Draft genome sequence data of the endophytic actinobacterium Streptomyces justiciae WPN32, a potential bioactive compounds producer

Streptomyces justiciae WPN32 is an endophytic actinobacterium isolated from the rhizosphere of turmeric field soil at the Botanical Garden of Suranaree University of Technology (Nakhon Ratchasima Province, Thailand). Here we present the draft genome sequence of S. justiciae WPN32. It was sequenced on the Illumina NextSeq 550 sequencer. The draft genome consisted of 123 contigs with a total size of 9,832,147 base pairs, an N50 of 237,572 base pairs and a GC content of 70.87%. The dDDH between WPN32 and Streptomyces justiciae 3R004T was 80.1%, identifying the strain as Streptomyces justiciae. The data presented here may aid microbial taxonomy, comparative genomics and identification of gene clusters associated with the synthesis of bioactive compounds. The draft genome sequence data has been deposited at NCBI under Bioproject accession number PRJNA680432.


a b s t r a c t
Streptomyces justiciae WPN32 is an endophytic actinobacterium isolated from the rhizosphere of turmeric field soil at the Botanical Garden of Suranaree University of Technology (Nakhon Ratchasima Province, Thailand).Here we present the draft genome sequence of S. justiciae WPN32.It was sequenced on the Illumina NextSeq 550 sequencer.The draft genome consisted of 123 contigs with a total size of 9,832,147 base pairs, an N50 of 237,572 base pairs and a GC content of 70.87%.The dDDH between WPN32 and Streptomyces justiciae 3R004 T was 80.1%, identifying the strain as Streptomyces justiciae .The data presented here may aid microbial taxonomy, comparative genomics and identification of gene clusters associated with the synthesis of bioactive compounds.The draft genome sequence data has been deposited at NCBI under Bioproject accession number PRJNA680432.Genomic DNA was extracted from a pure culture using the chloroform extraction method and sequenced on an Illumina NextSeq 550.AfterQC v0.9.6 was used for quality assessment, adapter trimming and quality filtering.De novo genome assembly was performed using Unicycler v0.5.0 and genome assembly metrics were determined using QUAST v5.0.2.Genome quality was assessed using CheckM v1.1.2.Digital DNA-DNA hybridisations and a phylogenomic tree were analysed using the Type (Strain) Genome Server.Genome annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline, and potential secondary metabolites were identified by genome mining using antiSMASH v7.0.1.

Data source location
Streptomyces justiciae WPN32 was isolated from soil collected from the Botanical Garden of Suranaree University of Technology, Nakhon Ratchasima Province, Thailand at 14.8712º N latitude and 102.0218ºE longitude.

Value of the Data
• The draft genome sequence of S. justiciae WPN32 could be valuable for research in microbial taxonomy and ecology, in particular for species identification and distribution.• The draft genome sequence of S. justiciae WPN32 has the potential to be beneficial in comparative genomic investigations with other species of Streptomyces .• Elucidating the genome sequence of S. justiciae WPN32 could potentially assist in identifying the gene clusters accountable for producing bioactive compounds.

Data Description
Here we present the draft genome sequence data of S. justiciae WPN32 ( Fig. 1 ), including its gene clusters with potential secondary metabolite biosynthesis.The genome consisted of 123 contigs with a total size of 9,832,147 bp, an N50 value of 237,572 bp and a GC content of 70.87% ( Table 1 ).The WPN32 draft genome was determined to be 99.14% complete with an estimated contamination of less than 1%.The digital DNA-DNA hybridisation (dDDH) value between WPN32 and Streptomyces justiciae 3R004 T was 80.1%, indicating that WPN32 is a Streptomyces justiciae strain.Fig. 2. The phylogenomic tree was reconstructed using the whole-genome sequence data of S. justiciae WPN32 and its closely related type strain on the TYGS platform.Branch numbers were determined based on pseudo-bootstrap support values greater than 70% from 100 replicates using Genome Blast Distance Phylogeny (GBDP), with average branch support at 93.6%.
Additionally, the study also demonstrates that WPN32 has potential to produce actinomycin D, a recognized anticancer agent [5] , as well as flaviolin 1,3,6,8-tetrahydroxynaphthalene, which exhibits properties of UV protection [6] .We believe that the draft genome sequence will fa- cilitate the characterisation of genes involved in the synthesis of bioactive compounds and the production of secondary metabolites in S. justiciae WPN32.

Bacterial Isolation
Strain WPN32 was isolated from the rhizosphere of turmeric field soil collected at Suranaree University of Technology, Nakhon Ratchasima Province, Thailand (14.8712ºN, 102.0218ºE).One gram of soil sample was suspended in 99 mL of sterile water in a 250 mL Erlenmeyer flask.The soil suspension was serially diluted and spread on International Streptomyces Project-2 (ISP-2) agar.Plates were incubated at 37 °C for 5 days or until streptomyces colonies appeared.A single colony of strain WPN32 was selected and purified by cross-streaking onto a new ISP-2 plate.

Genomic DNA Preparation
Genomic DNA (gDNA) was extracted from overnight cultures of strain WPN32 on ISP-2 medium.The cell pellet of the WPN32 strain was mixed with 50 μL of lysozyme (20 mg/mL) and 25 μL of RNase A (5 mg/mL).The mixture was incubated at 37 °C for 60 min, then 60 μL of 10% sodium dodecyl sulphate (SDS) and 80 μL of 500 μg/mL Proteinase K were added to the tube and incubated at 50 °C for 20 min.The suspension was mixed with 100 μL of 5M NaCl and centrifuged at 7,0 0 0 rpm for 15 min.The extraction of gDNA involved the combination of equal proportions of chloroform and isoamyl alcohol.Subsequently, the gDNA was recovered by adding an amount of 95% ethanol equal to twice its volume and placed in an incubator at -80 °C for 30 min.Following this, the mixture was centrifuged at 7,0 0 0 rpm for 15 min to obtain the gDNA.The supernatant was discarded, and the gDNA underwent three rounds of washing using a 70% ethanol solution.The gDNA pellet was air-dried before resuspension in 30 μL of TE buffer.The gDNA was subsequently evaluated for quality using agarose gel electrophoresis and NanoDrop spectrophotometry (Thermo Scientific, USA).

Whole Genome Sequencing and Assembly
Sequencing libraries were generated from 1 ng of DNA using the Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA).Raw sequencing reads were obtained through the NextSeq 550 sequencer by employing the NextSeq 500/550 high output kit v2.5 (300 cycles, 2 × 150-bp reads) (Illumina).AfterQC v0.9.6 with default parameters [7] was used for quality assessments, adapter trimming, and quality filtering.De novo genome assembly was conducted

Fig. 1 .
Fig. 1.The genome map for S. justiciae WPN32 was constructed using the CGView server ( https://proksee.ca/, accessed 28 September 2023).CDSs are represented by blue arrows, while contigs are represented by grey arrows.Green peaks represent GC skew + , purple peaks represent GC skew-and black peaks represent GC content.
© 2023 The Author(s).Published by Elsevier Inc.This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )

Table 1
Genomic features and assembly statistics for S. justiciae WPN32.

Table 2
Secondary metabolite biosynthesis gene clusters identified by antiSMASH.