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Genome expression dynamics reveals parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes

Martine Da Rocha, Caroline Bournaud, Julie Dazenière, Peter Thorpe, Clement Pellegrin, Marc Bailly-Bechet, Arthur Péré, Priscila Grynberg, Laetitia Perfus-Barbeoch, Sebastian Eves-van den Akker, View ORCID ProfileEtienne GJ Danchin
doi: https://doi.org/10.1101/2021.04.02.438169
Martine Da Rocha
1INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
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Caroline Bournaud
2Department of Plant Sciences, University of Cambridge, UK, CB2 3EA
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Julie Dazenière
1INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
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Peter Thorpe
3University of St. Andrews, School of Medicine, Medical & Biological Sciences, North Haugh, St Andrews, United Kingdom
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Clement Pellegrin
2Department of Plant Sciences, University of Cambridge, UK, CB2 3EA
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Marc Bailly-Bechet
1INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
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Arthur Péré
1INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
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Priscila Grynberg
4Embrapa Genetic Resources and Biotechnology, Brasília DF 70770-917, Brazil
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Laetitia Perfus-Barbeoch
1INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
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Sebastian Eves-van den Akker
2Department of Plant Sciences, University of Cambridge, UK, CB2 3EA
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Etienne GJ Danchin
1INRAE, Université Côte d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
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  • ORCID record for Etienne GJ Danchin
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Abstract

Root-knot nematodes are the major contributor to the crop losses caused by nematodes. Root-knot nematodes secrete effectors into the plant, derived from two sets of pharyngeal gland cells, to manipulate host physiology and immunity. Successful completion of the life cycle, involving successive molts from egg to adult, covers morphologically and functionally distinct stages and will require precise control of gene expression, including effectors. The details of how root-knot nematodes regulate transcription remain sparse.

Here, we report a life stage-specific transcriptome of Meloidogyne incognita. Combined with an available annotated genome, we explore the spatio-temporal regulation of gene expression. We reveal gene expression clusters and predicted functions that accompany the major developmental transitions. Focusing on effectors, we identify a putative cis-regulatory motif associated with expression in the dorsal glands: providing an insight into effector regulation. We combine the presence of this motif with several other criteria to predict a novel set of putative dorsal gland effectors. Finally, we show this motif, and thereby its utility, is broadly conserved across the Meloidogyne genus and termed it Mel-DOG.

Taken together, we provide the first genome-wide analysis of spatio-temporal gene expression in a root-knot nematode, and identify a new set of candidate effector genes that will guide future functional analyses.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • - All the supplementary data have now been publicly released and assigned proper DOIs. - An affiliation for one of the authors was corrected. - Some typos and mistakes were corrected.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted April 26, 2021.
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Genome expression dynamics reveals parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes
Martine Da Rocha, Caroline Bournaud, Julie Dazenière, Peter Thorpe, Clement Pellegrin, Marc Bailly-Bechet, Arthur Péré, Priscila Grynberg, Laetitia Perfus-Barbeoch, Sebastian Eves-van den Akker, Etienne GJ Danchin
bioRxiv 2021.04.02.438169; doi: https://doi.org/10.1101/2021.04.02.438169
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Genome expression dynamics reveals parasitism regulatory landscape of the root-knot nematode Meloidogyne incognita and a promoter motif associated with effector genes
Martine Da Rocha, Caroline Bournaud, Julie Dazenière, Peter Thorpe, Clement Pellegrin, Marc Bailly-Bechet, Arthur Péré, Priscila Grynberg, Laetitia Perfus-Barbeoch, Sebastian Eves-van den Akker, Etienne GJ Danchin
bioRxiv 2021.04.02.438169; doi: https://doi.org/10.1101/2021.04.02.438169

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