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De novo Transcriptome Assembly of Phomopsis liquidambari Provides Insights into Genes Associated with Different Lifestyles in Rice (Oryza sativa L.)

机译：拟南芥液体杆菌的从头转录组大会提供了与水稻（Oryza sativa L.）不同生活方式相关的基因的见解

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The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment. Fluorescence microscopy, confocal laser scanning microscopy and quantitative PCR investigated the colonization dynamics and biomass of P. liquidambari in rice in vivo. P. liquidambari formed infection structures similar to phytopathogens with infected vascular tissues that systematically spread to acrial parts. However, different from pathogenic infection, P. liquidambari colonization exhibits space restriction and quantity restriction. Direct comparison of a fungal transcriptome under three different habitats provided a better understanding of lifestyle conversion during plant-fungi interactions. The isolated total RNA of Ck (pure culture), EP (endophytic culture) and FP (saprophytic culture) was subjected to Illumina transcriptome sequencing. To the best of our knowledge, this study is the first to investigate Phomopsis sp. using RNA-seq technology to obtain whole transcriptome information. A total of 27,401,258 raw reads were generated and 22,700 unigenes were annotated. Functional annotation indicated that carbohydrate metabolism and biosynthesis of secondary metabolites played important roles. There were 2522 differentially expressed genes (DEGs) between the saprophytic and endophytic lifestyles. Quantitative PCR analysis validated the DEGs of RNA-seq. Analysis of DEGs between saprophytic and endophytic lifestyles revealed that most genes from amino acids metabolism, carbohydrate metabolism, fatty acid biosynthesis, secondary metabolism and terpenoid and steroid biosynthesis were up-regulated in EP. Secondary metabolites of these pathways may affect fungal growth and development and contribute to signaling communication with the host. Most pathways of xenobiotic biodegradation and metabolism were upregulated in FP. Cytochrome P450s play diverse vital roles in endophytism and saprophytism, as their highly specialized functions are evolutionarily adapted to various ecological niches. These results help to characterize the relationship between fungi and plants, the diversity of fungi for ecological adaptations and the application prospects for fungi in sustainable agriculture.
机译：触发从内生真菌向腐生真菌转变的机制在很大程度上尚待探索。在水稻的内生和腐生系统中建立了广泛的寄主液体拟南芥。内生假单胞菌促进水稻生长，提高水稻产量并提高氮肥效率。该物种的腐生物种可以分解水稻凋落物，促进凋落物有机物循环和养分的释放，并改善土壤微生物环境。荧光显微镜，共聚焦激光扫描显微镜和定量PCR研究了稻瘟病菌在水稻中的定殖动力学和生物量。南美白对虾形成了与植物病原体相似的感染结构，其受感染的血管组织系统地扩散到了肛门部分。然而，与致病性感染不同，液体伯氏疟原虫定殖具有空间限制和数量限制。直接比较三种不同生境下的真菌转录组，可以更好地理解植物-真菌相互作用过程中的生活方式转变。对分离的Ck（纯培养物），EP（内生培养物）和FP（腐生培养物）总RNA进行Illumina转录组测序。据我们所知，本研究是第一个研究Phomopsis sp。的研究。使用RNA-seq技术获得完整的转录组信息。总共产生了27,401,258个原始读数，并注释了22,700个单基因。功能注释表明碳水化合物的代谢和次生代谢产物的生物合成起着重要作用。在腐生性和内生性生活方式之间存在2522个差异表达基因（DEG）。定量PCR分析验证了RNA-seq的DEG。对腐生性和内生性生活方式之间的DEG的分析表明，来自氨基酸代谢，碳水化合物代谢，脂肪酸生物合成，次级代谢以及萜类和类固醇生物合成的大多数基因上调。这些途径的次生代谢产物可能会影响真菌的生长和发育，并有助于与宿主进行信号通讯。 FP中大多数异种生物降解和代谢途径均被上调。细胞色素P450在内生细菌和腐生植物中起着至关重要的作用，因为它们高度专业化的功能已进化适应各种生态位。这些结果有助于表征真菌与植物之间的关系，真菌对生态适应的多样性以及真菌在可持续农业中的应用前景。

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