Data from: The origin, deployment, and evolution of a plant-parasitic nematode effectorome

Eves-van den Akker, Sebastian1

Published Jan 31, 2024; Updated Jun 12, 2024 on Dryad. https://doi.org/10.5061/dryad.rfj6q57hn

Abstract

Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode.

To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode Heterodera schachtii at three key life-stages. We define 717 effector gene loci: 269 “known” high-confidence homologs of plant-parasitic nematode effectors, and 448 “novel” effectors with high gland cell expression. In doing so we define the most comprehensive “effectorome” of a plant-parasitic nematode to date.

Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.

README

README: The origin, deployment, and evolution of a plant-parasitic nematode effectorome.

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Data associated with the effectorome of the plant-parasitic nematode Heterodera schachtii. Principally annotated transcriptional network files for H. schachtii and Arabidopsis thaliana genes, and computationally predicted structures of all Heterodera schachtii and Globodera rostochiensis proteins (using AlphaFold).

Change log

This repository has been updated from the version associated with preprint, following peer review. The methods for effector definition in the manuscript were altered, which had an impact on the total number of effectors (659 to 717). As such, the associated network files have been re-computed and updated here, with no substantive changes. Alpha fold and Transcription factor files remain unchanged.

Description of the data and file structure

H. schachtii transcription factors predicted as described in Molloy et al. (H.schachtii_tfs.names.withzfc4.376.names)
Transcriptional network files showing correlations in gene expression across nematode infection (as outlined in Siddique et al. 2022) - above a threshold correlation co-efficient of 0.975 - between genes encoding:

i. H. schachtii effectors (717_putative_effectors_network_0975.gephi; 717_putative_effectors_network_0.975.gexf)

ii. H. schachtii effectors, with alternative edge thresholds (717_putative_effectors_network_0.950.gexf; 717_putative_effectors_network_0.955.gexf; 717_putative_effectors_network_0.960.gexf; 717_putative_effectors_network_0.965.gexf; 717_putative_effectors_network_0.970.gexf; 717_putative_effectors_network_0.975.gexf; 717_putative_effectors_network_0.980.gexf; 717_putative_effectors_network_0.985.gexf; 717_putative_effectors_network_0.990.gexf; 717_putative_effectors_network_0.995.gexf)

iii. H. schachtii transcription factors and effectors (effector_TF_network_0975.gephi; effector_TF_network_0975.gexf)

iv. H. schachtii effectors and A. thaliana genes. Genes involved in immunity (as defined in Molloy et al., 2024) are highlighted (effector_plant_network_0975.gephi; effectors_plant_network_0975.gexf)

.gephi and .gexf network files can be opened in Gephi v0.10, which can be downloaded for free from :https://gephi.org/(opens in new window).

3. AlphaFold predicted protein structures for all Heterodera schachtii and Globodera rostochiensis proteins.

i. AlphaFold predicted structures of H. schachtii effectors (BethEffectorRevised.zip)

ii. AlphaFold predicted proteome of G. rostochiensis (GloboRosAlphafold.zip)

iii. Alpha fold predicted proteome of H. schachtii (FullTranscriptomeAlphafoldhsch.zip)

.pdb files can be visualised using ChimeraX (https://www.cgl.ucsf.edu/chimerax/(opens in new window)), or any other software that supports PDB files. The JSON files can be opened by any text editor such as Notepad.

Sharing/Access information

Instructions for generating transcriptional networks are available here: https://github.com/BethMolloy/Effectorome_H_schachtii(opens in new window)

References

S. Siddique, et al., The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5. Nat. Commun. 13, 6190 (2022).

B. Molloy et al., The Origin, Deployment, and Evolution of a Plant-Parasitic Nematode Effectorome. BioRxiv. (2024).