Genome sequences of five Streptomyces type strains (Streptomyces argenteolus, Streptomyces pratensis, Streptomyces puniceus, Streptomyces spiroverticillatus, and Streptomyces sundarbansensis)

ABSTRACT

The genus Streptomyces is one of the largest prokaryotic taxa, including more than 800 species. Sequencing type strain genomes is essential to facilitate the identification of new isolates and the description of novel species. Here, we present the genome sequences of five Streptomyces type strains.

ANNOUNCEMENT

The genus Streptomyces is one of the most important sources of antibiotics and therapeutic drugs (1, 2). It is also one of the largest prokaryotic genera, comprising more than 800 species with validly published and correct names (3, 4). Generating high-quality genomes for all type strains is critical, as it facilitates the identification of new isolates and the description of novel species within this large and important genus. In this context, we sequenced the genomes of five Streptomyces type strains (Streptomyces argenteolus, Streptomyces pratensis, Streptomyces puniceus, Streptomyces spiroverticillatus, and Streptomyces sundarbansensis) that belong to—or are closely related to—the Streptomyces griseus clade and for which high-quality genomes were previously unavailable. These type strains were isolated from diverse habitats, including grassy field soil and mangrove forest sediments (5, 6).

The strains were obtained from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures in freeze-dried form. They were revived in tryptic soy broth (BD Difco) at 28°C under agitation (150 rpm). Genomic DNA was extracted from 5-day-old cultures using the DNeasy PowerLyzer Microbial Kit (Qiagen) following the manufacturer’s instructions. DNA quality and concentration were checked using a NanoDrop ND-1000 UV/Vis spectrophotometer. Library preparation and genome sequencing were performed at the Integrated Microbiome Resource (Halifax, NS, Canada). Genomic DNA was enzymatically fragmented and indexed using the LongPlex Long Fragment Multiplexing Kit (seqWell) according to the manufacturer’s instructions. The resulting DNA fragments (~8–10 kb) were cleaned up and pooled before undergoing library preparation using the SMRTbell Prep Kit 3.0 (Pacific Biosciences) as per the manufacturer’s instructions. Genome sequencing was performed on a Vega sequencer (Pacific Biosciences) loaded with one Vega SMRT Cell (Vega chemistry). SMRT Link v25.3 (Pacific Biosciences) was used for demultiplexing and adaptor trimming. FastQC v0.11.9 (7) was used to check the quality of the HiFi reads. No read filtering or error correction was performed. Genome assembly was performed with Flye v2.9.5-b1801 using the command “--pacbio-hifi.” The genomes were annotated by the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline v6.10 (8). Default parameters were used for all software unless otherwise specified. Sequencing, assembly metrics, and genome features are presented in Table 1.

TABLE 1.

Genome sequencing/assembly metrics and genome features^a

Data	Type strains
	DSM 40036T	DSM 40083T	DSM 40226T	DSM 42019T	DSM 105114T
Species	Streptomyces spiroverticillatus	Streptomyces puniceus (syn. Streptomyces californicus)	Streptomyces argenteolus	Streptomyces sundarbansensis	Streptomyces pratensis
Isolation date	1955	Unknown	Unknown	2001	Unknown
Origin	Soil, Japan	Unknown	Soil	Mangrove forest sediments, India	Grassy field soil, Charlotte, NC, USA
No. of HiFi reads	27,080	732,127	106,945	92,162	249,226
HiFi read N50 (bp)	5,410	8,187	5,641	5,423	6,226
Coverage (x)	13	259	75	59	175
Genome size (bp)	9,797,833	8,221,749	7,128,956	7,479,561	7,690,231
G + C content (%)	71.2	72.5	71.0	72.0	71.0
No. of contigs	20	3	4	2	12
Contig N50 (bp)	1,259,728	7,919,793	6,741,712	7,232,247	7,544,179
No. of coding DNA sequences	8,608	7,149	6,250	6,445	6,728
No. of pseudogenes	163	100	182	133	126
No. of rRNAs	23	18	18	18	18
No. of tRNAs	69	72	68	67	68
Closest type strain from another species (accession no.)	Streptomyces finlayi JCM 4637T (NZ_BMVC00000000.1)	Streptomyces californicus NRRL B-2098T (CP070241.1- CP070243.1)	Kitasatospora cinereorecta JCM 6916T (JBHUET000000000.1)	Streptomyces rubiginosohelvolus JCM 4415T (BMTW00000000.1)	Kitasatospora papulosa NRRL B-16504T (JNYQ00000000.1)
Digital DNA-DNA hybridization value (%)	99.8	87.5	96.5	50.6	94.8
GenBank accession no.	JBVQTE000000000	JBTRAP000000000	JBTRAO000000000	JBTRAN000000000	JBVQTD000000000
SRA accession no.	SRR36161494	SRR36161493	SRR36161492	SRR36161491	SRR36161490

^a The most closely related type strains were determined by TYGS, except for S. argenteolus DSM 40226^T. For this strain, the most closely related type strain (Kitasatospora cinereorecta JCM 6916^T) was identified by the taxonomy check performed by the NCBI.

The five genomes were assembled into 2–20 linear contigs, with total genome sizes ranging from 7.13 to 9.80 Mb and G + C content varying from 71.0% to 72.5%. To visualize the phylogenetic relationships of the five type strains with other Streptomyces species, a multilocus sequence analysis was performed (Fig. 1). Digital DNA-DNA hybridization (dDDH) values between the five type strains under study and closely related type strains were also calculated using the Type (Strain) Genome Server v408 (9, 10) and the Genome-to-Genome Distance Calculator software v4.0 (11). According to the dDDH values presented in Table 1, S. puniceus is a later heterotypic synonym of Streptomyces californicus, as previously suggested (12). S. spiroverticillatus, S. argenteolus, and S. pratensis are earlier heterotypic synonyms of Streptomyces finlayi, Kitasatospora cinereorecta, and Kitasatospora papulosa, respectively.

Fig 1.

Phylogenetic relationships between the five Streptomyces type strains under study and various Streptomyces type strains. Genomes of closely related Streptomyces type strains were downloaded from GenBank. The complete nucleotide sequences of five housekeeping genes (atpD, gyrB, recA, rpoB, and trpB) were extracted from each genome, aligned using Clustal Omega v1.2.2 (13), and subsequently concatenated. The resulting alignment was used to generate a phylogenetic tree using FastTree v2.1 (14) and the generalized time reversible model. The tree topology was verified by computing Shimodaira Hasegawa support values (15). Only support values above 0.5 are displayed at the nodes. Actinomyces bovis NCTC11535 ^T was used as an outgroup (not shown on the tree). The five strains whose genomes were sequenced in this study are highlighted in bold. The scale bar indicates sequence divergence.

DATA AVAILABILITY

The genome sequences of the five Streptomyces type strains (BioProject PRJNA1368964) have been deposited in GenBank. The versions described in this paper are the first versions. The raw sequencing data have been deposited in the Sequence Read Archive. Accession numbers are provided in Table 1.