The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes
The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes
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DOI：
10.1186/s12864-019-5485-8
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发表时间：
2019-02-07
期刊：
影响因子：
4.4
通讯作者：
Baum, Thomas J.
中科院分区：
文献类型：
--
作者：
Masonbrink, Rick;Maier, Tom R.;Baum, Thomas J.
大豆异尖线虫，俗称大豆胞囊线虫，是一种必须寄生的植物寄生虫，每年给大豆生产造成超过10亿美元的损失。虽然有遗传决定因素使大豆植株对某些线虫基因型产生抗性，但抗性大豆品种越来越无效，因为它们的多年使用选择了毒力较强的大豆种群。甜菜夜蛾寄生的成功依赖于侵染部位向合胞体的全面重组，以及寄主防御的长期抑制以确保合胞体的生存。在这些复杂的分子相互作用的最前沿是效应器，即由甘氨酸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，需要了解效应器获取、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障碍。结果在这里，我们使用PacBio长读技术将738个重叠群的大豆基因组组装成123Mb，并对29,769个基因进行注释。基因组包含大量的重复序列(34%)、串联重复序列(18.7Mb)和水平基因转移事件(151个基因)。在大豆孢囊线虫基因组中发现了大量可能的效应因子(431个基因)，其中许多是在转座子中发现的。结论这一进展揭示了引起大豆孢囊线虫毒力基因的多种机制，包括：包含超过总基因总数五分之一的串联复制，转座子中搭载的毒力基因，以及107个水平基因转移，这些基因在其他植物寄生线虫中尚未见报道。通过对甘氨酸杆菌基因组的广泛表征，我们提供了对甘氨酸杆菌生物学的新见解，并揭示了复杂的宿主-寄生虫相互作用的奥秘。这一基因组序列是能够产生新的抗药性或控制措施的工作的重要前提。
BackgroundHeterodera 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.ResultsHere, we use PacBio long-read technology to assemble a H. glycines genome of 738 contigs into 123Mb with annotations for 29,769 genes. The genome contains significant numbers of repeats (34%), tandem duplicates (18.7Mb), 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.ConclusionsThis 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.