ABSTRACT
We report the genomic DNA sequence of the actinomycete Streptomyces auratus DSM 41897. The genome assembled as two linear chromosomal contigs (4,434,406 bp and 3,992,024 bp) and a circular plasmid (12,008 bp), with an overall GC content of 71.2%, and 33 predicted biosynthetic gene clusters for potential secondary metabolites.
KEYWORDS: Streptomyces auratus, genome, antibiotics
ANNOUNCEMENT
The Actinomycetota phylum is a source of diverse bacteria known to produce highly sought-after secondary metabolites for clinical and industrial use (1). Within this group, Streptomyces have particularly been exploited for their production of antibiotics and other bioactive compounds (2, 3). The type strain Streptomyces auratus DSM 41897 was sequenced as part of the “Sequencing the genomes of 1,000 Actinobacteria strains” project at the U.S. Department of Energy (DOE) Joint Genome Institute to provide insight into the pharmacological potential of this species.
S. auratus DSM 41897 was provided by the Leibniz Institute DSMZ and cultured in Trypticase soy broth (DSMZ medium 535) at 28°C for 3 days with shaking at 120 rpm (4). Genomic DNA was extracted using the MasterPure gram-positive DNA Purification Kit (Biosearch Technologies). Genomic DNA was sheared to 10 kb using Covaris g-Tube. An SMRTbell template library was sequenced on a Pacific Biosciences (PacBio) Sequel II sequencer using 8M 1 SMRT cells and Version 1.0 sequencing chemistry with 1 × 900 sequencing movie run times (5). PacBio’s SMRT Link software performed quality control and adapter trimming under default conditions. Read error correction was performed by the Flye assembler (6). A total of 5,108,190 filtered subreads (read N50 = 5855 bases) were assembled using Flye v.2.8.1 under the following settings: –asm-coverage 100 –plasmid –genome-size 5000000 t 64 –pacbio-raw (fasta list). The resulting assembly totaled 8,438,454 bp (71.2% GC) in three contigs: a 4,434,406 bp linear chromosomal contig, a 3,992,024 bp linear chromosomal contig, and a 12,008 bp circular plasmid. Circularity of the plasmid assembly was confirmed with Circlator (7). The average coverage was 2,279×. CheckM2 was used to assess genome completeness (100%) and possible contamination (0.32%) (8).
The S. auratus DSM 41897 genome was annotated by the integrated microbial genomes genome annotation pipeline version 5.0.23 (9). A total of 7,454 genes were identified, including 7,300 protein-coding genes, 19 rRNA genes, and 71 tRNA genes. The sequence showed 98.6% average nucleotide identity (10) to the S. auratus AGR0001 draft genome sequence (GenBank accession no. CP072931) (11), but the DSM 41897 assembly is consolidated to three scaffolds, compared to 238 for AGR0001. Accurate prediction of biosynthetic gene clusters (BGCs) is facilitated by high-quality genome assemblies (12). BGCs in S. auratus DSM 41897 were identified using antiSMASH v.7.1.0 (13) with default software parameters. The genome contains 33 high-confidence BGCs (Table 1) (14), including nine with 80% or greater similarity to known clusters in the MIBig v.4.0 database (15). These BGCs may encode bioactive compounds with potential for biotechnological research applications.
TABLE 1.
Biosynthetic gene cluster distribution of S. auratus DSM 41897
| BGC class | Total | Products of most similar known cluster(s) |
|---|---|---|
| Non-ribosomally synthesized peptides | 1 | No prediction |
| Polyketides | 9 | iso-migrastatin/migrastatin/dorrigocin A/dorrigocinB/13-epi-dorrigocin A; naringenin;https://mibig.secondarymetabolites.org/go/BGC0000242/1lysolipin I;https://mibig.secondarymetabolites.org/go/BGC0000123/1phoslactomycin B;https://mibig.secondarymetabolites.org/go/BGC0002051/1antipain |
| Ribosomally synthesized and post- translationally modified peptides |
6 | radamycin/globimycin;https://mibig.secondarymetabolites.org/go/BGC0001550/1citrulassin D |
| Terpenes | 3 | No prediction |
| Other | 10 | legonoxamine A/desferrioxamine B/legonoxamine B,https://mibig.secondarymetabolites.org/go/BGC0002052/1Ectoine |
| Hybrid | 4 | Ulleungdin |
ACKNOWLEDGMENTS
The work (proposal DOI [https://doi.org/10.46936/10.25585/60001044]) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under contract no. DE-AC02-05CH11231.
This announcement was largely prepared by undergraduate students, and we gratefully acknowledge JGI for initiating and supporting it as an educational project (the “Adopt-a-Genome” Project).
Contributor Information
Craig Stephens, Email: cstephens@scu.edu.
Julie C. Dunning Hotopp, University of Maryland School of Medicine, Baltimore, Maryland, USA
DATA AVAILABILITY
The genome of Streptomyces auratus DSM 41897 is deposited in GenBank under accession number NZ_JBNGCB000000000, with the respective annotated DNA sequences available as JBNGCB010000001.1, JBNGCB010000002.1, and JBNGCB010000003.1. Raw data are available as SRA accession numberhttps://www.ncbi.nlm.nih.gov/sra/SRX7194182%5Baccn%5DSRX7194182.
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Associated Data
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Data Availability Statement
The genome of Streptomyces auratus DSM 41897 is deposited in GenBank under accession number NZ_JBNGCB000000000, with the respective annotated DNA sequences available as JBNGCB010000001.1, JBNGCB010000002.1, and JBNGCB010000003.1. Raw data are available as SRA accession numberhttps://www.ncbi.nlm.nih.gov/sra/SRX7194182%5Baccn%5DSRX7194182.