The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat

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BTA 1-131 was isolated from the marine sponge Melophlus sarasinorum collected in Indonesia. The crude extracts of this strain displayed antibacterial and cytotoxic activity, and therefore, to further investigate the bioactive potential of the strain, whole genome sequencing was performed in this study. The whole genome sequencing of Streptomyces sp. BTA 1-131 was conducted using both Illumina NextSeq and Oxford Nanopore platforms with a de novo hybrid assembly approach. The high-quality genome obtained is 10.23 Mbp with a GC content of 71.57%. It is organised into a single chromosomal contig, two linear plasmids, and one circular plasmid. Interestingly, a long-terminal inverted repeat (L-TIR) sequence of 1.5 Mbp has been confirmed in the strain genome. Phylogenomic analysis suggested that the strain BTA 1-131 likely represents a new species within the genus Streptomyces. To the best of our knowledge, the genome data described here would be the first report on the hybrid genome sequence of Streptomyces associated with the rarely reported sponge Melophlus sarasinorum from Indonesia, with a unique feature of L-TIR. The complete genome data generated here will provide compelling information for further analysis of the biosynthetic potential of the strain BTA 1-131 to produce new bioactive compounds." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/14-1303", "name": "The first whole-genome sequence of a prospective novel sponge-associated..." } } ] } Home Browse The first whole-genome sequence of a prospective novel sponge-associated... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Pratama R, Sukmarini L, Atikana A et al. The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.12688/f1000research.173356.3 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Genome Note Revised The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] Rahadian Pratama https://orcid.org/0000-0002-2709-7370 1 , Linda Sukmarini https://orcid.org/0000-0001-8154-7996 2,3 , Akhirta Atikana https://orcid.org/0000-0002-4863-629X 2-4 , Shanti Ratnakomala 3,5 , Fahrurrozi Fahrurrozi https://orcid.org/0000-0002-9230-0347 6 , Puspita Lisdiyanti 3,5 Rahadian Pratama https://orcid.org/0000-0002-2709-7370 1 , Linda Sukmarini https://orcid.org/0000-0001-8154-7996 2,3 , [...] Akhirta Atikana https://orcid.org/0000-0002-4863-629X 2-4 , Shanti Ratnakomala 3,5 , Fahrurrozi Fahrurrozi https://orcid.org/0000-0002-9230-0347 6 , Puspita Lisdiyanti 3,5 PUBLISHED 24 Jan 2026 Author details Author details 1 Department of Biochemistry, IPB University, Bogor, West Java, Indonesia 2 Research Centre for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia 3 Indonesian Biofilm Research and Collaboration Centre, Yogyakarta, Yogyakarta, Indonesia 4 Laboratory of Microbiology, Wageningen University & Research, Wageningen, Gelderland, The Netherlands 5 Research Centre for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia 6 Research Centre for Freshwater, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia Rahadian Pratama Roles: Data Curation, Formal Analysis, Investigation, Methodology, Resources, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Linda Sukmarini Roles: Conceptualization, Data Curation, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Akhirta Atikana Roles: Data Curation, Investigation, Methodology, Project Administration, Resources, Validation, Writing – Review & Editing Shanti Ratnakomala Roles: Resources, Writing – Review & Editing Fahrurrozi Fahrurrozi Roles: Data Curation, Resources, Writing – Review & Editing Puspita Lisdiyanti Roles: Resources, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Genomics and Genetics gateway. Abstract Streptomyces sp. BTA 1-131 was isolated from the marine sponge Melophlus sarasinorum collected in Indonesia. The crude extracts of this strain displayed antibacterial and cytotoxic activity, and therefore, to further investigate the bioactive potential of the strain, whole genome sequencing was performed in this study. The whole genome sequencing of Streptomyces sp. BTA 1-131 was conducted using both Illumina NextSeq and Oxford Nanopore platforms with a de novo hybrid assembly approach. The high-quality genome obtained is 10.23 Mbp with a GC content of 71.57%. It is organised into a single chromosomal contig, two linear plasmids, and one circular plasmid. Interestingly, a long-terminal inverted repeat (L-TIR) sequence of 1.5 Mbp has been confirmed in the strain genome. Phylogenomic analysis suggested that the strain BTA 1-131 likely represents a new species within the genus Streptomyces. To the best of our knowledge, the genome data described here would be the first report on the hybrid genome sequence of Streptomyces associated with the rarely reported sponge Melophlus sarasinorum from Indonesia, with a unique feature of L-TIR. The complete genome data generated here will provide compelling information for further analysis of the biosynthetic potential of the strain BTA 1-131 to produce new bioactive compounds. READ ALL READ LESS Keywords Melophlus sarasinorum, sponge-associated Streptomyces, de novo assembly, whole genome, L-TIR Corresponding Author(s) Linda Sukmarini ( [email protected] ) Close Corresponding author: Linda Sukmarini Competing interests: No competing interests were disclosed. Grant information: Rumah Program Biodiversitas, ORHL-BRIN” (9/III/HK/2022 to LS) and “Rumah Program Artificial, Intelligence, Big Data & Teknologi Komputasi, OREI-BRIN (B-1409/III.6/PR.03.06/4/2023 to LS) and continuously financed by “Riset dan Inovasi untuk Indonesia Maju—Indonesia Endowment Funds for Education (LPDP) (37/II.7/HK/2023; B-3838/II.7.7/FR.06.00.112023 to LS) The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2026 Pratama R et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Pratama R, Sukmarini L, Atikana A et al. The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.12688/f1000research.173356.3 ) First published: 24 Nov 2025, 14 :1303 ( https://doi.org/10.12688/f1000research.173356.1 ) Latest published: 24 Jan 2026, 14 :1303 ( https://doi.org/10.12688/f1000research.173356.3 ) Revised Amendments from Version 2 The version 3 include more information in the methods section and results of generated sequencing data The version 3 include more information in the methods section and results of generated sequencing data See the authors' detailed response to the review by Matsapume Detcharoen See the authors' detailed response to the review by Arzu Karahan READ REVIEWER RESPONSES Introduction Streptomycetes represent a group of metabolically diverse bacteria known for their ability to produce natural products of considerable importance in human health, veterinary medicine, and agriculture. The genus Streptomyces primarily synthesises bioactive secondary metabolites that include antibiotics, as well as antifungal, antiviral, and anthelmintic agents, anticancer drugs, immunosuppressants, and herbicides. 1 However, Streptomyces spp. demonstrate notable GC content exceeding 70% and show high repetition within secondary metabolite biosynthetic gene clusters (BGCs). 2 These provide issues in sequencing and high-quality genome assembly for in-depth genome mining, which are presently addressed through intensive sequencing efforts. Advances in genome sequencing technology have uncovered a multitude of hitherto unexamined metabolic capabilities inside Streptomyces genomes. The advent of fast and efficient genome sequencing tools has allowed for the examination of more profound and comprehensive bacterial genomic data. Thus, the data rely on the thoroughly curated genome sequence characterised by high contiguity and improved annotation. In recent years, the emergence of long-read sequencing technologies has led to the integration of both Illumina (short) and Nanopore or PacBio (long) reads, potentially enhancing the completeness of genome assemblies relative to those constructed based solely on Illumina reads. 3 Streptomyces sp. BTA 1-131 was isolated from an Indonesian sponge, namely MS5, identified as Melophlus sarasinorum. The marine sponge M. sarasinorum is widely distributed in the Indo-Pacific region, including Indonesia, Palau, Guam, Papua New Guinea, and the Solomon Islands. 4 A multiomics analysis of M. sarasinorum leads to the exploration of the previously unknown natural products derived from the sponge M. sarasinorum and the bacterial symbiont. 5 Indeed, our initial study showed the potential extracts of sponge M. sarasinorum MS5 to inhibit the growth of gram-positive pathogenic bacteria, and the abundance of actinobacteria is significantly correlated to the sponge bioactivity. 6 Further investigation observed antibacterial activity in the methanolic extracts of the sponge-associated actinobacterium Streptomyces sp. BTA 1-131 against the gram-positive S. aureus ATCC 13240. Additionally, the methanolic extracts of Streptomyces sp. BTA 1-131 also demonstrated cytotoxic effects on the MDA-MDB231 human breast cancer cells and the Caco-2 colorectal adenocarcinoma cell. 7 The study confirmed that potential bioactivity was present between the sponge-associated actinobacterium Streptomyces and its sponge host. Molecular identification using the 16S rRNA gene sequence revealed that the strain BTA 1-131 is 98% similar to S. kunmingensis NBRC 14463. 7 A study by Wei et al. (2017) 8 reported the potential of S. kunmingensis YIM 121234 , which originated from soil, to produce bioactive compounds with potent cytotoxic activity towards the MCF-7 human breast cancer cells. Moreover, another reported strain, S. kunmingensis MR03, originated from marine sediment and showed its potential to synthesise cadmium sulphide nanoparticles that were active against biofilm-forming bacteria such as S. aureus, E. coli, P. aeruginosa, and Enterecoccus spp. 9 The diversity of Streptomyces and their novel compounds originating from marine biospheres remains less explored. 10 Indeed, the analysis of secondary metabolite BGCs demonstrated by Almeida et al. (2019) 11 suggests that while the marine isolates share a close genomic relationship with their terrestrial counterparts, they may have the capacity to produce distinct compounds. Considering the atypical origin of the culturable sponge symbiont Streptomyces sp. BTA 1-131, similarity of the strain to known Streptomyces (≤ 98.7%), and our intention to further evaluate its biosynthetic capabilities, we sequenced the whole genome of Streptomyces sp. BTA 1-131, using a de novo approach based on the hybrid Illumina and Nanopore platform. This has allowed us to generate a complete chromosome sequence. To the best of our knowledge, this is the first study to publish the complete genome of a sponge-associated Streptomyces strain from the marine sponge M. sarasinorum of Indonesian origin. The reported data provides the basis for further analysis to explore the strain as a putative new Streptomyces species and reveals the biosynthetic capabilities of its bioactive compounds. Methods Bacterial isolation and culture condition Streptomyces sp. BTA 1-131 was previously isolated from marine sponge M. sarasinorum in December 2015. The sponge was collected in Tanjung Batu Angus, Lembeh Strait, Bitung, North Sulawesi, Indonesia (1.50572° N, 125.24541° E; depth 13 m) as described in the previous study. 6 The strain BTA 1-131 was previously identified by sequencing the 16S rRNA gene and is closely related to soil-derived S. kunmingensis NBRC 14463. 7 The nucleotide sequence of the 16S rRNA was deposited in the NCBI GenBank database under accession number MT280129, and the cultivable isolate was deposited in the Indonesian Culture Collection BRIN (InaCC) under accession number A1205. 7 In this study, the strain BTA 1-131 was revived from a glycerol stock stored at –80 °C. Prior to genomic DNA extraction, the strain BTA 1-131 was grown on an International Streptomyces Project (ISP)-recommended medium, ISP2 agar medium, at 28 °C, for 14 days. The ISP2 medium contains yeast extract (BD Difco, USA; 4 g L −1 ), malt extract (BD Difco, USA; 10 g L −1 ), and dextrose (BD Difco, USA; 4 g L −1 ). The medium was prepared in 1 L of seawater with an addition of bacteriological agar (BD Difco, USA; 20 g L −1 ). DNA extraction and sequencing Genomic DNA was extracted from Streptomyces sp. BTA 1-131 colonies grown on ISP2 medium agar plate using the Quick-DNA TM HMW MagBead kit according to the manufacturer’s instructions (Zymoresearch, USA). The integrity of the extracted genomic DNA was assessed by gel electrophoresis (0.8% tris borate-EDTA agarose w/v), while its quality and quantity were analysed by a NanoDrop spectrophotometer (Thermo Fischer Scientific, USA) and a Qubit 4 fluorometer (Thermo Fischer Scientific, USA) using the Qubit TM dsDNA High Sensitivity assay kit (Thermo Fischer Scientific, USA), respectively. Moreover, total gDNA was used for the input of library preparation for both short read-based Illumina sequencing and long read-based Oxford Nanopore Technologies (ONT) sequencing platforms. To sequence the genome of the strain BTA 1-131 on the Illumina platform, the DNA library was prepared using the Illumina NextSeq500 system with the NextSeq 500/550 kit v2.5 (300 cycles) to generate 2 x 150 bp paired-end sequence reads following the manufacturer’s protocol (Illumina, USA). For the ONT platform, the DNA library was prepared for GridION ONT using the SQK-NBD114.24 ligation sequencing kit according to the manufacturer’s recommendation (Oxford Nanopore Technology, UK). Kit from NEBNext, FFPE Repair Mix (NEB M6630, UK) and Ultra II End repair module (NEB E7546, UK) were employed in the library preparation. In brief, total gDNA was repaired using an end-prep enzyme mix (NEB M6630 & NEB E7546), generating DNA with 5’ phosphorylated, 3’ dA-tailed ends. Barcodes were ligated with an ONT-compatible adapter. The library was quantified with a Qubit Fluorometer before loading to the FLO-MIN114 flow cell. Sequencing control was conducted in MINKNOW v23.04.6 following default sequencing run from ONT (72 h). The output raw reads were set to POD5 for a separate basecalling process. Data processing and hybrid assembly Illumina read processing Illumina-generated FASTQ files were initially processed using Fastp v0.24.0 12 to assess read quality and remove low-quality bases (Data file 1). 13 Reads were filtered with the parameters -q 30 -l 100 -c , ensuring only high-quality reads were retained (Data file 2). 14 Unpaired reads (those lacking a mate from either R1 or R2) were kept using the flags –unpaired1 sample_unpaired1.fastq.gz --unpaired2 sample_unpaired2.fastq.gz and were included alongside paired reads for subsequent hybrid assembly with the ONT data. ONT read processing and hybrid assembly Raw POD5 files were basecalled at super accuracy using Dorado v0.8.2, generating a simplex BAM file. This BAM file was converted to FASTQ format using Samtools v1.21. 15 Read quality distributions were assessed with NanoPlot v1.44.0, 16 (Data file 1). 13 Hybrid assembly began by assembling ONT reads first using Flye v2.9.5, 17 (Data file 3). 18 Parameters included --nano-hq -g 8m --asm-coverage 50 , reflecting an estimated 8 Mbp genome size and a coverage limit set to 50X. Assembly graphs were visualised with Bandage v0.9.0, 19 (Data file 4). 20 Moreover, to refine the ONT-based assembly, Medaka v2.0.1 (Medaka consensus) was applied with recommended settings optimised for v14 reagent kit reads. A final hybrid assembly was then generated by polishing the ONT assembly with the high-quality Illumina reads using Pilon v1.24. 21 Three iterative polishing steps were performed; in the first iteration, the Illumina was aligned to the Medaka-polished ONT assembly using Bowtie v2.5.4, 22 and alignments were processed with Samtools v1.21. The resulting consensus contigs become assembly sources for the second iteration and continue until three iterations of polishing are reached. After these three polishing rounds constituted the final hybrid assembly for subsequent analyses. Assembly statistics and completeness Assembly metrics were obtained with the quality assessment tool for genome assembly (QUAST) v5.2.0, 23 reporting the number of contigs, N50, and GC content; gene predictions were disabled for this step (Data file 5). 24 Genome completeness was evaluated using the benchmarking universal single-copy orthologs (BUSCO) v5.8.2 25 in genome mode, employing the Streptomyces_odb12 lineage dataset (Data file 6). 26 The identified single-copy orthologs were visualised via the generate_plot.py script included with BUSCO. CheckM v1.2.3 27 was used with the lineage_wf workflow to estimate completeness and contamination, summarised in a table of reported statistics (qa) (Data file 7). 28 Assemblies with >95% completeness and <5% contamination were considered high-quality. Bioinformatic analysis Genome visualisation and annotation Genome visualisation was performed using GenoVi v02.16, 29 which generated circular genome maps depicting sequence features, contig boundaries, and genomic architecture. Functional annotation of clusters of orthologous groups (COGs) categories was conducted using the integrated DeepNOG 30 within GenoVi, with gene sequences queried against the COG database to assign functional categories and identify orthologous proteins across genomes (Data file 8). 31 The resulting visualisations provided both an overview of overall genomic organisation and detailed functional annotation profiles for downstream analysis. TIR and plasmid identification To examine the linear inverted repeats on the strain BTA 1-131 chromosome, a basic local alignment search tool (BLAST) was conducted using the parameters described previously by Jørgensen et al. (2024). 32 While putative plasmid contigs were identified with PLASme v1.1 33 using the default database and the “balance” mode parameter. All other settings were kept at default values. Any candidate plasmid contigs were verified by examining the assembly graph in Bandage to confirm their circular topology or unique structural features. Taxonomic inference and phylogenomic analysis Taxonomic assignment was carried out on the type (strain) genome server (TYGS) 34 by submitting the polished genome assembly (Data file 9). 35 Additional inferences were made using GTBD-Tk v2.1.0, 36 incorporating Streptomyces kunmingensis strains and the type strain S. albus NRRL B-1811 (ASM72588v1), as well as some selected Streptomyces strains associated with marine sponges reported by Xu et al. (2019) 37 for comparative analysis. Moreover, Deferribacter desulfuricans SSM1 was chosen as an outgroup. The resulting genome BLAST distance phylogeny (GBDP) tree was visualised in iToL v7. 38 The TYGS webserver also provided a DNA-DNA hybridization (dDDH) score. To assess the genomic similarity between the polished genome assembly of the strain BTA 1-131 and one of the reference S. kunmingensis DSM 41681 (the nearest strain based on the genome-scale GBDP tree), average nucleotide identity (ANI) was calculated using FastANI. 39 The reference genome sequence of S. kunmingensis DSM 41681 (ASM3561610v1) was obtained from publicly available genomic repositories, and the strain BTA 1-131 genome assembly was prepared using the following command: FastANI -q assembly_genome.fasta -r reference_genome.fasta -o ani_output.txt , where -q specifies the query genome (the polished genome assembly of the strain BTA 1-131), - r denotes the reference genome ( S. kunmingensis DSM 41681), and -o defines the output file storing ANI results. The ANI percentage from the analysis result was used to determine the genomic relatedness between the assembly and the reference strain. Results were interpreted based on established ANI thresholds (90–95%) for bacterial species delineation. 39 Results Complete assembled genome description Sequencing of Streptomyces sp. BTA1-131 performed on both Illumina and ONT platform. The Illumina sequencing generated 11.25 million reads with a total base of 1.67 Gbp; the mean length was 149 bp, with a peak insert size of 261 bp. The filtering process resulted in 82.04% of reads (9.23 million reads) passing filtering (>Q30, >100 bp); the remaining reads were categorized as low quality (15.2%), too short (2.7%), and too many N (0.06%). The ONT sequencing generated 561,346 reads with a total base of 1.46 Gbp; reads N50 was 5,672 Kbp and more than 97% reads were >Q10. No filtering process was applied to ONT reads as the Flye assembler will use all data input from ONT raw reads. The whole genome sequence of Streptomyces sp. BTA 1-131 was obtained from a total of 561,346 sequence reads from the ONT long-read assembly, followed by polishing with the Illumina short-read assembly. This hybrid assembly resulted in a 10,234,869 bp genome size with an N50 median of 9,496,435 bp and a GC content of 71.62%, consisting of one large chromosomal contig and three small contigs. Based on the CheckM analysis, the genome was 99.89% complete with a contamination level of 0.21%. In addition, the overall average coverage of the complete assembled genome was noted to be approximately 170.7X. This finding is supported by BUSCO result, 99.8% complete BUSCOs from Streptomyces_odb12 lineage dataset. Moreover, both linear and circular topologies were found in the genome of Streptomyces sp. BTA 1-131. The BLAST analysis revealed that a linear chromosomal genome of the strain BTA 1-131 contains a long-terminal inverted repeat (L-TIR) of up to 1.5 Mbp at the chromosome end (9,496,435–7,999,105; 1,497,730 bp), resulting in a loop-like feature ( Figure 1 ). Two additional small linear contigs, 386.1 Kbp and 301.8 Kbp in size, along with the smallest circular contig at 50.5 Kbp, were identified as plasmids. In total, there were 8,986 protein-coding genes (CDSs) with the average open reading frame (ORF) length of 995 bp. Within the genome Streptomyces sp. BTA 1-131, 21 rRNA and 92 tRNA operons were also predicted ( Table 1 ). Figure 1. Streptomyces sp. BTA 1-131 assembly using Flye with high assembly depth. (A) Schematic representation of the Streptomyces sp. BTA 1-131 genome detected, adding up to 1.5 Mbp in length to chromosome size. In addition, a circular and two linear plasmids were detected from the strain BTA 1-131 assembly. (B) L-TIR is indicated with a reverse arrow (pink colour) from the end of chromosome (9,496,435–7,999,105; 1,497,324 bp). Table 1. Genomic features of Streptomyces sp. BTA 1-131, S. kunmingensis DSM 41681, and S. albus NRRL B-1811 T . BTA 1-131 DSM 41681 NRRL B-1811 T Genome topology a linear linear linear Contigs 4 379 104 Genome size (bp) 10,234,869 9,797,351 7,633,340 N50 9,496,435 57,076 245,715 GC content (%) 71.62 70.73 72.74 Protein coding genes (CDS) 8,986 8,633 6,405 rRNA genes 21 4 6 tRNA genes 92 83 81 Genes assigned to COG 87 78 36 a Chromosome, T Type strain. Table 2. Overview of data files/dataset generated in this study. Label Data Type of data Data file 1 Figshare: Quality distribution of the BTA1-131 reads from Illumina and ONT sequencing This data contains the raw data read quality score, GC content (%), and general statistics of the reads https://doi.org/10.6084/m9.figshare.24204633 Web report (HTML) Attribution: CC BY 4.0 Data file 2 Figshare: High-quality reads resulted from Illumina raw read filtering (Q > 20, length > 200) https://doi.org/10.6084/m9.figshare.24204720 Reads (FASTQ) Attribution: CC BY 4.0 Data file 3 Figshare: Draft assembly from ONT raw read This data contains fasta file, graph file, and assembly statistic. https://doi.org/10.6084/m9.figshare.30563048 Draft assembly (FASTA) Attribution: CC BY 4.0 Data file 4 Figshare: Topology hybrid assembly of Streptomyces sp. BTA 1-131 https://doi.org/10.6084/m9.figshare.30542942 Image (PNG) Attribution: CC BY 4.0 Data file 5 Figshare: Hybrid assembly statistic report https://doi.org/10.6084/m9.figshare.24204789 Report (ZIP) Attribution: CC BY 4.0 Data file 6 Figshare: Identification of BUSCO genes to assess genome completeness https://doi.org/10.6084/m9.figshare.24204855 Report (TXT) Attribution: CC BY 4.0 Data file 7 Figshare: Genome completeness and contamination assessment with CheckM https://doi.org/10.6084/m9.figshare.30563456 Report (TXT) Attribution: CC BY 4.0 Data file 8 Figshare: Genome visualisations including identified COGs https://doi.org/10.6084/m9.figshare.30564893 Report (PDF) Attribution: CC BY 4.0 Data file 9 Figshare: Identification for potential new species using TYGS https://doi.org/10.6084/m9.figshare.30563564 Report (PDF) Attribution: CC BY 4.0 Data set 1 NCBI GenBank: The nucleotide sequence of 16S rRNA gene of the strain BTA 1-131 NCBI accession number MT280129.1 https://www.ncbi.nlm.nih.gov/nuccore/MT280129 Contigs (FASTA) Data set 2 The cultivable isolate: The Indonesian Culture Collection BRIN (InaCC), accession number A1205 This data contains a deposition data sheet of the isolate BTA 1-131 in InaCC https://hdl.handle.net/20.500.12690/RIN/UKGE4I Report (PDF) Attribution: CC BY-NC-ND 4.0 Data set 3 Raw reads from Illumina and ONT sequencers This data contains raw reads deposited in the DNA Data Bank of Japan (DDBJ) and Indonesian national scientific repository (RIN Dataverse) DDBJ Bioproject: PRJDB16533 https://ddbj.nig.ac.jp/search/entry/bioproject/PRJDB16533 RIN Dataverse: https://hdl.handle.net/20.500.12690/RIN/UQP1WS GenBank collection (FASTQ) Furthermore, the general genome features of Streptomyces sp. BTA 1-131 are summarised in comparison to its closely related neighbour strain S. kunmingensis DSM 41681 and the type strain S. albus NRRL B-1811 in Table 1 , while the schematic of circular maps of the genome, including the annotated COG categories, is presented in Figure 2 . Figure 2. A circular map of each contig from the Streptomyces sp. BTA 1-131 assembly. Contig of L-TIR displayed together as one chromosome. Labelling from outside to the inside: contigs; COGs on the forward strand; CDS, rRNAs, and tRNAs on the forward strand; CDS, rRNAs, and tRNAs on the reverse strand; GC content; GC skew. Phylogenomic analysis As aforementioned, the strain BTA 1-131 was previously identified by sequencing the 16S rRNA gene and is closely related to S. kunmingensis NBRC 14463 with the sequence similarity of 98.4%. Indeed, the results of TYGS species identification suggested a potential novel Streptomyces species for the strain BTA 1-131, as indicated by the dDDH value below the threshold for classification as the same species as the nearest strain, S. kunmingensis DSM 41681 (<70%) ( Figure 3 ). Moreover, the ANI score between the BTA 1-131 genome assembly and S. kunmingensis DSM 41681 was 89.15%. Figure 3. Phylogenomic tree construct based on whole genome sequence data of Streptomyces sp. BTA 1-131 and other Streptomyces strains. Limitations The main limitation in this study is that although the phylogenomic analysis showed a possibility of the strain BTA 1-131 as a new Streptomyces species, a follow-up taxonomical confirmation through polyphasic study is necessary to establish its species status. Additional taxonomical investigations, including chemotaxonomic, morphological, and biochemical characterisation, would be required to definitively confirm the novelty of this strain and validate its classification within the genus Streptomyces. Ethical considerations Not applicable. Data availability The data generated from this study is available in Table 2 . The sequence read archives are deposited in Genbank: 16S rRNA (Accession no. MT280129.1), 40 Illumina and ONT reads (Bioproject PRJDB16533). 41 The raw reads are also accessible in the Indonesian national scientific repository (RIN Dataverse): https://hdl.handle.net/20.500.12690/RIN/UQP1WS . The cultivable isolate was deposited in the Indonesian Culture Collection BRIN (InaCC) under accession number InaCC A1205DNA and is accessible in RIN Dataverse: https://hdl.handle.net/20.500.12690/RIN/UKGE4I . 42 Acknowledgements The authors acknowledge BRIN’s High Performance Computing (HPC)–Mahameru for scientific computing services. 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Reference Source Comments on this article Comments (0) Version 3 VERSION 3 PUBLISHED 24 Nov 2025 ADD YOUR COMMENT Comment Author details Author details 1 Department of Biochemistry, IPB University, Bogor, West Java, Indonesia 2 Research Centre for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia 3 Indonesian Biofilm Research and Collaboration Centre, Yogyakarta, Yogyakarta, Indonesia 4 Laboratory of Microbiology, Wageningen University & Research, Wageningen, Gelderland, The Netherlands 5 Research Centre for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia 6 Research Centre for Freshwater, National Research and Innovation Agency (BRIN), Bogor, West Java, Indonesia Rahadian Pratama Roles: Data Curation, Formal Analysis, Investigation, Methodology, Resources, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Linda Sukmarini Roles: Conceptualization, Data Curation, Funding Acquisition, Investigation, Methodology, Project Administration, Resources, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Akhirta Atikana Roles: Data Curation, Investigation, Methodology, Project Administration, Resources, Validation, Writing – Review & Editing Shanti Ratnakomala Roles: Resources, Writing – Review & Editing Fahrurrozi Fahrurrozi Roles: Data Curation, Resources, Writing – Review & Editing Puspita Lisdiyanti Roles: Resources, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information Rumah Program Biodiversitas, ORHL-BRIN” (9/III/HK/2022 to LS) and “Rumah Program Artificial, Intelligence, Big Data & Teknologi Komputasi, OREI-BRIN (B-1409/III.6/PR.03.06/4/2023 to LS) and continuously financed by “Riset dan Inovasi untuk Indonesia Maju—Indonesia Endowment Funds for Education (LPDP) (37/II.7/HK/2023; B-3838/II.7.7/FR.06.00.112023 to LS) The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Article Versions (3) version 3 Revised Published: 24 Jan 2026, 14:1303 https://doi.org/10.12688/f1000research.173356.3 version 2 Revised Published: 16 Jan 2026, 14:1303 https://doi.org/10.12688/f1000research.173356.2 version 1 Published: 24 Nov 2025, 14:1303 https://doi.org/10.12688/f1000research.173356.1 Copyright © 2026 Pratama R et al . 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COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 2 VERSION 2 PUBLISHED 16 Jan 2026 Revised Views 0 Cite How to cite this report: Karahan A. Reviewer Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.195110.r450494 ) The direct URL for this report is: https://f1000research.com/articles/14-1303/v2#referee-response-450494 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 21 Jan 2026 Arzu Karahan , Middle East Technical University, Erdemli-Mersin, Turkey Approved VIEWS 0 https://doi.org/10.5256/f1000research.195110.r450494 I don't have further comment; ... Continue reading READ ALL I don't have further comment; this version can be accepted for publication. Competing Interests: No competing interests were disclosed. Reviewer Expertise: tunicates, aging, whole body regeneration, transcriptomics, metagenomics. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Karahan A. Reviewer Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.195110.r450494 ) The direct URL for this report is: https://f1000research.com/articles/14-1303/v2#referee-response-450494 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Version 1 VERSION 1 PUBLISHED 24 Nov 2025 Views 0 Cite How to cite this report: Detcharoen M. Reviewer Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.191165.r442272 ) The direct URL for this report is: https://f1000research.com/articles/14-1303/v1#referee-response-442272 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 12 Jan 2026 Matsapume Detcharoen , Prince of Songkla University, Songkhla, Thailand Approved VIEWS 0 https://doi.org/10.5256/f1000research.191165.r442272 This Genome Note reports a high-quality hybrid Illumina and Oxford Nanopore whole-genome assembly of Streptomyces sp. BTA 1-131, a sponge-associated strain isolated from the Indonesian marine sponge Melophlus sarasinorum. The genome is about 10 Mbp with an unusually long 1.5 ... Continue reading READ ALL This Genome Note reports a high-quality hybrid Illumina and Oxford Nanopore whole-genome assembly of Streptomyces sp. BTA 1-131, a sponge-associated strain isolated from the Indonesian marine sponge Melophlus sarasinorum. The genome is about 10 Mbp with an unusually long 1.5 Mbp terminal inverted repeat and plasmids. Define “ONT” at first use. Specify the end-prep chemistry and kits used prior to ONT library construction. Explain why barcodes were used, identify the barcode kit, and clarify whether multiplexing was performed. Report how many libraries were constructed, the number and type of flow cells used, and the duration of the sequencing run. Clearly describe ONT data quality control, including read filtering, trimming, and summary statistics such as read N50 and quality scores. The rationale for the estimated genome size used during Flye assembly should be explained. Given the unusually long 1.5 Mbp terminal inverted repeat (TIR), stronger validation is warranted, such as read-level support across TIR boundaries or additional assembly diagnostics, to confirm that this feature is not an assembly artifact. The manuscript inconsistently refers to the reference strain as “NRRL B-181” and “NRRL B-1811.” This must be corrected throughout. Although BUSCO and CheckM analyses were performed, BUSCO results are not clearly summarized in the main text. Data set 2 and 3 are not yet public. Clarify inconsistencies in Illumina read filtering thresholds between the Methods section and Table 2. Correct typographical errors, including the misspelling of Streptomyces kunmingensis in Table 1. Figure 3 requires a scale bar and an explanation of color coding. The manuscript does not clearly describe how the phylogenetic tree shown in Figure 3 was reconstructed. a brief summary of predicted secondary metabolite biosynthetic gene clusters would strengthen the manuscript Are the rationale for sequencing the genome and the species significance clearly described? Partly Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Genomics, molecular ecology I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Detcharoen M. Reviewer Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.191165.r442272 ) The direct URL for this report is: https://f1000research.com/articles/14-1303/v1#referee-response-442272 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 16 Jan 2026 Linda Sukmarini , Research Centre for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia 16 Jan 2026 Author Response Thank you Reviewer for the critical input to our manuscript. Below are our responds to the comments: We have updated the manuscript to the third version (v3), however, we are ... Continue reading Thank you Reviewer for the critical input to our manuscript. Below are our responds to the comments: We have updated the manuscript to the third version (v3), however, we are waiting for the second version (v2) to be published first. We have already submitted the v2 before receiving your comments. 1. We have updated manuscript (v3) to define "ONT" on first use 2. The End-prep chemistry have been added to the method section 3. The sequencing process of BTA1-131 with ONT platform was joined with other projects (multiplexing), therefore barcodes were used. The barcode kit already mentioned in the methods section (SQK-NBD114.24). 4. Only one library was generated. The flowcell used already mentioned in the methods section (FLO-MIN114). The sequencing run was executed for 72 hours 5. The summary statistics for ONT quality control have been revised in the manuscript. We did not perform filtering or trimming, since the Flye assembler need to use all data for the assembly. 6. Genome size estimation during assembly process was calculated from the average of Streptomyces spp. genome size. We believe that the high coverage number from the assembly result, support the finding of TIR region 7. We have updated the manuscript (v3) for "NRRL B-1811" consistently written 8. We have updated manuscript (v3) to include BUSCO result after CheckM result. 9. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. 10. We have updated the manuscript (v3) to correct the inconsistency for Illumina filtering thresold. 11. The scale bar revision have been submitted alongside v2 manuscript. The color coding was default to TYGS result, such as the species cluster, subspecies cluster, and other parameters which is described in the TYGS paper (doi.org/10.1038/s41467-019-10210-3). We do not receive detailed explanation from the TYGS results (Data File 9) 12. The construction of Phylogenetic tree is already mentioned in the methods section, under " Taxonomic inference and phylogenomic analysis ". This tree was part of the TYGS results, we just better visualized using iTOL (also described already) 13. As mentioned earlier in the introduction, this manuscript focuses on the finding of the complete genome of a sponge-associated Streptomyces strain from the marine sponge M. sarasinorum of Indonesian origin. We highlight the TIR feature and species delineation. The secondary metabolite analysis is already prepared in the follow up publication. Thank you Reviewer for the critical input to our manuscript. Below are our responds to the comments: We have updated the manuscript to the third version (v3), however, we are waiting for the second version (v2) to be published first. We have already submitted the v2 before receiving your comments. 1. We have updated manuscript (v3) to define "ONT" on first use 2. The End-prep chemistry have been added to the method section 3. The sequencing process of BTA1-131 with ONT platform was joined with other projects (multiplexing), therefore barcodes were used. The barcode kit already mentioned in the methods section (SQK-NBD114.24). 4. Only one library was generated. The flowcell used already mentioned in the methods section (FLO-MIN114). The sequencing run was executed for 72 hours 5. The summary statistics for ONT quality control have been revised in the manuscript. We did not perform filtering or trimming, since the Flye assembler need to use all data for the assembly. 6. Genome size estimation during assembly process was calculated from the average of Streptomyces spp. genome size. We believe that the high coverage number from the assembly result, support the finding of TIR region 7. We have updated the manuscript (v3) for "NRRL B-1811" consistently written 8. We have updated manuscript (v3) to include BUSCO result after CheckM result. 9. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. 10. We have updated the manuscript (v3) to correct the inconsistency for Illumina filtering thresold. 11. The scale bar revision have been submitted alongside v2 manuscript. The color coding was default to TYGS result, such as the species cluster, subspecies cluster, and other parameters which is described in the TYGS paper (doi.org/10.1038/s41467-019-10210-3). We do not receive detailed explanation from the TYGS results (Data File 9) 12. The construction of Phylogenetic tree is already mentioned in the methods section, under " Taxonomic inference and phylogenomic analysis ". This tree was part of the TYGS results, we just better visualized using iTOL (also described already) 13. As mentioned earlier in the introduction, this manuscript focuses on the finding of the complete genome of a sponge-associated Streptomyces strain from the marine sponge M. sarasinorum of Indonesian origin. We highlight the TIR feature and species delineation. The secondary metabolite analysis is already prepared in the follow up publication. Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 16 Jan 2026 Linda Sukmarini , Research Centre for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia 16 Jan 2026 Author Response Thank you Reviewer for the critical input to our manuscript. Below are our responds to the comments: We have updated the manuscript to the third version (v3), however, we are ... Continue reading Thank you Reviewer for the critical input to our manuscript. Below are our responds to the comments: We have updated the manuscript to the third version (v3), however, we are waiting for the second version (v2) to be published first. We have already submitted the v2 before receiving your comments. 1. We have updated manuscript (v3) to define "ONT" on first use 2. The End-prep chemistry have been added to the method section 3. The sequencing process of BTA1-131 with ONT platform was joined with other projects (multiplexing), therefore barcodes were used. The barcode kit already mentioned in the methods section (SQK-NBD114.24). 4. Only one library was generated. The flowcell used already mentioned in the methods section (FLO-MIN114). The sequencing run was executed for 72 hours 5. The summary statistics for ONT quality control have been revised in the manuscript. We did not perform filtering or trimming, since the Flye assembler need to use all data for the assembly. 6. Genome size estimation during assembly process was calculated from the average of Streptomyces spp. genome size. We believe that the high coverage number from the assembly result, support the finding of TIR region 7. We have updated the manuscript (v3) for "NRRL B-1811" consistently written 8. We have updated manuscript (v3) to include BUSCO result after CheckM result. 9. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. 10. We have updated the manuscript (v3) to correct the inconsistency for Illumina filtering thresold. 11. The scale bar revision have been submitted alongside v2 manuscript. The color coding was default to TYGS result, such as the species cluster, subspecies cluster, and other parameters which is described in the TYGS paper (doi.org/10.1038/s41467-019-10210-3). We do not receive detailed explanation from the TYGS results (Data File 9) 12. The construction of Phylogenetic tree is already mentioned in the methods section, under " Taxonomic inference and phylogenomic analysis ". This tree was part of the TYGS results, we just better visualized using iTOL (also described already) 13. As mentioned earlier in the introduction, this manuscript focuses on the finding of the complete genome of a sponge-associated Streptomyces strain from the marine sponge M. sarasinorum of Indonesian origin. We highlight the TIR feature and species delineation. The secondary metabolite analysis is already prepared in the follow up publication. Thank you Reviewer for the critical input to our manuscript. Below are our responds to the comments: We have updated the manuscript to the third version (v3), however, we are waiting for the second version (v2) to be published first. We have already submitted the v2 before receiving your comments. 1. We have updated manuscript (v3) to define "ONT" on first use 2. The End-prep chemistry have been added to the method section 3. The sequencing process of BTA1-131 with ONT platform was joined with other projects (multiplexing), therefore barcodes were used. The barcode kit already mentioned in the methods section (SQK-NBD114.24). 4. Only one library was generated. The flowcell used already mentioned in the methods section (FLO-MIN114). The sequencing run was executed for 72 hours 5. The summary statistics for ONT quality control have been revised in the manuscript. We did not perform filtering or trimming, since the Flye assembler need to use all data for the assembly. 6. Genome size estimation during assembly process was calculated from the average of Streptomyces spp. genome size. We believe that the high coverage number from the assembly result, support the finding of TIR region 7. We have updated the manuscript (v3) for "NRRL B-1811" consistently written 8. We have updated manuscript (v3) to include BUSCO result after CheckM result. 9. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. 10. We have updated the manuscript (v3) to correct the inconsistency for Illumina filtering thresold. 11. The scale bar revision have been submitted alongside v2 manuscript. The color coding was default to TYGS result, such as the species cluster, subspecies cluster, and other parameters which is described in the TYGS paper (doi.org/10.1038/s41467-019-10210-3). We do not receive detailed explanation from the TYGS results (Data File 9) 12. The construction of Phylogenetic tree is already mentioned in the methods section, under " Taxonomic inference and phylogenomic analysis ". This tree was part of the TYGS results, we just better visualized using iTOL (also described already) 13. As mentioned earlier in the introduction, this manuscript focuses on the finding of the complete genome of a sponge-associated Streptomyces strain from the marine sponge M. sarasinorum of Indonesian origin. We highlight the TIR feature and species delineation. The secondary metabolite analysis is already prepared in the follow up publication. Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Karahan A. Reviewer Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.191165.r436015 ) The direct URL for this report is: https://f1000research.com/articles/14-1303/v1#referee-response-436015 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 27 Dec 2025 Arzu Karahan , Middle East Technical University, Erdemli-Mersin, Turkey Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.191165.r436015 In the article, Streptomyces sp. BTA 1-131, isolated from the rare marine sponge Melophlus sarasinorum, is sequenced using a hybrid Illumina-Nanopore approach, resulting in a high-quality genome assembly. Based on the phylogenomic analyses, the strain is suggested to represent a ... Continue reading READ ALL In the article, Streptomyces sp. BTA 1-131, isolated from the rare marine sponge Melophlus sarasinorum, is sequenced using a hybrid Illumina-Nanopore approach, resulting in a high-quality genome assembly. Based on the phylogenomic analyses, the strain is suggested to represent a new species. Overall, this is a well-prepared manuscript; however, a few issues need to be addressed: - The scale bar in Figure 3 is missing. - Datasets 2 and 3 require a password for access, preventing verification of the associated data. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly Competing Interests: No competing interests were disclosed. Reviewer Expertise: tunicates, aging, whole body regeneration, transcriptomics, metagenomics. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Karahan A. Reviewer Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.191165.r436015 ) The direct URL for this report is: https://f1000research.com/articles/14-1303/v1#referee-response-436015 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 20 Jan 2026 Linda Sukmarini , Research Centre for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia 20 Jan 2026 Author Response Thank you reviewer for your kind report. To answer your questions: 1. We have revised the phylogenetic tree figure to include the tree scale. The figure will be included ... Continue reading Thank you reviewer for your kind report. To answer your questions: 1. We have revised the phylogenetic tree figure to include the tree scale. The figure will be included in the second version of article 2. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. Thank you reviewer for your kind report. To answer your questions: 1. We have revised the phylogenetic tree figure to include the tree scale. The figure will be included in the second version of article 2. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 20 Jan 2026 Linda Sukmarini , Research Centre for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia 20 Jan 2026 Author Response Thank you reviewer for your kind report. To answer your questions: 1. We have revised the phylogenetic tree figure to include the tree scale. The figure will be included ... Continue reading Thank you reviewer for your kind report. To answer your questions: 1. We have revised the phylogenetic tree figure to include the tree scale. The figure will be included in the second version of article 2. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. Thank you reviewer for your kind report. To answer your questions: 1. We have revised the phylogenetic tree figure to include the tree scale. The figure will be included in the second version of article 2. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Comments on this article Comments (0) Version 3 VERSION 3 PUBLISHED 24 Nov 2025 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 2 Version 3 (revision) 24 Jan 26 Version 2 (revision) 16 Jan 26 read Version 1 24 Nov 25 read read Arzu Karahan , Middle East Technical University, Erdemli-Mersin, Turkey Matsapume Detcharoen , Prince of Songkla University, Songkhla, Thailand Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2026 Karahan A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 21 Jan 2026 | for Version 2 Arzu Karahan , Middle East Technical University, Erdemli-Mersin, Turkey 0 Views copyright © 2026 Karahan A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions I don't have further comment; this version can be accepted for publication. Competing Interests No competing interests were disclosed. Reviewer Expertise tunicates, aging, whole body regeneration, transcriptomics, metagenomics. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (0) Karahan A. Peer Review Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.195110.r450494) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/14-1303/v2#referee-response-450494 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2026 Detcharoen M. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 12 Jan 2026 | for Version 1 Matsapume Detcharoen , Prince of Songkla University, Songkhla, Thailand 0 Views copyright © 2026 Detcharoen M. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions This Genome Note reports a high-quality hybrid Illumina and Oxford Nanopore whole-genome assembly of Streptomyces sp. BTA 1-131, a sponge-associated strain isolated from the Indonesian marine sponge Melophlus sarasinorum. The genome is about 10 Mbp with an unusually long 1.5 Mbp terminal inverted repeat and plasmids. Define “ONT” at first use. Specify the end-prep chemistry and kits used prior to ONT library construction. Explain why barcodes were used, identify the barcode kit, and clarify whether multiplexing was performed. Report how many libraries were constructed, the number and type of flow cells used, and the duration of the sequencing run. Clearly describe ONT data quality control, including read filtering, trimming, and summary statistics such as read N50 and quality scores. The rationale for the estimated genome size used during Flye assembly should be explained. Given the unusually long 1.5 Mbp terminal inverted repeat (TIR), stronger validation is warranted, such as read-level support across TIR boundaries or additional assembly diagnostics, to confirm that this feature is not an assembly artifact. The manuscript inconsistently refers to the reference strain as “NRRL B-181” and “NRRL B-1811.” This must be corrected throughout. Although BUSCO and CheckM analyses were performed, BUSCO results are not clearly summarized in the main text. Data set 2 and 3 are not yet public. Clarify inconsistencies in Illumina read filtering thresholds between the Methods section and Table 2. Correct typographical errors, including the misspelling of Streptomyces kunmingensis in Table 1. Figure 3 requires a scale bar and an explanation of color coding. The manuscript does not clearly describe how the phylogenetic tree shown in Figure 3 was reconstructed. a brief summary of predicted secondary metabolite biosynthetic gene clusters would strengthen the manuscript Are the rationale for sequencing the genome and the species significance clearly described? Partly Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Genomics, molecular ecology I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (1) Author Response 16 Jan 2026 Linda Sukmarini, Research Centre for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia Thank you Reviewer for the critical input to our manuscript. Below are our responds to the comments: We have updated the manuscript to the third version (v3), however, we are waiting for the second version (v2) to be published first. We have already submitted the v2 before receiving your comments. 1. We have updated manuscript (v3) to define "ONT" on first use 2. The End-prep chemistry have been added to the method section 3. The sequencing process of BTA1-131 with ONT platform was joined with other projects (multiplexing), therefore barcodes were used. The barcode kit already mentioned in the methods section (SQK-NBD114.24). 4. Only one library was generated. The flowcell used already mentioned in the methods section (FLO-MIN114). The sequencing run was executed for 72 hours 5. The summary statistics for ONT quality control have been revised in the manuscript. We did not perform filtering or trimming, since the Flye assembler need to use all data for the assembly. 6. Genome size estimation during assembly process was calculated from the average of Streptomyces spp. genome size. We believe that the high coverage number from the assembly result, support the finding of TIR region 7. We have updated the manuscript (v3) for "NRRL B-1811" consistently written 8. We have updated manuscript (v3) to include BUSCO result after CheckM result. 9. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. 10. We have updated the manuscript (v3) to correct the inconsistency for Illumina filtering thresold. 11. The scale bar revision have been submitted alongside v2 manuscript. The color coding was default to TYGS result, such as the species cluster, subspecies cluster, and other parameters which is described in the TYGS paper (doi.org/10.1038/s41467-019-10210-3). We do not receive detailed explanation from the TYGS results (Data File 9) 12. The construction of Phylogenetic tree is already mentioned in the methods section, under " Taxonomic inference and phylogenomic analysis ". This tree was part of the TYGS results, we just better visualized using iTOL (also described already) 13. As mentioned earlier in the introduction, this manuscript focuses on the finding of the complete genome of a sponge-associated Streptomyces strain from the marine sponge M. sarasinorum of Indonesian origin. We highlight the TIR feature and species delineation. The secondary metabolite analysis is already prepared in the follow up publication. View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Detcharoen M. Peer Review Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.191165.r442272) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/14-1303/v1#referee-response-442272 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Karahan A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 27 Dec 2025 | for Version 1 Arzu Karahan , Middle East Technical University, Erdemli-Mersin, Turkey 0 Views copyright © 2025 Karahan A. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Approved With Reservations info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions In the article, Streptomyces sp. BTA 1-131, isolated from the rare marine sponge Melophlus sarasinorum, is sequenced using a hybrid Illumina-Nanopore approach, resulting in a high-quality genome assembly. Based on the phylogenomic analyses, the strain is suggested to represent a new species. Overall, this is a well-prepared manuscript; however, a few issues need to be addressed: - The scale bar in Figure 3 is missing. - Datasets 2 and 3 require a password for access, preventing verification of the associated data. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Partly Competing Interests No competing interests were disclosed. Reviewer Expertise tunicates, aging, whole body regeneration, transcriptomics, metagenomics. I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. reply Respond to this report Responses (1) Author Response 20 Jan 2026 Linda Sukmarini, Research Centre for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia Thank you reviewer for your kind report. To answer your questions: 1. We have revised the phylogenetic tree figure to include the tree scale. The figure will be included in the second version of article 2. For access to the dataset 2 and 3 of RIN Dataverse, the project has been published, however access to the raw data is available by request. For dataset 3, access to the DDBJ bioproject PRJDB16533 will be released after manuscript been published. The same data are mirrored in the RIN Dataverse (dataset 3) and available upon request in the system. View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Karahan A. Peer Review Report For: The first whole-genome sequence of a prospective novel sponge-associated Streptomyces strain from Indonesia with a long 1.5 Mbp terminal inverted repeat [version 3; peer review: 2 approved] . F1000Research 2026, 14 :1303 ( https://doi.org/10.5256/f1000research.191165.r436015) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/14-1303/v1#referee-response-436015 Alongside their report, reviewers assign a status to the article: Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. 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