A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrix

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained the sustainable production of Arabica coffee for over 150 years. The ability of H. vastatrix to overcome resistance in coffee cultivars and evolve new races is inexplicable for a pathogen that supposedly only utilizes clonal reproduction. Understanding the evolutionary complexity between H. vastatrix and its only known host, including determining how the pathogen evolves virulence so rapidly is crucial for disease management. Achieving such goals relies on the availability of a comprehensive and high-quality genome reference assembly. To date, two reference genomes have been assembled and published for H. vastatrix that, while useful, remain fragmented and do not represent chromosomal scaffolds. Here, we present a complete scaffolded pseudochromosome-level genome resource for H. vastatrix strain 178a (Hv178a). Our initial assembly revealed an unusually high degree of gene duplication (over 50% BUSCO basidiomycota_odb10 genes). Upon inspection, this was predominantly due to a single scaffold that itself showed 91.9% BUSCO Completeness. Taxonomic analysis of predicted BUSCO genes placed this scaffold in Exobasidiomycetes and suggests it is a distinct genome, which we have named Hv178a associated fungal genome (Hv178a AFG). The high depth of coverage and close association with Hv178a raises the prospect of symbiosis, although we cannot completely rule out contamination at this time. The main Ca. 546 Mbp Hv178a genome was primarily (97.7%) localised to 11 pseudochromosomes (51.5 Mb N50), building the foundation for future advanced studies of genome structure and organization. Citation: https://doi.org/10.1101/2022.07.29.502101

由真菌病原菌咖啡驼孢锈菌（Hemileia vastatrix）引发的咖啡叶锈病周期性流行，已制约阿拉比卡咖啡的可持续生产长达150余年。该病原菌能够突破咖啡品种的抗性并演化出新的生理小种，这对于理论上仅能进行无性繁殖的病原菌而言，其机制长期以来难以解释。解析咖啡驼孢锈菌与其唯一已知宿主之间的演化复杂性，尤其是阐明该病原菌快速演化毒性的核心机制，对于病害防控工作至关重要。而达成上述研究目标，有赖于获取全面且高质量的基因组参考组装序列。截至目前，已有两份咖啡驼孢锈菌的参考基因组被组装并发表，但它们虽具备一定应用价值，却仍存在片段化缺陷，且未达到染色体级支架（scaffold）水平。本研究报道了咖啡驼孢锈菌菌株178a（Hv178a）的完整支架化假染色体（pseudochromosome）级基因组资源。初始组装结果显示，该基因组存在异常高的基因重复比例，其中超过50%的担子菌门odb10基准通用单拷贝同源基因基准集（BUSCO）基因发生了重复。经核查，该现象主要源于一条单独的支架序列，该序列自身的BUSCO完整度达91.9%。对预测得到的BUSCO基因开展分类学分析后发现，该支架序列归类于外担子菌纲（Exobasidiomycetes），且提示其为一个独立的基因组，我们将其命名为Hv178a关联真菌基因组（Hv178a AFG）。该序列的高覆盖深度以及与Hv178a的紧密关联，提示二者可能存在共生关系，但目前尚无法完全排除污染的可能性。主体约546 Mb的Hv178a基因组中，97.7%的序列被锚定至11条假染色体（N50为51.5 Mb），为后续开展基因组结构与组织形式的深入研究奠定了坚实基础。引用信息：https://doi.org/10.1101/2022.07.29.502101