Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites

Abstract

Background: 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. Results: 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. Conclusions: 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.

Infection Process and Genome Assembly Provide Insights into the Pathogenic Mechanism of Destructive Mycoparasite Calcarisporium cordycipiticola with Host Specificity

“…The resulting assembly yielded an N50 length of 5.45 Mbp and a total size around 34.51 Mbp (Table 1), which was similar to Calcarisporium sp. 525 (36.8 Mbp) [63] and C. militaris (32.2 Mbp) [18], less than that of C. arbuscula (45.0 Mbp) [64]. The sequenced data were assembled into eight scaffolds, an approximate chromosomelevel, with three of these scaffolds containing characteristic telomeric (CCCTAA)n or (TTAGGG)n repeats on both the 5 and 3 ends of the sequence, and four having telomeric repeats on one of the 5 or 3 ends of the sequence.…”

“…Sixty-six SMs were identified in the genome of C. cordycipiticola (Table 3), similar to 60 SMs in marine fungus Calcarisporium sp. KF525 [63] and 65 in mushroom-endophytic fungus C. arbuscula NRRL 3705 [64]. However, compared to the sequenced species in Cordyciptaceae, the number of SMs in C. cordycipiticola (66) was much more than 30 SMs in C. militaris [18], 45 in B. bassiana [68].…”

“…The repeat sequence of congeneric fungi, Calcarisporium sp. KF525 and C. arbuscula NRRL 3705, only accounted for 1.28% and 3.08% of their genome sizes, respectively [63,64]. It was reported that two mycoparasite species, Trichoderm atroviride and T. virens, only had 0.49% and 0.48% repeat sequences [14].…”

Using Next-Generation Sequencing Technology to Explore Genetic Pathways in Endophytic Fungi in the Syntheses of Plant Bioactive Metabolites

“…To date, NGS technologies have been employed in the field of endophytic fungi for taxonomic identification and studies on their ecology (resistance to heavy metals and high salinity, communication with other fungi and bacteria, etc.) [14][15][16][17][18][19], interactions with hosts, lifestyle and functional heterogeneity [20][21][22][23][24][25][26], biosynthetic pathways of secondary metabolites [27][28][29][30][31][32][33], bioprospecting for biofuel production [34,35], evolution [36], and many other aspects.…”

A Cell Factory of a Fungicolous Fungus Calcarisporium arbuscula for Efficient Production of Natural Products

“…Calcarisporium arbuscula NRRL 3705, a fungicolous fungus of Russulaceae , belongs to the class Sordariomycota and primarily produces highly reduced polyketide type mycotoxins aurovertins, which show potent bioactivity against root-knot nematodes and breast cancer as inhibitors of F0F1-ATP synthase. , Though 65 gene clusters have been identified by antiSMASH based on genome sequencing, the mutant with deletion of the polyketide synthetase gene aurA ( ΔaurA ) showed null production of aurovertins and a clear chemo-background, suggesting that most endogenous BGCs are silent and that this mutant has a potential to be a cell factory for activation or heteroexpression of other BGCs for natural product production. , In addition, convenient genetic manipulations have been established in this fungus, also guaranteeing efficient introduction of BGCs from other nonmodel fungi …”