 17:124. [PMID: 27286965 PMCID: PMC4901422 DOI: 10.1186/s13059-016-0985-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/12/2016] [Indexed: 11/23/2022] Open
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. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0985-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Peter Thorpe
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | | | - Etienne G J Danchin
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Martine Da Rocha
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Corinne Rancurel
- INRA, University Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, 06900, Sophia Antipolis, France
| | - Nancy E Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | - Amir Szitenberg
- School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Eric Grenier
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Josselin Montarry
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Benjamin Mimee
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Marc-Olivier Duceppe
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Ian Boyes
- Sidney Laboratory, Canadian Food Inspection Agency (CFIA), 8801 East Saanich Rd, Sidney, BC, V8L 1H3, Canada
| | | | - Laura M Jones
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Hazijah B Yusup
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Joël Lafond-Lapalme
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Magali Esquibet
- INRA, UMR1349 IGEPP (Institute for Genetics, Environment and Plant Protection), 35653, Le Rheu, France
| | - Michael Sabeh
- Agriculture and Agri-food Canada, Horticulture Research and Development Centre, 430 Bboul. Gouin, St-Jean-sur-Richelieu, Quebec, J3B 3E6, Canada
| | - Michael Rott
- Sidney Laboratory, Canadian Food Inspection Agency (CFIA), 8801 East Saanich Rd, Sidney, BC, V8L 1H3, Canada
| | - Hein Overmars
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Anna Finkers-Tomczak
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | | | - Vivian Blok
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Sophie Mantelin
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Peter J A Cock
- Information and Computational Sciences Group, James Hutton Institute, Dundee, UK
| | - Wendy Phillips
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Bernard Henrissat
- CNRS UMR 7257, INRA, USC 1408, Aix-Marseille University, AFMB, 13288, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Peter E Urwin
- Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - John T Jones
- Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Dundee, DD2 5DA, UK.,School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9TZ, UK
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