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）是一种具有重大全球经济影响的毁灭性植物病原线虫。这类活体营养型寄生线虫从咽腺分泌效应因子，其中部分效应因子是通过水平基因转移（horizontal gene transfer）获得的，用以调控宿主生理过程并促进寄生。马铃薯金线虫可分为不同致病型，各自具有不同的植物抗性打破表型。
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，鉴定了候选效应因子与水平基因转移事件，以关键寄生转换阶段为重点绘制了其生活史中的基因表达图谱，并对包括4个额外致病型在内的8个种群的基因组进行测序以鉴定遗传变异。水平基因转移贡献了其预测基因的3.5%，其中约8.5%以效应因子的形式发挥功能。超过三分之一的效应因子基因在基因组中聚集于21个候选“效应因子岛”内。本研究鉴定出一种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，并据此预测了与该基序相关的效应因子全集。我们通过原位杂交（in situ hybridisation）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编录了携带背腺启动子元件的效应因子。对不同致病型间效应因子多样性的比较分析显示，其与植物抗性打破表型存在显著相关性。
结论：本研究获得的马铃薯金线虫基因组资源将推动对线虫寄生植物机制的研究取得重大进展。携带背腺启动子元件的效应因子处于植物与寄生虫间进化军备竞赛的前沿，而先验性预测腺细胞表达的能力有望快速推动对这些效应因子的功能与作用机制的研究。