The fungal genus Plectosphaerella comprises species and strains with different lifestyles on plants, such as P. cucumerina, which has served as model for the characterization of Arabidopsis thaliana basal and nonhost resistance to necrotrophic fungi. We have sequenced, annotated, and compared the genomes and transcriptomes of three Plectosphaerella strains with different lifestyles on A. thaliana, namely, PcBMM, a natural pathogen of wild-type plants (Col-0), Pc2127, a nonpathogenic strain on Col-0 but pathogenic on the immunocompromised cyp79B2 cyp79B3 mutant, and P0831, which was isolated from a natural population of A. thaliana and is shown here to be nonpathogenic and to grow epiphytically on Col-0 and cyp79B2 cyp79B3 plants. The genomes of these Plectosphaerella strains are very similar and do not differ in the number of genes with pathogenesis-related functions, with the exception of secreted carbohydrate-active enzymes (CAZymes), which are up to five times more abundant in the pathogenic strain PcBMM. Analysis of the fungal transcriptomes in inoculated Col-0 and cyp79B2 cyp79B3 plants at initial colonization stages confirm the key role of secreted CAZymes in the necrotrophic interaction, since PcBMM expresses more genes encoding secreted CAZymes than Pc2127 and P0831. We also show that P0831 epiphytic growth on A. thaliana involves the transcription of specific repertoires of fungal genes, which might be necessary for epiphytic growth adaptation. Overall, these results suggest that in-planta expression of specific sets of fungal genes at early stages of colonization determine the diverse lifestyles and pathogenicity of Plectosphaerella strains.

真菌嗜油杆菌属（Plectosphaerella）包括植物上具有不同生活方式的物种和菌株，例如黄瓜枯草杆菌（P. cucumerina），该菌株已作为拟南芥对基础和对病原性真菌的非宿主抗性表征的模型。我们测序，注释，比较了三种基因组转录和Plectosphaerella菌株与不同的生活方式拟南芥，即PcBMM，野生型植物（Col-0中），Pc2127，对同事一个致病性菌株的天然病原体0，但对免疫受损的cyp79B2 cyp79B3突变体和P0831具有致病性，该突变体是从拟南芥的自然种群中分离出来的并且在此处显示是非致病性的，并且在Col-0和cyp79B2 cyp79B3植物上附生生长。这些Plectosphaerella菌株的基因组非常相似，并且具有与发病相关的功能的基因数量没有差异，只有分泌的碳水化合物活性酶（CAZymes）除外，其在致病性菌株PcBMM中的含量高出五倍。 。在最初的定殖阶段，对接种的Col-0和cyp79B2 cyp79B3植物中的真菌转录组进行分析，证实了分泌的CAZymes在坏死性相互作用中的关键作用，因为PcBMM比编码Pc2127和P0831表达更多的基因编码分泌的CAZymes。我们还显示了拟南芥中的P0831附生生长涉及真菌基因特定库的转录，这可能对于附生生长适应是必需的。总体而言，这些结果表明，在定殖早期，特定真菌基因组在植物体内的表达决定了嗜油假单胞菌菌株的多样生活方式和致病性。