Comparative transcriptome analysis between enophytic and pathogenic Colletotrichum species isolated from field-grown healthy Brassicaceae plants

In nature, plants are constantly associated with a rich diversity of microbes, ranging from potentially harmful pathogens to beneficial endophytes, typically without discernible disease symptoms. However, it remains poorly understood how the potential pathogenesis of pathogens that colonize inside the plant is suppressed. Here, we show that the root endophyte Colletotrichum fructicola (CfE), isolated from field-grown healthy Brassicaceae plants, inhibits the pathogenic growth of Colletotrichum fungi in Arabidopsis thaliana. Remarkably, CfE displays the antifungal function specifically in the host plants but not in axenic culture conditions. Isolation of C. gloeosporioides, a pathogenic relative to CfE, called CgP, from healthy Brassicaceae individuals accommodating CfE enables comparative genome and in-planta transcriptome analyses between the two fungi. This reveals a degree of divergence in their genome sequences and >700 CfE genes (4.34% of CfE whole genes) that are specifically induced in A. thaliana following co-inoculation with CgP. This indicates that large-scale transcriptome reprograming is induced in CfE during its suppression of CgP growth and pathogenesis in the host roots. In particular, strong activation of CfE genes for the biosynthesis and efflux of fungal toxins raises the possibility that CfE outcompetes phytopathogenic fungi with these fungal toxins, thereby conferring plant protection.

在自然界中，植物始终与丰富多样的微生物类群形成共生关系，这些微生物涵盖潜在有害的病原菌与有益的内生菌（endophyte），且宿主植物通常不会表现出可见的病害症状。然而，学界对于定殖于植物体内的病原菌的潜在致病力如何被抑制这一科学问题，仍知之甚少。本研究证实，从田间种植的健康十字花科（Brassicaceae）植物中分离得到的根内生真菌果生炭疽菌（Colletotrichum fructicola，CfE），可在拟南芥（Arabidopsis thaliana）体内抑制炭疽菌属真菌的致病生长。值得注意的是，CfE仅在宿主植物体内展现出抗真菌活性，而在无菌纯培养（axenic culture）条件下并无此类功能。从携带有CfE的健康十字花科植株中，我们分离得到与CfE亲缘关系紧密的病原菌胶孢炭疽菌（Colletotrichum gloeosporioides，CgP），这为开展二者的比较基因组学分析与植物体内转录组学分析提供了条件。该分析揭示了二者基因组序列的分化程度，同时发现，在与CgP共接种后，拟南芥体内的CfE有超过700个基因（占CfE全基因总数的4.34%）被特异性诱导表达。这表明，在CfE抑制宿主根系内CgP的生长与致病力的过程中，CfE发生了大规模的转录组重编程（transcriptome reprogramming）。尤为关键的是，参与真菌毒素生物合成与外排的CfE基因被显著激活，这提示CfE可能通过这类真菌毒素竞争排斥植物病原真菌，从而为植物提供病害防护能力。