Comparative transcriptomics analyses of fruiting body development in Fusarium species. Comparative transcriptomics analyses of fruiting body development in Fusarium species

Fusarium neocosmosporiellum (formerly Neocosmospora vasinfecta) has been reported as a fruit- and root-rot pathogen of numerous field crops, although it is not known to cause significant losses on any crop. This cosmopolitan species has also been reported as an opportunistic human pathogen, from infected soybean cyst nematodes, deer dung, and soil, and it possesses a highly active CO2 fixation mechanism. To better understand the metabolic potential of this fungus, we sequenced the genome of one isolate of F. neocosmosporiellum and compared its gene content with previously published Fusarium genomes. The predicted gene numbers were similar to F. graminearum, but the F. neocosmosporiellum genome contained more carbohydrate metabolism-related and transmembrane transport genes, and it appears to have a greater ability to utilize resources in the environment as a cosmopolitan saprotroph. Transcriptome data during perithecium development was compared with that of the model plant pathogen F. graminearum. The F. neocosmosporiellum genome included both MAT1-1 and MAT1-2 idiomorphs, as in the homothallic F. graminearum, however MAT gene organization and their expression patterns during perithecium development differed in these species. We also found that many transmembrane transport genes were differentially expressed during perithecium development, which may account for the larger perithecia of F. neocosmosporiellum. Finally, comparative analysis of the secondary metabolite gene clusters identified several polyketide synthase genes that were induced during perithecium development. Deletion of a novel polyketide synthase gene in F. neocosmosporiellum resulted in a defective perithecium phenotype. In summary, comparative analysis of the transcriptional programs during perithecium development has provided novel insights into morphological and physiological diversification in F. neocosmosporiellum. Overall design: Time-series mRNA profiles during the perithecial development for the Fusarium neocosmosporiellum strain NRRL_22166 were generated by deep sequencing, in triplicate, using the Illumina HiSeq 2500 system.

新壳囊孢镰孢菌（Fusarium neocosmosporiellum，曾用名Neocosmospora vasinfecta）已被报道为多种大田作物的果腐病与根腐病病原菌，但目前尚未见其对任何作物造成重大经济损失的相关报道。该广布性物种还被报道为机会性人类致病菌，分离来源包括受侵染的大豆胞囊线虫、鹿粪以及土壤，且该菌拥有一套活性极高的二氧化碳固定机制。为深入解析该真菌的代谢潜能，本研究对一株新壳囊孢镰孢菌菌株进行了全基因组测序，并将其基因组成分与已发表的镰孢菌属基因组进行了比对分析。预测的基因数量与禾谷镰孢菌（F. graminearum）相近，但新壳囊孢镰孢菌基因组中参与碳水化合物代谢与跨膜转运的基因数量更多，作为广布性腐生真菌，其环境资源利用能力似乎更强。本研究将该菌在子囊壳发育过程中的转录组数据与模式植物病原菌禾谷镰孢菌的转录组数据进行了比对。与同宗配合的禾谷镰孢菌类似，新壳囊孢镰孢菌基因组同时携带MAT1-1和MAT1-2交配型异型基因座（idiomorph），但二者的基因座结构以及子囊壳发育过程中的表达模式在两个物种间存在显著差异。本研究还发现，大量跨膜转运基因在子囊壳发育过程中呈现差异表达，这或许是新壳囊孢镰孢菌子囊壳体积更大的原因。最后，通过对次生代谢产物基因簇的比较分析，本研究鉴定出多个在子囊壳发育过程中被诱导表达的聚酮合酶（polyketide synthase, PKS）基因。对新壳囊孢镰孢菌中一个新型聚酮合酶基因进行敲除后，菌株出现了子囊壳发育缺陷的表型。综上，对子囊壳发育过程中转录调控程序的比较分析，为解析新壳囊孢镰孢菌的形态与生理分化机制提供了全新的认识。实验设计概述：本研究采用Illumina HiSeq 2500测序平台，对新壳囊孢镰孢菌菌株NRRL_22166的子囊壳发育过程进行了三次生物学重复的深度测序，以获取该过程中的时序性mRNA表达谱。