Transposable elements create distinct genomic niches for effector evolution among Magnaporthe oryzae lineages

Draft genome assemblies: De novo draft assemblies were generated using the software SPAdes v3.15.5 (Bankevich et al., 2012) with the “careful” method and automated k-mer selection. Assemblies are identified by their NCBI SRA accession ID. Abstract: Plant-pathogen interactions are characterized by evolutionary arms races. At the molecular level, fungal effectors can target important plant functions, while plants evolve to improve effector recognition. Rapid evolution in genes encoding effectors can be facilitated by transposable elements (TEs). In Magnaporthe oryzae, the causal agent of blast disease in several cereals and grasses, TEs play important roles in chromosomal evolution as well as the gain or loss of effector genes in host specialized lineages. However, a global understanding of TE dynamics driving effector evolution at population scale and across lineages is lacking. Here, we focus on 16 AVR effector loci assessed across a global sampling of 11 reference genomes and 447 newly generated draft genome assemblies across all major M. oryzae lineages and outgroups. We classified each effector based on evidence for duplication, deletion and translocation processes among M. oryzae lineages. Next, we determined AVR gain and loss dynamics across lineages allowing for a broad categorization of effector dynamics. Each AVR was integrated in a distinct genomic niche determined by the TE activity profile contributing to the diversification at the locus. We quantified TE contributions to effector niches and found that TE identity helped diversify AVR loci. We used the large genomic dataset to recapitulate the evolution of the rice blast AVR1-CO39 locus. Taken together, our work demonstrates how TE dynamics are an integral component of M. oryzae effector evolution, likely facilitating escape from host recognition. In-depth tracking of effector loci is a valuable tool to predict the durability of host resistance.基因组草图组装：本研究采用SPAdes v3.15.5软件（Bankevich等，2012）的"careful"组装模式与自动化k-mer选择流程，完成de novo（从头）基因组草图组装。所有组装结果以其NCBI SRA（Sequence Read Archive，序列读取存档）登录号进行标识。 研究摘要：植物与病原菌的互作以进化军备竞赛为典型特征。在分子层面，真菌效应蛋白可靶向宿主植物的关键生理功能，而植物则通过演化提升对效应蛋白的识别能力。转座元件（transposable elements, TEs）可推动效应蛋白编码基因的快速演化。在引发多种谷类作物与草本植物稻瘟病的稻瘟病菌（*Magnaporthe oryzae*）中，转座元件在染色体演化以及寄主专化谱系内效应蛋白编码基因的获得与丢失过程中发挥重要作用。然而，目前学界尚缺乏在种群尺度与跨谱系维度上解析驱动效应蛋白演化的转座元件动态的全局认知。 本研究聚焦于16个AVR（avirulence）效应蛋白基因座，对全球采样获得的11个参考基因组，以及覆盖稻瘟病菌所有主要谱系与外类群的447个新构建的基因组草图展开分析。我们基于稻瘟病菌各谱系间的基因重复、缺失与易位事件证据，对每个效应蛋白基因座进行分类。随后，我们解析了跨谱系的AVR基因获得与丢失动态，实现了对效应蛋白演化动态的广谱分类。每个AVR基因均整合于由转座元件活性特征决定的独特基因组生态位中，这一特征推动了该基因座的序列多样化。我们量化了转座元件对效应蛋白基因组生态位的贡献，发现转座元件的类型差异可促进AVR基因座的多样化。我们利用该大型基因组数据集，重构了稻瘟病菌AVR1-CO39基因座的演化历程。综上，本研究证实转座元件动态是稻瘟病菌效应蛋白演化的核心组成部分，或可助力病原菌逃避宿主的免疫识别。对效应蛋白基因座的深度追踪，可作为预测宿主抗病性持久性的有效工具。