Draft Genome Sequence Data of Streptomyces anulatus, Strain K-31

Abstract

Streptomyces anulatus is a typical representative of the Streptomyces genus synthesizing a large number of biologically active compounds. In this study, the draft genome of Streptomyces anulatus, strain K-31 is presented, generated from Illumina reads by SPAdes software. The size of the assembled genome was 8.548838 Mb. Annotation of the S. anulatus genome assembly identified C. hemipterus genome 7749 genes, including 7149 protein-coding genes and 92 RNA genes. This genome will be helpful to further understand Streptomyces genetics and evolution and can be useful for obtained biological active compounds.

Dataset: The raw genome sequencing data of Illumina MiSeq were submitted to NCBI SRA database in FASTQ format with BioSample: SAMN35538655, under BioProject PRJNA977889. The assembled genome available in NCBI GeneBank under CP127386.1.

Dataset License: CC0

1. Summary

Actinobacteria are typical representatives of soil and water samples [1,2,3]. They take part in the cycle of organic substances and in the carbon cycle. In addition, more than half of clinically used antibiotics, including aminoglycosides, lactamybean anthracyclines, macrolides, etc., are synthesized by representatives of actinomycetes. To date, more than 7600 compounds are known to be synthesized by this group of microorganisms [1,2,3]. The genome Streptomycetes have biosynthesis gene clusters encode enzymes that are responsible for the synthesis of several classes of compounds, including nonribosomal peptides, polyketides, phenazines, terpenes, etc. [4]. Streptomyces anulatus can produces actinomycin C, cactinomycin, endophenazine A, endophenazine B, endophenazine C, epocarbazolin A, epocarbazolin B, tubermycin B, dextranase, and telomestatin; therefore, a draft genome of a new strain may be of interest to many groups of investigators.

2. Data Description (Required)

Streptomyces anulatus, strain k-31 was isolated from soil “Solonetzes”, Kazakhstan, Kostanay region “52.179274 N 64.069596 E”. The draft genome characteristics are summarized in

Table 1. Characteristics of draft genome assembly of Streptomyces anulatus, strain K-31 [5,6,7,8].

Total genome size	8,548,838
Number of contigs about 100,000 bp	1754
N50 contig number	9871
Genes (total)	7749
CDSs (total)	7657
CDSs (with protein)	7143
Genes (RNA)	92
tRNAs	71

. The size of the genome was 8548838 bp. Based on genome annotation, there were 7749 genes, including 92 RNA genes and 27 numbers of subsystem sequences (Table 1, Figure 1).

Additionally, in the genome Streptomyces anulatus, strain K-31, the presence of gene clusters synthesizing secondary metabolites was determined by antiSMASH 7.0 program [9]. Thirty-two gene clusters were determined (

Table 2. Putative region clusters coding for secondary metabolites detected by antiSMASH annotation of Streptomyces anulatus K-31 [9].

Region	Type	from	to	Similarity	MIBiG Accession	Short Description
Region 1	butyrolactone	40,583	51,527	8%	BGC0000038	coelimycin P1, Polyketide, biosynthetic gene cluster from Streptomyces coelicolor A3(2)
Region 2	terpene	85,010	105,914	100%	BGC0001181	geosmin biosynthetic gene cluster from Streptomyces coelicolor A3(2)
Region 3	NRP-metallophore	232,803	291,365	81%	BGC0000325	coelichelin biosynthetic gene cluster from Streptomyces coelicolor A3(2)
Region 4	T3PKS	359,289	398,962	100%	BGC0001310	naringenin biosynthetic gene cluster from Streptomyces clavuligerus ATCC 27064
Region 5	NRPS	655,387	698,449	9%	BGC0000031	borrelidin biosynthetic gene cluster from Streptomyces parvulus
Region 6	PKS-like	717,893	758,951	5%	BGC0001036	polyoxypeptin biosynthetic gene cluster from Streptomyces sp. MK498-98F14
Region 7	Anthracycline	1,035,068	1,054,288	19%	BGC0000273	steffimycin D biosynthetic gene cluster from Streptomyces steffisburgensis
Region 8	ectoine	1,509,035	1,519,433	100%	BGC0000853	ectoine biosynthetic gene cluster from Streptomyces anulatus
Region 9	lanthipeptide-class-ii, iii	2,543,034	2,574,357	9%	BGC0000603	cyclothiazomycin biosynthetic gene cluster from Streptomyces hygroscopicus
Region 10	NI-siderophore	2,629,509	2,639,744	80%	BGC0000941	desferrioxamin B biosynthetic gene cluster from Streptomyces griseus subsp. griseus NBRC 13350
Region 11	lanthipeptide-class-i	3,978,552	4,003,814
Region 12	NRPS	4,330,299	4,424,130	63%	BGC0002676	skyllamycin D biosynthetic gene cluster from Streptomyces anulatus
Region 13	arylpolyene	4,769,141	4,810,541	13%	BGC0000698	hygromycin A biosynthetic gene cluster from Streptomyces hygroscopicus
Region 14	NRPS-like	5,353,507	5,406,855	10%	BGC0000341	enduracidin biosynthetic gene cluster from Streptomyces fungicidicus
Region 15	thiopeptide	5,418,638	5,447,540	11%	BGC0002376	bombyxamycin A biosynthetic gene cluster from Streptomyces sp
Region 16	melanin	5,465,624	5,474,333	100%	BGC0000912	melanin biosynthetic gene cluster from Streptomyces griseus subsp. griseus NBRC 13350
Region 17	lanthipeptide-class-iii	5,516,282	5,538,933	100%	BGC0000496	AmfS biosynthetic gene cluster from Streptomyces griseus subsp. griseus NBRC 13350
Region 18	terpene	5,922,704	5,942,363
Region 19	NI-siderophore	6,342,962	6,357,683	20%	BGC0002683	schizokinen biosynthetic gene cluster from Nostoc sp. PCC 7120 = FACHB-418
Region 20	NRPS	6,543,237	6,624,407	97%	BGC0001438	warkmycin CS1 biosynthetic gene cluster from Streptomyces sp. CS057
Region 21	Polyketide	6,931,020	6,950,554	11%	BGC0001590	formicamycins A m biosynthetic gene cluster from Streptomyces sp. KY5
Region 22	terpene	7,370,054	7,396,451	61%	BGC0000663	hopene biosynthetic gene cluster from Streptomyces coelicolor A3(2)
Region 23	linaridin	7,463,339	7,483,947	9%	BGC0001735	pentostatine biosynthetic gene cluster from Streptomyces antibioticus
Region 24	T1PKS	7,546,793	7,595,910	100%	BGC0001043	SGR PTMs biosynthetic gene cluster from Streptomyces griseus subsp. griseus NBRC 13350
Region 25	RiPP-like	7,611,006	7,621,267	3%	BGC0000163	tetronasin biosynthetic gene cluster from Streptomyces longisporoflavus
Region 26	T1PKS	7,720,816	7,765,658	16%	BGC0001584	C-1027 biosynthetic gene cluster from Streptomyces sp. CB02366
Region 27	RiPP-like	7,854,078	7,865,445	58%	BGC0002115	streptamidine biosynthetic gene cluster from Streptomyces albidoflavus J1074
Region 28	melanin	7,866,288	7,876,767	100%	BGC0000911	melanin biosynthetic gene cluster from Streptomyces griseus subsp. griseus NBRC 13350
Region 29	T3PKS	7,911,501	7,952,553	100%	BGC0000282	alkylresorcinol biosynthetic gene cluster from Streptomyces griseus subsp. griseus NBRC 13350
Region 30	NRPS-like	7,991,666	8,068,947	61%	BGC0000175	cycloheximide biosynthetic gene cluster from Streptomyces sp. YIM 56141
Region 31	T1PKS	8,129,275	8,182,159	11%	BGC0000290	A-47934 biosynthetic gene cluster from Streptomyces toyocaensis
Region 32	NRPS	8,242,727	8,329,466	100%	BGC0000664	isorenieratene biosynthetic gene cluster from Streptomyces griseus subsp. griseus NBRC 13350

). The presented genes included type I, II, and III polyketides synthase (PKS) and non-ribosomal polypeptide synthetase (NRPS). Polyketide synthases (PKSs) produce highly diverse polyketide chains by sequential condensation of the starter units with extender units, followed by reduction, cyclization, aromatization, and tailoring reactions to synthesis aromatic core with several annulated rings. There is coelimycin, coelichelin, borrelidin, steffimycin, etc.

The 16S rRNA phylogenetic analysis revealed that Streptomyces anulatus K-31 is closely related to the CP 110539 Streptomyces anulatus strain YUW1 (97.07%), CP061072 Streptomyces sp. (97.07%), and CP096281 Streptomyces sp. WAC00303 (100%).

This genome will be helpful in further understanding the evolutions of Streptomyces genetics and can be useful for obtained biological active compounds.

3. Methods

3.1. Sample Collection and Isolation of Streptomyces

Natural soil sample (muds and rhizosphere) was collected from the extreme habitats of northern (Kostanay region, 52.179274 N 64.069596 E) Kazakhstan. The soil sample collected was of the solonetz type. Solonetz are soils with a high content of exchangeable sodium and/or magnesium ions. The soil sample was collected at the depth of 10 cm (~4 inches). The samples were packed in sterile plastic containers, transported to the laboratory, and refrigerated at 4 °C (39 °F) until ready for analysis [10].

Soil samples were plated using the standard method. Actinomycetes samples were isolated on two variants of modified Bennett’s agar: glucose (0.2%), peptone (0.2%), yeast extract (0.1%), and agar (2.0%), with 5% NaCl, pH 7.2 (variant #1), or with 0.5% Na₂CO₃, pH 9.0 (variant #2). The medium was adjusted with NaOH to pH 9.0 after sterilization. The purity of the isolated strains was confirmed using the standard microbiological method. The culture was stored in 20% glycerol stock at −80 °C.

3.2. DNA Isolation, Genome Sequencing, Assembly, and Annotation

Genomic DNA was isolated using the PureLink Genomic DNA Mini Kit according to the manufacturer’s instructions (ThermoFisher Scientific, Waltham, MA, USA). A whole-genome sequencing library was prepared using the Nextera XT DNA library preparation kit following the manufacturer’s instructions (Illumina, Cambridge, UK). The libraries were sequenced using the Miseq platform (Illumina, Cambridge, UK) to generate 2 × 300 paired end reads. The raw reads adapters were trimmed by Trimmomatic version 0.38.0 [11]. Low-quality sequences (<Q30) were deleted. After trimming, reads were contained from 50 to 250 bp. Genome assembly was performed using SPAdes version 3.12.0 [6]. After assembly, the quality of the genome was checked by the software Geneious Prime 2023 by mapping to the reference genome [12]. The annotation genome was determined by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP), GeneMarkS-2+, RAST, and Bacta [5,7,8]. The secondary metabolites biosynthetic gene clusters of the strain K-31 draft genome were identified using antiSMASH version 7.0 [9].