Comparative Analysis of Clinical and Environmental Strains ofExophiala spiniferaby Long-Reads Sequencing and RNAseq Reveal Adaptive Strategies
Comparative Analysis of Clinical and Environmental Strains ofExophiala spiniferaby Long-Reads Sequencing and RNAseq Reveal Adaptive Strategies
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通过长读长测序和 RNAseq 对 Exophiala spinifera 的临床和环境菌株进行比较分析，揭示适应性策略
DOI：
10.3389/fmicb.2020.01880
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发表时间：
2020-07-31
影响因子：
5.2
通讯作者：
Li, Ruoyu
中科院分区：
文献类型：
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作者：
Song, Yinggai;Du, Minghao;Li, Ruoyu
外瓶霉spinifera，胶囊生产的黑色酵母，是过度代表作为传播感染的代理人在人类遗传性功能障碍的CARD 9基因。在对已发表的含半胱天冬酶募集结构域蛋白9（CARD 9）缺乏症病例的综述中，黑色真菌与酵母菌和皮肤真菌病例中常见的突变无关，并且发现对更大的细胞因子有反应。在这里，我们对来自CARD 9缺陷患者的BMU 08022和两种环境菌株BMU 00051和BMU 00047的基因组进行了测序和注释。我们对这些分离株进行了基因组和转录组学分析，包括已发表的黑酵母基因组，使用长读（PACBIO）和短读（Illumina）测序技术与混合组装策略的组合。我们用RNAseq技术鉴定了菌株之间的毒力因子、适应性以及主要的遗传和基因表达差异。基因组组装达到亚染色体水平，预测基因在12，043和12，130之间。在临床菌株中鉴定的插入缺失的数量高于在环境菌株中观察到的。我们确定了一个相对较大的核心基因组，有9,887个基因。此外，检测到CARD 9相关分离物中支架I和III的大量同线重排。17个基因簇参与了次生代谢产物的产生。在临床菌株中始终发现不存在PKS-簇17。比较转录组分析表明，16个单拷贝基因在脑心浸液肉汤与沙氏葡萄糖肉汤孵育后显着差异表达。脑心灌注（BHI）上调的大多数单拷贝基因是转运蛋白。在两种不同培养基中，有48个独特的基因仅对临床菌株差异表达，包括来自各种代谢过程和转录调控的基因。基因本体论（Gene Ontology，GO）富集的临床菌株中表达上调的基因主要涉及跨膜转运、生物合成过程和代谢过程。这项研究提供了新的见解，了解菌株的内在毒力的物种的差异，并表明种内变异可能与栖息地的选择。这表明E.黑刺酵母在易感患者群体中引起感染的倾向不同，并为未来研究探索黑酵母在免疫缺陷患者中的致病和适应性策略的机制提供了线索。
Exophiala spinifera, a capsule-producing black yeast, is overrepresented as agent of disseminated infection in humans with inherited dysfunction of the CARD9 gene. In a review of published caspase recruitment domain-containing protein 9 (CARD9) deficiency cases, black fungi were linked to mutations other than those prevalent in yeast and dermatophyte cases, and were found to respond to a larger panel of cytokines. Here, we sequenced and annotated the genomes of BMU 08022 from a patient with CARD9 deficiency and two environmental strains, BMU 00051 and BMU 00047. We performed genomic and transcriptomic analysis for these isolates including published black yeasts genomes, using a combination of long-read (PACBIO) and short-read (Illumina) sequencing technologies with a hybrid assembly strategy. We identified the virulence factors, fitness, and the major genetic and gene expression differences between the strains with RNAseq technology. Genome assembly reached sub-chromosome level with between 12,043 and 12,130 predicted genes. The number of indels identified in the clinical strain was higher than observed in environmental strains. We identify a relatively large core genome of 9,887 genes. Moreover, substantial syntenic rearrangements of scaffolds I and III in the CARD9-related isolate were detected. Seventeen gene clusters were involved in the production of secondary metabolites. PKS-cluster 17 was consistently found to be absent in the clinical strain. Comparative transcriptome analysis demonstrated that 16 single-copy genes were significantly differentially expressed upon incubation in brain-heart infusion broth vs. Sabouraud glucose broth. Most of the single-copy genes upregulated with Brain Heart Infusion (BHI) were transporters. There were 48 unique genes differentially expressed exclusively to the clinical strain in two different media, including genes from various metabolic processes and transcriptional regulation. Up-regulated genes in the clinical strain with Gene Ontology (GO) enrichment are mainly involved in transmembrane transport, biosynthetic process and metabolic process. This study has provided novel insights into understanding of strain-differences in intrinsic virulence of the species and indicated that intraspecific variability may be related to habitat choice. This indicates that strains of E. spinifera are differentially prone to cause infection in susceptible patient populations, and provides clues for future studies exploring the mechanisms of pathogenic and adaptive strategies of black yeasts in immunodeficient patients.