Dual RNAseq analysis of the interaction between the plant pathogen Pythium myriotylum and the mycoparasite Pythium oligandrum

Biological control is a promising approach to control diseases caused by Pythium species. Unusually for a single genus, the Pythium genus also includes species that can antagonise Pythium plant pathogens, such as Pythium oligandrum. These Pythium plant pathogens are commonly found in the soil such as the broad host-range pathogen Pythium myriotylum and cause various diseases of important crops. While P. oligandrum genes expressed in the interaction with oomycete plant pathogens have been identified previously, the transcriptional response of an oomycete plant pathogen to P. oligandrum has not been investigated. An isolate of P. oligandrum, GAQ1, recovered from soil could antagonise P. myriotylum in a plate-based confrontation assay. The P. oligandrum isolate had a strong disease control effect on soft-rot of ginger caused by P. myriotylum. We investigated the transcriptional interaction between P. myriotylum and P. oligandrum. As part of the transcriptional response of P. myriotylum to the presence of P. oligandrum, putative effector genes such as a sub-set of Kazal-type protease inhibitors were strongly upregulated. P. myriotylum cellulases and elicitin-like putative effectors were also upregulated. In P. oligandrum, cellulases, peroxidases, proteases and NLP effectors were upregulated. The transcriptional response of P. myriotylum suggests clear features of a counter-attacking strategy that may contribute to the variable success and durability of biological attempts to control diseases caused by Pythium species. Whether aspects of this counter-attack could inhibit aspects of this virulence of P. myriotylum is another interesting aspect for future studies. Overall design: Nine RNA samples in total were analyzed from three conditions (self-confrontation of P. oligandum, P. myriotylum, and the cross-species confrontation) in triplicate.生物防治（biological control）是防治疫霉属（Pythium）物种引发病害的极具潜力的策略。尤为特殊的是，在疫霉属这一单菌属中，竟存在可拮抗疫霉属植物病原菌的物种，如寡雄腐霉（Pythium oligandrum）。这类疫霉属植物病原菌广泛存在于土壤环境中，例如寄主范围广泛的芋疫霉（Pythium myriotylum），可侵染多种重要作物并引发各类病害。尽管此前已有研究鉴定出寡雄腐霉在与卵菌（oomycete）植物病原菌互作过程中表达的基因，但目前尚未有针对卵菌植物病原菌对寡雄腐霉的转录响应的相关研究。本研究从土壤中分离得到一株寡雄腐霉菌株GAQ1，在平板对峙实验中该菌株可有效拮抗芋疫霉。该寡雄腐霉菌株对芋疫霉引发的生姜软腐病具有显著的防治效果。本研究针对芋疫霉与寡雄腐霉之间的转录互作展开了系统分析。在芋疫霉对寡雄腐霉存在的转录响应中，包括部分Kazal型蛋白酶抑制剂亚类在内的假定效应基因均被显著上调表达。芋疫霉的纤维素酶及类激发素（elicitin）假定效应基因同样呈现上调表达。在寡雄腐霉中，纤维素酶、过氧化物酶、蛋白酶以及NLP效应因子均被上调表达。芋疫霉的转录响应展现出清晰的反击策略特征，这或可解释为何疫霉属病害的生物防治效果存在波动且持效性参差不齐。此类反击策略是否能够抑制芋疫霉的部分致病能力，仍是未来研究值得深入探索的有趣方向。实验设计：本研究共分析9份RNA样本，覆盖3种培养条件并设置3次生物学重复，分别为寡雄腐霉自身对峙组、芋疫霉自身对峙组以及跨物种对峙组。