The soybean cyst nematode (Heterodera glycines) is a sedentary plant parasite that exceeds billion USD annually in yield losses. This problem is exacerbated by H. glycines populations overcoming the limited sources of natural resistance in soybean and by the lack of effective and safe alternative treatments. Although there are genetic determinants that render soybeans resistant to nematode genotypes, resistant soybeans are increasingly ineffective because their multiyear usage has selected for virulent H. glycines populations. Successful H. glycines infection relies on the comprehensive re-engineering of soybean root cells into a syncytium, as well as the long-term suppression of host defences to ensure syncytial viability. At the forefront of these complex molecular interactions are effectors, the proteins secreted by H. glycines into host root tissues. The mechanisms that control genomic effector acquisition, diversification, and selection are important insights needed for the development of essential novel control strategies. As a foundation to obtain this understanding, we created a nine-scaffold, 158 Mb pseudomolecule assembly of the H. glycines genome using PacBio, Chicago, and Hi-C sequencing. A Mikado consensus gene prediction produced an annotation of 22,465 genes using short- and long-read expression data. To evaluate assembly and annotation quality, we cross-examined synteny among H. glycines assemblies, and compared BUSCO across related species. To describe the predicted proteins involved in H. glycines’ secretory pathway, we contrasted expression between preparasitic and parasitic stages with functional gene information. Here, we present the results from our assembly and annotation of the H. glycines genome and contribute this resource to the scientific community.

中文翻译：

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大豆胞囊线虫基因组的染色体组装


大豆胞囊线虫（大豆胞囊线虫）是一种定植植物寄生虫，每年造成的产量损失超过十亿美元。由于大豆嗜血杆菌种群克服了大豆中有限的天然抗性来源，并且缺乏有效和安全的替代治疗方法，这一问题变得更加严重。尽管存在使大豆对线虫基因型具有抗性的遗传决定因素，但抗性大豆越来越无效，因为它们的多年使用选择了有毒的大豆异丙酚种群。成功的甘氨酸感染依赖于将大豆根细胞全面重新改造为合胞体，以及长期抑制宿主防御以确保合胞体活力。在这些复杂分子相互作用的最前沿是效应子，即由甘氨酸分泌到宿主根组织中的蛋白质。控制基因组效应子获取、多样化和选择的机制是开发重要的新型控制策略所需的重要见解。作为获得这一认识的基础，我们使用 PacBio、Chicago 和 Hi-C 测序创建了甘氨酸基因组的 9 个支架、158 Mb 假分子组装体。 Mikado 共识基因预测使用短读和长读表达数据生成了 22,465 个基因的注释。为了评估组装和注释质量，我们交叉检查了H之间的同线性。甘氨酸组装，并比较了相关物种的 BUSCO。描述H中涉及的预测蛋白质。 为了研究甘氨酸的分泌途径，我们将寄生前和寄生阶段之间的表达与功能基因信息进行了对比。在这里，我们展示了甘氨酸基因组的组装和注释结果，并将这一资源贡献给科学界。