Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence

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 present upstream of 26 out of 28 representative 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.

背景：马铃薯金线虫（Globodera rostochiensis）是一种具有全球经济重要性的毁灭性植物病原物。这类活体营养型寄生物从咽腺分泌效应因子（effector），其中部分通过水平基因转移（horizontal gene transfer）获得，以调控宿主生理过程、促进寄生。该线虫可划分为具有不同破植物抗性表型的致病型（pathotype）。
结果：本研究完成了马铃薯金线虫致病型Ro1的高质量基因组组装，鉴定了推定效应因子与水平基因转移事件，聚焦关键寄生转换阶段绘制其整个生活史的基因表达谱，并对包含4个额外致病型在内的8个种群进行基因组测序以鉴定遗传变异。水平基因转移占预测基因总数的3.5%，其中约8.5%作为效应因子发挥功能。超过三分之一的效应因子基因在基因组中聚集为21个推定的“效应因子岛”。本研究鉴定到一类背腺启动子元件基序（dorsal gland promoter element motif），该基序存在于28个代表性背腺效应因子家族中的26个的上游区域，并据此预测了一个与该基序相关的推定效应因子超集。我们通过原位杂交验证了两个新基因的腺细胞表达特性，并从已公开的胞囊线虫基因组中收录了携带背腺启动子元件的效应因子。不同致病型间的效应因子多样性比较结果显示，其与植物抗性破断表型存在显著相关性。
结论：上述马铃薯金线虫的基因组资源将推动线虫植物寄生机制研究的重大进展。携带背腺启动子元件的效应因子处于植物与寄生物间进化军备竞赛的前沿，而先验预测腺细胞表达特性的能力，有望为解析这些效应因子的功能与作用机制带来快速突破。