Department of Plant Pathology, Iowa State University, Ames, IA, USA.
Genome Informatics Facility, Iowa State University, Ames, IA, USA.
BMC Genomics. 2019 Feb 7;20(1):119. doi: 10.1186/s12864-019-5485-8.
Heterodera glycines, commonly referred to as the soybean cyst nematode (SCN), is an obligatory and sedentary plant parasite that causes over a billion-dollar yield loss to soybean production annually. Although there are genetic determinants that render soybean plants resistant to certain nematode genotypes, resistant soybean cultivars are increasingly ineffective because their multi-year usage has selected for virulent H. glycines populations. The parasitic success of H. glycines relies on the comprehensive re-engineering of an infection site into a syncytium, as well as the long-term suppression of host defense 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 of effector acquisition, diversification, and selection need to be understood before effective control strategies can be developed, but the lack of an annotated genome has been a major roadblock.
Here, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123 Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7 Mb), and horizontal gene transfer events (151 genes). A large number of putative effectors (431 genes) were identified in the genome, many of which were found in transposons.
This advance provides a glimpse into the host and parasite interplay by revealing a diversity of mechanisms that give rise to virulence genes in the soybean cyst nematode, including: tandem duplications containing over a fifth of the total gene count, virulence genes hitchhiking in transposons, and 107 horizontal gene transfers not reported in other plant parasitic nematodes thus far. Through extensive characterization of the H. glycines genome, we provide new insights into H. glycines biology and shed light onto the mystery underlying complex host-parasite interactions. This genome sequence is an important prerequisite to enable work towards generating new resistance or control measures against H. glycines.
大豆胞囊线虫（SCN）通常被称为大豆囊线虫，是一种专性和定居性植物寄生虫，每年导致大豆产量损失超过 10 亿美元。虽然有一些遗传决定因素使大豆植株对某些线虫基因型具有抗性，但由于多年来使用抗性大豆品种，导致毒性更强的 H. glycines 种群的选择。H. glycines 的寄生成功依赖于将感染部位全面重新构建为合胞体，以及长期抑制宿主防御以确保合胞体的存活。在这些复杂的分子相互作用中处于前沿的是效应子，即 H. glycines 分泌到宿主根组织中的蛋白质。在开发有效的控制策略之前，需要了解效应子的获取、多样化和选择的机制，但缺乏注释的基因组一直是一个主要的障碍。
在这里，我们使用 PacBio 长读技术将 H. glycines 基因组组装成 738 个 contigs，大小为 123Mb，包含 29769 个基因的注释。该基因组包含大量的重复序列（34%）、串联重复（18.7Mb）和水平基因转移事件（151 个基因）。在基因组中鉴定出大量的假定效应子（431 个基因），其中许多位于转座子中。
这一进展通过揭示导致大豆胞囊线虫毒力基因的多种机制，提供了宿主与寄生虫相互作用的一个视角，这些机制包括：包含超过五分之一总基因数的串联重复， hitchhiking 在转座子中的毒力基因，以及迄今为止在其他植物寄生线虫中尚未报道的 107 个水平基因转移。通过对 H. glycines 基因组的广泛表征，我们提供了对 H. glycines 生物学的新见解，并揭示了复杂的宿主-寄生虫相互作用背后的奥秘。该基因组序列是开发针对 H. glycines 的新抗性或控制措施的重要前提。
