Oomycetes include many devastating plant pathogens. Across oomycete diversity, plant-infecting lineages are interspersed by non-pathogenic ones. Unfortunately, our understanding of the evolution of lifestyle switches is hampered by a scarcity of data on the molecular biology of saprotrophic oomycetes, ecologically important primary colonizers of dead tissue that can serve as informative reference points for understanding the evolution of pathogens. Here, we established Salisapilia sapeloensis as a tractable system for the study of saprotrophic oomycetes. We generated multiple transcriptomes from S. sapeloensis and compared them to (a) 22 oomycete genomes and (b) the transcriptomes of eight pathogenic oomycetes grown under 13 conditions. We obtained a global perspective on gene expression signatures of oomycete lifestyles. Our data reveal that oomycete saprotrophs and pathogens use similar molecular mechanisms for colonization but exhibit distinct expression patterns. We identify S. sapeloensis’ specific array and expression of carbohydrate-active enzymes and putative regulatory differences, highlighted by distinct expression levels of transcription factors. S. sapeloensis expresses only a small repertoire of candidates for virulence-associated genes. Our analyses suggest lifestyle-specific gene regulatory signatures and that, in addition to variation in gene content, shifts in gene regulatory networks underpin the evolution of oomycete lifestyles.

中文翻译：

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比较对Salisapilia sapeloensis和多种植物病原性卵菌的腐生性揭示了生活方式特异性基因表达。

卵菌纲包括许多破坏性的植物病原体。在卵菌多样性中，感染植物的谱系散布着非致病性的谱系。不幸的是，缺乏对腐生性卵菌的分子生物学数据的了解阻碍了我们对生活方式转换的理解，腐殖性卵菌是死组织的重要生态重要定居者，可以作为了解病原体进化的信息参考点。在这里，我们建立了Salisapilia sapeloensis作为研究腐生卵菌的易于处理的系统。我们从沙门氏菌中产生了多个转录组并将其与（a）22个卵菌基因组和（b）在13种条件下生长的8种致病卵菌的转录组进行比较。我们获得了卵菌生活方式的基因表达特征的全球视角。我们的数据表明卵菌腐生物和病原体使用相似的分子机制定植，但表现出不同的表达模式。我们确定沙棘链球菌的特异性阵列和糖活性酶的表达和推定的调节差异，通过转录因子的不同表达水平突出显示。沙棘表达与毒力相关的基因的候选基因的一小部分。我们的分析表明特定生活方式的基因调控特征，除了基因含量的变化外，基因调控网络的变化也为卵菌生活方式的发展提供了支撑。