Supplementary file 1_Whole genome sequencing of Phomopsis asparagi reveals molecular basis of asparagus stem blight pathogenesis.docx

Asparagus (Asparagus officinalis L.), a nutritionally and medicinally valuable crop, faces significant yield and quality losses due to stem blight disease caused by the fungal pathogen Phomopsis asparagi (syn. Diaporthe asparagi). Despite the implementation of various control measures—including agronomic practices, resistant cultivars, chemical treatments, and biological controls—the lack of comprehensive understanding of the pathogen’s molecular pathogenesis has hindered the development of effective management strategies. In this study, we present the first whole-genome assembly of P. asparagi (50.94 Mb) through Illumina sequencing, which contains 4,362 predicted protein-coding genes. Functional annotation identified key virulence-associated pathways, particularly those related to oxidative stress response, reactive oxygen species (ROS) metabolism, cell wall remodeling, and programmed cell death (PCD). Given the known temperature sensitivity of disease development, we performed comparative transcriptomic profiling under optimal (25 °C) and heat-stress (32 °C) conditions. Our findings reveal that thermal stress triggers a sophisticated molecular response cascade in P. asparagi: initial environmental sensing through WRKY transcription factors and MAPK signaling activates coordinated stress adaptation mechanisms involving ROS generation, DNA damage repair, metabolic reprogramming (lipid and carbohydrate metabolism), proteolytic activity, and cell wall degradation enzymes. This multifaceted response ultimately culminates in host cell dysfunction and PCD, facilitating fungal invasion. This work provides fundamental genomic resources and mechanistic insights into P. asparagi pathogenicity, offering new targets for developing science-based disease control approaches in asparagus cultivation.

石刁柏（Asparagus officinalis L.）是兼具营养与药用价值的重要作物，但其种植生产常受真菌病原菌天门冬拟茎点霉（Phomopsis asparagi，异名Diaporthe asparagi）引发的茎枯病影响，面临严重的产量与品质损失。尽管已采取农艺栽培、抗病品种选育、化学防治及生物防治等多种防控措施，但由于对该病原菌的分子致病机制缺乏全面认知，有效防控策略的开发仍受到极大阻碍。本研究通过Illumina测序首次完成了天门冬拟茎点霉的全基因组组装，组装得到的基因组大小为50.94 Mb，共预测得到4362个蛋白编码基因。功能注释鉴定出多条关键的致病相关通路，尤以与氧化应激应答、活性氧（reactive oxygen species, ROS）代谢、细胞壁重塑以及程序性细胞死亡（programmed cell death, PCD）相关的通路最为突出。考虑到病害发展对温度的敏感性，本研究在适宜温度（25℃）与热胁迫（32℃）条件下开展了比较转录组分析。结果显示，热胁迫会触发天门冬拟茎点霉复杂的分子响应级联反应：首先通过WRKY转录因子与MAPK信号通路完成初始环境感知，随后激活协同的胁迫适应机制，涵盖活性氧生成、DNA损伤修复、脂质与碳水化合物代谢相关的代谢重编程、蛋白水解活性以及细胞壁降解酶的表达调控。这种多维度响应最终导致宿主细胞功能失常与程序性细胞死亡，从而促进真菌侵染。本研究为天门冬拟茎点霉的致病性提供了基础基因组资源与机制解析，为芦笋栽培中基于科学依据的病害防控手段开发提供了全新靶点。