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Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites.
BMC Genomics ( IF 3.5 ) Pub Date : 2020-06-24 , DOI: 10.1186/s12864-020-06813-6
Jin-Tao Cheng 1, 2 , Fei Cao 1, 2 , Xin-Ai Chen 1, 2 , Yong-Quan Li 1, 2 , Xu-Ming Mao 1, 2
Affiliation  

Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals. However, there is currently little understanding of endophytic fungi at the omics levels about their potential in secondary metabolites. Calcarisporium arbuscula, an endophytic fungus from the fruit bodies of Russulaceae, produces a variety of secondary metabolites with anti-cancer, anti-nematode and antibiotic activities. A comprehensive survey of the genome and transcriptome of this endophytic fungus will help to understand its capacity to biosynthesize secondary metabolites and will lay the foundation for the development of this precious resource. In this study, we reported the high-quality genome sequence of C. arbuscula NRRL 3705 based on Single Molecule Real-Time sequencing technology. The genome of this fungus is over 45 Mb in size, larger than other typical filamentous fungi, and comprises 10,001 predicted genes, encoding at least 762 secretory-proteins, 386 carbohydrate-active enzymes and 177 P450 enzymes. 398 virulence factors and 228 genes related to pathogen-host interactions were also predicted in this fungus. Moreover, 65 secondary metabolite biosynthetic gene clusters were revealed, including the gene cluster for the mycotoxin aurovertins. In addition, several gene clusters were predicted to produce mycotoxins, including aflatoxin, alternariol, destruxin, citrinin and isoflavipucine. Notably, two independent gene clusters were shown that are potentially involved in the biosynthesis of alternariol. Furthermore, RNA-Seq assays showed that only expression of the aurovertin gene cluster is much stronger than expression of the housekeeping genes under laboratory conditions, consistent with the observation that aurovertins are the predominant metabolites. Gene expression of the remaining 64 gene clusters for compound backbone biosynthesis was all lower than expression of the housekeeping genes, which partially explained poor production of other secondary metabolites in this fungus. Our omics data, along with bioinformatics analysis, indicated that C. arbuscula NRRL 3705 contains a large number of biosynthetic gene clusters and has a huge potential to produce a profound number of secondary metabolites. This work also provides the basis for development of endophytic fungi as a new resource of natural products with promising biological activities.

中文翻译:

内生真菌丛生Calcarisporium arbuscula NRRL 3705的基因组和转录组学调查及其次级代谢产物的潜在概况。

作为内生真菌天然产物的次生代谢产物是重要的药物来源。但是,目前在组学水平上对内生真菌在次生代谢产物中的潜力了解甚少。芸香科植物内生真菌——Calcarisporium arbuscula会产生多种具有抗癌,抗线虫和抗生素活性的次级代谢产物。对该内生真菌的基因组和转录组进行全面调查将有助于了解其生物合成次生代谢物的能力,并将为开发这种宝贵资源奠定基础。在这项研究中,我们报告了基于单分子实时测序技术的C. arbuscula NRRL 3705的高质量基因组序列。这种真菌的基因组大小超过45 Mb,它比其他典型的丝状真菌大,并且包含10001个预测基因,编码至少762种分泌蛋白,386种碳水化合物活性酶和177种P450酶。在该真菌中还预测到398个毒力因子和228个与病原体-宿主相互作用有关的基因。此外,揭示了65个次级代谢产物生物合成基因簇,包括真菌毒素aurovertins的基因簇。此外,预测有几个基因簇会产生霉菌毒素,包括黄曲霉毒素,交替烯醇,destruxin,citrinin和异黄病毒素。值得注意的是,显示了两个独立的基因簇,它们可能与交替烯醇的生物合成有关。此外,RNA-Seq分析显示,在实验室条件下,仅aurovertin基因簇的表达要强于管家基因的表达,这与aurovertins是主要代谢产物的观察结果一致。用于化合物主链生物合成的其余64个基因簇的基因表达均低于管家基因的表达,这部分解释了该真菌中其他次级代谢产物的产生较差。我们的组学数据以及生物信息学分析表明,棉铃虫NRRL 3705包含大量的生物合成基因簇,并且具有产生大量次级代谢产物的巨大潜力。这项工作也为内生真菌作为具有前景的生物活性的天然产物的新资源的发展提供了基础。与aurovertins是主要代谢产物的观察结果一致。用于化合物主链生物合成的其余64个基因簇的基因表达均低于管家基因的表达,这部分解释了该真菌中其他次级代谢产物的产生较差。我们的组学数据以及生物信息学分析表明,棉铃虫NRRL 3705包含大量的生物合成基因簇,并且具有产生大量次级代谢产物的巨大潜力。这项工作也为内生真菌作为具有前景的生物活性的天然产物的新资源的发展提供了基础。与aurovertins是主要代谢产物的观察结果一致。用于化合物主链生物合成的其余64个基因簇的基因表达均低于管家基因的表达,这部分解释了该真菌中其他次级代谢产物的产生较差。我们的组学数据以及生物信息学分析表明,棉铃虫NRRL 3705包含大量的生物合成基因簇,并且具有产生大量次级代谢产物的巨大潜力。这项工作也为内生真菌作为具有前景的生物活性的天然产物的新资源的发展提供了基础。用于化合物主链生物合成的其余64个基因簇的基因表达均低于管家基因的表达,这部分解释了该真菌中其他次级代谢产物的产生较差。我们的组学数据以及生物信息学分析表明,棉铃虫NRRL 3705包含大量的生物合成基因簇,并且具有产生大量次级代谢产物的巨大潜力。这项工作也为内生真菌作为具有前景的生物活性的天然产物的新资源的发展提供了基础。用于化合物主链生物合成的其余64个基因簇的基因表达均低于管家基因的表达,这部分解释了该真菌中其他次级代谢产物的产生较差。我们的组学数据以及生物信息学分析表明,棉铃虫NRRL 3705包含大量的生物合成基因簇,并且具有产生大量次级代谢产物的巨大潜力。这项工作也为内生真菌作为具有前景的生物活性的天然产物的新资源的发展提供了基础。灌木丛NRRL 3705包含大量的生物合成基因簇,并且具有产生大量次生代谢产物的巨大潜力。这项工作也为内生真菌作为具有前景的生物活性的天然产物的新资源的发展提供了基础。灌木丛NRRL 3705包含大量的生物合成基因簇,并且具有产生大量次生代谢产物的巨大潜力。这项工作也为内生真菌作为具有前景的生物活性的天然产物的新资源的发展提供了基础。
更新日期:2020-06-24
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