The SOAPdenovo (version 2.04,, accessed on 10 February 2022) software was used to assemble and construct the scaffold sequence, while the GapCloser (, accessed on 20 February 2022) program was deployed to fill the sequence gap. Sequencing was performed on the Illumina MiSeq platform and resulted in paired-end raw data in FASTQ format, followed by decontamination using Adapter Removal (version 1.5.4, Copenhagen, Denmark) by and quality correction using the SOAPec (version 2.0,, accessed on 3 February 2022) software. Strain, Cultivation, and Crude Extracts PreparationĪ total of 400 bp DNA fragment library was constructed using the whole-genome shotgun (WGS) method. Additionally, an antibiotic and secondary metabolite analysis database (antiSMASH) was used to determine the SM biosynthetic potential of strain SPS-2. Its gene annotation was extensively predicted using various BLAST databases, including non-redundant (Nr) protein sequence, Swiss-Prot, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and EuKaryotic Orthologous Groups (KOG), and Carbohydrate-Active Enzyme (CAZy) databases. ![]() To better understand this endophytic fungus and explore its SM biosynthetic potential, in this study, whole-genome sequencing and assembly were conducted by hybridizing next-generation sequencing (NGS) and using the Illumina MiSeq platform. In our continuous search for new SMs from endophytic fungi, an endophytic Alternaria strain SPS-2 was obtained from Echrysantha chrysantha Lindl., one of the traditional Chinese medicine used for the treatment of the swelling of the eye, ophthalmalgia, delacrimation, nephelium of the eye, and nocturnal emission. Thus far, however, the detailed genomic features and SM biosynthetic potential of the Alternaria strain have been seldom reported. Additionally, these SMs are biosynthesized via an assembly line process that is catalyzed by modular polyketide synthases (PKSs), non-ribosomal peptide synthetase (NRPS), NRPS-PKS, terpene, and ribosomally synthesized and post-translationally modified peptides (RiPPs). Structurally, the SM inventory of the genus Alternaria consists of diverse groups, including terpenes, pyrones, cyclopeptides, nitrogen-containing compounds, and miscellaneous, which showed a variety of biological activities, such as antimicrobial effect, phytotoxicity, and cytotoxicity. Alternaria strains are commonly detected in plants and have been shown to be a treasure trove of secondary metabolites (SMs) since as many as 482 substances have been isolated and structurally elucidated from this genus by extensively searching the Dictionary of Natural Products database (accessed on 10 July 2022). LS–MS/MS and GNPS-based analyses suggested that this endophytic fungus is a potential producer of bioactive SMs and merits further exploration and development.Įndophytes have been recognized as one of the important sources of bioactive natural products with therapeutic potential. ![]() ![]() The antiSMASH results indicated that strain SPS-2 harbored 22 SM biosynthetic gene clusters (BGCs), 14 of which are cryptic and unknown. The results of this study suggested that the genome of strain SPS-2 was 33.4 Mb in size with a GC content of 51% and an N50 scaffold of 2.6 Mb, and 9789 protein-coding genes, including 644 CAZyme-encoding genes, were discovered in strain SPS-2 through KEGG enrichment analysis. and gene annotation using various bioinformatic tools. SPS-2 derived from Echrysantha chrysantha Lindl. The present work focuses on the whole-genome sequencing and assembly of an endophytic strain Alternaria sp. However, its detailed genomic features and SM biosynthetic potential have not been extensively studied thus far. As one of the commonly isolated endophytic fungi, Alternaria has been known for the production of numerous secondary metabolites (SMs).
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