Abstract
BackgroundSecondary 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.ResultsIn 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.ConclusionsOur 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.
Highlights
Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals
Most gene clusters are silent under laboratory conditions and the fungi are unable to produce corresponding secondary metabolites. To further understand this endophytic fungus, its potential in production of secondary metabolites, we report here a the genome sequence of C. arbuscula NRRL 3705, which was generated bythe high quality Single Molecule Real-Time (SMRT) sequencing technology
The genome was assembled with a size of approximately 45.01 Mb, comprising 91 contigs as displayed by circos-plots (Fig. 1) with an N50 length of 1,530,317 bp,which is larger than the genome size of Calcarisporium sp. (Table 1) [22]
Summary
Secondary metabolites as natural products from endophytic fungi are important sources of pharmaceuticals. Fungi are important sources of natural product-derived drugs, such as penicillin, cephalosporins, lovastatin and cyclosporin A [1, 2] Endophytic fungi are those that live in various tissues and organs of healthy hosts at a certain stage or all stages of their life history, and generally do not confer external symptoms to the infected hosts [3]. There is currently little research on the biosynthesis capacity of endophytic fungi and its secondary metabolites, especially at the omics levels, which has limited our understanding and development of these resources. Calcarisporium, a genus of fungi founded by Preuss, is characterized by a transparent, conical, spore-like sporophyte with spores [12] Most research on this genus has focused on species classification and bio-morphological studies. No details about the genomic information of relevant species in this genus have been reported
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