Genome Sequencing of Inonotus Obliquus Reveals Insights Into Candidate Genes Involved In Secondary Metabolite Biosynthesis

Abstract Background: Inonotus obliquus is an important edible and medicinal mushroom that was shown to have many pharmacological activities in preclinical trials, including anti-inflammatory, antitumor, immunomodulatory, and antioxidant effects. However, the biosynthesis of these pharmacological components has rarely been reported. The reason for this is that there have been no relevant reports on its genome information.Results: we report the genome of I. obliquus using a combined high-throughput Illumina NovaSeq with Oxford Nanopore PromethION sequencing platform. The de novo assembled 38.18 Mb I. obliquus genome was determined to harbor 12525 putative genes, with 81.83% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed a close evolutionary relationship between I. obliquus and Fomitiporia mediterranea and Sanghuangporus baumii in the core Hymenochaetales clade. The I. obliquus genome was found to encode a repertoire of enzymes involved in carbohydrate metabolism, along with 135 cytochrome P450 proteins. Other annotated genes included those encoding key enzymes for secondary metabolite biosynthesis, such as those from polysaccharide, melanin, and triterpenoid pathways. Among them, the I. obliquus genome was particularly enriched in sesquiterpenoid biosynthesis genes and gene clusters.Conclusions: This study presents the first genome analysis of an important medical mushroom, I. obliquus, which can provide insights into the usefulness of this organism and its secondary metabolites in medicine.

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An atlas of bacterial secondary metabolite biosynthesis gene clusters

Environmental Microbiology ◽

10.1111/1462-2920.15761 ◽

2021 ◽

Author(s):

Bin Wei ◽

Ao‐Qi Du ◽

Zhen‐Yi Zhou ◽

Cong Lai ◽

Wen‐Chao Yu ◽

...

Keyword(s):

Secondary Metabolite ◽

Gene Clusters ◽

Biosynthesis Gene ◽

Secondary Metabolite Biosynthesis

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De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.)

Scientific Reports ◽

10.1038/s41598-021-01906-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bhagyashree Biswal ◽

Biswajit Jena ◽

Alok Kumar Giri ◽

Laxmikanta Acharya

Keyword(s):

Secondary Metabolite ◽

De Novo ◽

Differentially Expressed Gene ◽

Homology Search ◽

Biosynthesis Pathway ◽

Terpenoid Biosynthesis ◽

De Novo Transcriptome ◽

Illumina Hiseq ◽

Secondary Metabolite Biosynthesis ◽

Root Tissues

AbstractThis study reported the first-ever de novo transcriptome analysis of Operculina turpethum, a high valued endangered medicinal plant, using the Illumina HiSeq 2500 platform. The de novo assembly generated a total of 64,259 unigenes and 20,870 CDS (coding sequence) with a mean length of 449 bp and 571 bp respectively. Further, 20,218 and 16,458 unigenes showed significant similarity with identified proteins of NR (non-redundant) and UniProt database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. A total of 17,444 DEGs were identified among which majority of the DEGs (Differentially Expressed Gene) involved in secondary metabolite biosynthesis were found to be significantly upregulated in stem as compared to root tissues. The qRT-PCR validation of 9 unigenes involved in phenylpropanoid and terpenoid biosynthesis also showed a similar expression pattern. This finding suggests that stem tissues, rather than root tissues, could be used to prevent uprooting of O. turpethum in the wild, paving the way for the plant's effective conservation. Moreover, the study formed a valuable repository of genetic information which will provide a baseline for further molecular research.

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A Complete Genome Sequence of the Wood Stem Endophyte Bacillus velezensis BY6 Strain Possessing Plant Growth-Promoting and Antifungal Activities

BioMed Research International ◽

10.1155/2021/3904120 ◽

2021 ◽

Vol 2021 ◽

pp. 1-9

Author(s):

Ping Zhang ◽

Jian Diao ◽

Guangqiang Xie ◽

Ling Ma ◽

Lihai Wang

Keyword(s):

Secondary Metabolite ◽

Single Molecule ◽

Complete Genome ◽

Pathogenic Fungus ◽

Gc Content ◽

Endophytic Bacterium ◽

Gene Clusters ◽

Bacillus Velezensis ◽

Sequencing Platform ◽

Plant Growth Promoting

An endophytic bacterium Bacillus velezensis BY6 was isolated from the wood stems of healthy Populus davidiana × P. alba var. pyramidalis (PdPap). The BY6 strain can inhibit pathogenic fungus Alternaria alternate in PdPap and promote growth of PdPap seedlings. In the present study, we used the Pacific Biosciences long-read sequencing platform, a single-molecule real-time (SMRT) technology for strain BY6, to perform complete genome sequencing. The genome size was 3,898,273 bp, the number of genes was 4,045, and the average GC content was 47.33%. A complete genome of strain BY6 contained 110 secondary metabolite gene clusters. Nine of the secondary metabolite gene clusters exhibited antifungal activity and promoted growth functions primarily involved in the synthesis of surfactin, bacteriocins, accumulated iron ions, and related antibiotics. Gene clusters provide genetic resources for biotechnology and genetic engineering, and enhance understanding of the relationship between microorganisms and plants.

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antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

Nucleic Acids Research ◽

10.1093/nar/gkr466 ◽

2011 ◽

Vol 39 (suppl_2) ◽

pp. W339-W346 ◽

Cited By ~ 899

Author(s):

Marnix H. Medema ◽

Kai Blin ◽

Peter Cimermancic ◽

Victor de Jager ◽

Piotr Zakrzewski ◽

...

Keyword(s):

Secondary Metabolite ◽

Gene Clusters ◽

Rapid Identification ◽

Fungal Genome ◽

Genome Sequences ◽

Biosynthesis Gene ◽

Secondary Metabolite Biosynthesis

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Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products

Frontiers in Microbiology ◽

10.3389/fmicb.2020.00437 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 1

Author(s):

Jaime Felipe Guerrero-Garzón ◽

Martin Zehl ◽

Olha Schneider ◽

Christian Rückert ◽

Tobias Busche ◽

...

Keyword(s):

Secondary Metabolite ◽

Marine Sponge ◽

Gene Clusters ◽

Streptomyces Spp ◽

Biosynthesis Gene ◽

Secondary Metabolite Biosynthesis

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De novo sequencing and detection of secondary metabolite gene clusters of Penicillium griseofulvum

Acta Horticulturae ◽

10.17660/actahortic.2016.1144.22 ◽

2016 ◽

pp. 157-162

Author(s):

H. Banani ◽

M. Marcet-Houben ◽

A.-R. Ballester ◽

P. Abbruscato ◽

L. González-Candelas ◽

...

Keyword(s):

Secondary Metabolite ◽

De Novo ◽

Gene Clusters ◽

De Novo Sequencing ◽

Penicillium Griseofulvum

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Divergence of pigments in three phylogenetically close Monascus species (M. pilosus, M. ruber, and M. purpureus) based on secondary metabolite biosynthetic gene clusters

10.21203/rs.2.22197/v1 ◽

2020 ◽

Author(s):

YUKI HIGA ◽

Young-Soo Kim ◽

Md. Altaf-Ul-Amin ◽

Ming Huan ◽

Naoaki Ono ◽

...

Keyword(s):

Secondary Metabolite ◽

Food Industry ◽

Gene Clusters ◽

Illumina Miseq ◽

Biosynthetic Gene ◽

Asian Countries ◽

Biosynthetic Gene Clusters ◽

Natural Pigments ◽

Secondary Metabolite Biosynthesis ◽

Paired End Sequencing

Abstract Background: Species under the genus Monascus are considered as economically important and have been widely used in the production of yellow and red food colorants. In particular, three Monascus species, namely, M. pilosus , M. purpureus , and M. ruber , are used for food fermentation in the cuisine of East Asian countries such as China, Japan, and Korea. These species have also been utilized in the production of various kinds of natural pigments. Results: We examined the diversity of pigment-related biosynthetic pathways in three Monascus species ( M. pilosus , M. purpureus , and M. ruber ) at the metabolome and genome levels. Illumina MiSeq 300 bp paired-end sequencing generated 17 million high-quality short reads in each species, corresponding to 200 times the genome size. We measured the pigments and their related metabolites using potato dextrose liquid (PDL) media. The colors in the PDL media corresponding to the pigments and their related metabolites produced by the three species are very different from each other. The gene clusters for secondary metabolite biosynthesis of the three Monascus species also diverged, confirming that M. pilosus and M. purpureus are chemotaxonomically different. M. ruber has similar biosynthetic gene clusters for citrinin, monacolin K, and Monascus azaphilone pigments with M. pilosus and M. purpureus. The comparison of secondary metabolites produced also revealed divergence in the three species. Conclusions: Our findings are important for improving the utilization of Monascus species in the food industry and industrial field. However, in view of food safety, we need to determine if the toxins produced by some Monascus strains exist in the genome or in the metabolome.

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Transcriptome Comparison of Secondary Metabolite Biosynthesis Genes Expressed in Cultured and Lichenized Conditions of Cladonia rangiferina

Diversity ◽

10.3390/d13110529 ◽

2021 ◽

Vol 13 (11) ◽

pp. 529

Author(s):

Natalia Sveshnikova ◽

Michele D. Piercey-Normore

Keyword(s):

Secondary Metabolite ◽

Environmental Changes ◽

Gene Clusters ◽

Biosynthetic Gene Clusters ◽

Secondary Metabolite Biosynthesis ◽

Metabolite Synthesis ◽

Transcriptome Comparison ◽

Encoding Genes ◽

Cladonia Rangiferina ◽

Active Genes

Lichen secondary metabolites are natural products of high medicinal and industrial value, which are produced by the fungal symbiont (mycobiont) of lichens in response to environmental changes. It has been shown that the cultured mycobiont is capable of secondary metabolite production, specifically polyketides, and polyketide production is affected by the presence or absence of the algal or cyanobacterial symbiont (photobiont). Identification of polyketide synthases encoding genes is, in turn, key for understanding the regulation of secondary metabolite synthesis. Using a previously established method of resynthesis for Cladonia rangiferina as well as the sequenced and assembled genome of that species, we compared transcriptomes of C. rangiferina cultured alone and resynthesized with the photobiont (Asterochloris glomerata) to reveal transcriptionally active genes in secondary metabolic gene clusters, as well some of the neighbouring genes, induced by the presence of the photobiont and events of lichenization. The results identify potential candidates for PKS genes in C. rangiferina, identify potential neighbouring genes in the PKS cluster, and offer insights into further research. The study provides preliminary insights into the activity of several identified biosynthetic gene clusters (BGC) as well as interactions of genes within those clusters.

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