DOI: 10.5061/dryad.rfj6q57hn
title: Data from: The origin, deployment, and evolution of a plant-parasitic nematode effectorome

description: 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.
description: Instructions for the generation of transcriptional networks are
 available here: https://github.com/BethMolloy/Effectorome_H_schachtii
description: ## **README: The origin, deployment, and evolution of a plant-parasitic
 nematode effectorome.** Access this dataset on Dryad (opens in new window)
 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** 1. *H. schachtii* transcription factors predicted as
 described in Molloy et al. (H.schachtii_tfs.names.withzfc4.376.names) 2.
 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)](https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgephi.org%2F&data=05%7C02%7Cse389%40cam.ac.uk%7C9b791c26ba4f4cf23f5408dc8954a0c9%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638536243765848734%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=wHt08khh2yrhJG%2BBeYcbvN7g7gsDWTsVIf4WrF2b6zs%3D&reserved=0 "Original URL: https://gephi.org/. Click or tap if you trust this link.").         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)](https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cgl.ucsf.edu%2Fchimerax%2F&data=05%7C02%7Cse389%40cam.ac.uk%7C9b791c26ba4f4cf23f5408dc8954a0c9%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638536243765856419%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=9muUX%2FqNSjsc%2FxoPJzQvlMU6k%2BsV607iDr8llpGFGsg%3D&reserved=0 "Original URL: https://www.cgl.ucsf.edu/chimerax/. Click or tap if you trust this link.")), 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)](https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBethMolloy%2FEffectorome_H_schachtii&data=05%7C02%7Cse389%40cam.ac.uk%7C9b791c26ba4f4cf23f5408dc8954a0c9%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638536243765862479%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=prdPOk8EN%2BXk%2Fb%2BHNm7dl878ET22vRfZOTOhe05YV44%3D&reserved=0 "Original URL: https://github.com/BethMolloy/Effectorome_H_schachtii. Click or tap if you trust this link.") ### **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).