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

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 659 effector gene loci: 293 “known” high-confidence homologs of plant-parasitic nematode effectors, and 366 “novel” effectors with high gland cell expression. In doing so we define a comprehensive “effectorome” of a plant-parasitic nematode. Using this effector definit..., Instructions for the generation of transcriptional networks are available here: https://github.com/BethMolloy/Effectorome_H_schachtii, , # The origin, deployment, and evolution of a plant-parasitic nematode effectorome. [Access this dataset on Dryad] (DOI:10.5061/dryad.rfj6q57hn) Data associated with the effectorome of the plant-parasitic nematode Heterodera schachtii. Principally annotated transcriptional network files, and computationally predicted structures of all Heterodera schachtii and Globodera rostochiensis proteins (using Alpha fold and ESM fold). ## 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 (659_effectors_network_BM_0.975.gephi; 659_effectors_network_BM_0.975.gexf) ii. H. schachtii transcription factors and effectors (3d_network_TFs_and...植物寄生线虫威胁全球粮食安全。在寄生过程中，它们会从两类咽腺细胞（pharyngeal gland cells）中将效应蛋白（effector）分泌至宿主植物体内。这些效应蛋白会引发宿主生物学特性发生显著改变，以抑制宿主免疫并构建独特的取食器官，供线虫从中获取营养。尽管效应蛋白在线虫寄生过程中至关重要，但此前尚未有针对任意植物寄生线虫的效应蛋白组（effectorome）进行全面鉴定与特征注释的研究。 为解决这一问题，本研究优化了腺细胞分离与转录组分析技术，对三个关键生命阶段的甜菜孢囊线虫（Heterodera schachtii）的推定效应蛋白进行了严格注释。本研究共鉴定出659个效应蛋白基因位点：其中293个为植物寄生线虫效应蛋白的高置信度同源‘已知’效应蛋白，另有366个在腺细胞中高表达的‘新型’效应蛋白。借此，本研究首次完成了植物寄生线虫的完整效应蛋白组（effectorome）注释。 基于该效应蛋白组，转录网络（transcriptional network）构建的操作说明可参见：https://github.com/BethMolloy/Effectorome_H_schachtii，# 植物寄生线虫效应蛋白组的起源、部署与演化。 [可在Dryad平台获取本数据集]（DOI:10.5061/dryad.rfj6q57hn） 本数据集关联甜菜孢囊线虫效应蛋白组的相关数据，主要包含注释后的转录网络文件，以及所有甜菜孢囊线虫与马铃薯金线虫（Globodera rostochiensis）蛋白质的计算机预测结构（采用阿尔法折叠（AlphaFold）与ESM折叠（ESM Fold）进行预测）。 ### 数据与文件结构说明 1. 按Molloy等人的研究方法预测的甜菜孢囊线虫转录因子（transcription factor）（对应文件：H.schachtii_tfs.names.withzfc4.376.names） 2. 转录网络文件，展示线虫侵染过程中基因表达的相关性（详见Siddique等2022年研究），筛选阈值为相关系数≥0.975，涉及以下编码基因的相关性： i. 甜菜孢囊线虫效应蛋白编码基因（对应文件：659_effectors_network_BM_0.975.gephi；659_effectors_network_BM_0.975.gexf） ii. 甜菜孢囊线虫转录因子与效应蛋白编码基因（对应文件：3d_network_TFs_and...）