Table_6_Infection Strategies Deployed by Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer as a Function of Tomato Fruit Ripening Stage.XLSX

Worldwide, 20–25% of all harvested fruit and vegetables are lost annually in the field and throughout the postharvest supply chain due to rotting by fungal pathogens. Most postharvest pathogens exhibit necrotrophic or saprotrophic lifestyles, resulting in decomposition of the host tissues and loss of marketable commodities. Necrotrophic fungi can readily infect ripe fruit leading to the rapid establishment of disease symptoms. However, these pathogens generally fail to infect unripe fruit or remain quiescent until host conditions stimulate a successful infection. Previous research on infections of fruit has mainly been focused on the host’s genetic and physicochemical factors that inhibit or promote disease. Here, we investigated if fruit pathogens can modify their own infection strategies in response to the ripening stage of the host. To test this hypothesis, we profiled global gene expression of three fungal pathogens that display necrotrophic behavior—Botrytis cinerea, Fusarium acuminatum, and Rhizopus stolonifer—during interactions with unripe and ripe tomato fruit. We assembled and functionally annotated the transcriptomes of F. acuminatum and R. stolonifer as no genomic resources were available. Then, we conducted differential gene expression analysis to compare each pathogen during inoculations versus in vitro conditions. Through characterizing patterns of overrepresented pathogenicity and virulence functions (e.g., phytotoxin production, cell wall degradation, and proteolysis) among the differentially expressed genes, we were able to determine shared strategies among the three fungi during infections of compatible (ripe) and incompatible (unripe) fruit tissues. Though each pathogen’s strategy differed in the details, interactions with unripe fruit were commonly characterized by an emphasis on the degradation of cell wall components, particularly pectin, while colonization of ripe fruit featured more heavily redox processes, proteolysis, metabolism of simple sugars, and chitin biosynthesis. Furthermore, we determined that the three fungi were unable to infect fruit from the non-ripening (nor) tomato mutant, confirming that to cause disease, these pathogens require the host tissues to undergo specific ripening processes. By enabling a better understanding of fungal necrotrophic infection strategies, we move closer to generating accurate models of fruit diseases and the development of early detection tools and effective management strategies.

全球范围内，每年有20%至25%的采收果蔬因真菌病原体侵染腐烂，在田间及采后供应链全过程中发生损耗。多数采后病原真菌以死体营养型（necrotrophic）或腐生营养型（saprotrophic）方式生存，导致宿主组织分解、可售商品损失。死体营养型真菌可轻易侵染成熟果实，快速引发病害症状。但此类病原体通常无法侵染未成熟果实，或保持休眠状态，直至宿主生理条件触发成功侵染。此前关于果蔬侵染的研究多聚焦于宿主调控病害发生与否的遗传与理化因素。本研究旨在探究果蔬病原真菌是否可根据宿主果实的成熟阶段调整自身侵染策略。为验证该假说，我们针对3种死体营养型病原真菌——灰葡萄孢（Botrytis cinerea）、尖孢镰孢菌（Fusarium acuminatum）、匍枝根霉（Rhizopus stolonifer）——在与未成熟及成熟番茄果实互作过程中的全局基因表达谱进行了分析。由于此前尚无尖孢镰孢菌与匍枝根霉的基因组资源，我们对二者的转录组进行了组装与功能注释。随后，我们开展差异基因表达分析，对比各病原真菌在果实接种与体外培养条件下的基因表达差异。通过解析差异基因中富集的致病力与毒力功能（如植物毒素合成、细胞壁降解、蛋白水解）模式，我们明确了3种真菌在侵染亲和性（成熟）与非亲和性（未成熟）果实组织时的共有侵染策略。尽管各病原真菌的策略细节存在差异，但与未成熟果实的互作通常以降解细胞壁组分（尤其是果胶）为核心；而侵染成熟果实则更侧重于氧化还原过程、蛋白水解、单糖代谢与几丁质生物合成。此外，我们发现3种真菌均无法侵染非成熟突变体（nor）番茄的果实，证实此类病原体要引发病害，需宿主组织完成特定的成熟进程。本研究有助于深化对真菌死体营养型侵染策略的认知，为构建精准的果蔬病害模型、开发早期检测工具与高效防控策略奠定了基础。