Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies

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Siregar" } ], "publisher": { "@type": "Organization", "name": "F1000Research", "logo": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 480, "width": 60 } }, "image": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 1200, "width": 150 }, "description": " Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) belongs to the Magnoliids group and is mainly distributed in Indonesia and Southeast Asia. The complete chloroplast (cp) genome of C. burmanni sampled from Indonesia was assembled and annotated for the first time in this study. The length of the cp genome is 152,765 bp with a GC content of 39%, and it consists of four subregions: a large single-copy (LSC) region of 93,636 bp, a small single-copy (SSC) region of 18,893 bp and two inverted repeats (IR) regions (IRA 20,121 bp; IRB 20,115 bp) . The cp genome of C. burmanni encodes a total of 173 unique genes, which are 96 protein-coding genes, 19 rRNA genes, and 68 tRNA genes that can be utilized for advanced genetic and genomic studies of the species." } { "@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/13-127/v3", "name": "Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni..." } } ] } Home Browse Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Salindeho RA, Dwiyanti FG, Pratama R et al. Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.12688/f1000research.145790.3 ) 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 Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] Richard Andreas Salindeho https://orcid.org/0000-0003-3897-4671 1 , Fifi Gus Dwiyanti https://orcid.org/0000-0003-0366-3259 1,2 , Rahadian Pratama https://orcid.org/0000-0002-2709-7370 2,3 , Deden Derajat Matra 2,4 , Muhammad Majiidu https://orcid.org/0000-0002-1996-6580 2 , Iskandar Z. Siregar https://orcid.org/0000-0003-0278-5887 1,2 Richard Andreas Salindeho https://orcid.org/0000-0003-3897-4671 1 , Fifi Gus Dwiyanti https://orcid.org/0000-0003-0366-3259 1,2 , [...] Rahadian Pratama https://orcid.org/0000-0002-2709-7370 2,3 , Deden Derajat Matra 2,4 , Muhammad Majiidu https://orcid.org/0000-0002-1996-6580 2 , Iskandar Z. Siregar https://orcid.org/0000-0003-0278-5887 1,2 PUBLISHED 16 Dec 2025 Author details Author details 1 Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, West Java, 16680, Indonesia 2 Molecular Science Research Group, Advanced Research Laboratory, IPB University, Bogor, West Java, 16680, Indonesia 3 Department of Biochemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, West Java, 16680, Indonesia 4 Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, West Java, 16680, Indonesia Richard Andreas Salindeho Roles: Data Curation, Formal Analysis, Investigation, Visualization, Writing – Original Draft Preparation Fifi Gus Dwiyanti Roles: Project Administration, Resources, Validation, Writing – Review & Editing Rahadian Pratama Roles: Data Curation, Methodology, Validation, Writing – Review & Editing Deden Derajat Matra Roles: Methodology, Validation, Writing – Review & Editing Muhammad Majiidu Roles: Data Curation, Methodology Iskandar Z. Siregar Roles: Conceptualization, Funding Acquisition, Supervision, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Nanopore Analysis gateway. This article is included in the Genomics and Genetics gateway. Abstract Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) belongs to the Magnoliids group and is mainly distributed in Indonesia and Southeast Asia. The complete chloroplast (cp) genome of C. burmanni sampled from Indonesia was assembled and annotated for the first time in this study. The length of the cp genome is 152,765 bp with a GC content of 39%, and it consists of four subregions: a large single-copy (LSC) region of 93,636 bp, a small single-copy (SSC) region of 18,893 bp and two inverted repeats (IR) regions (IRA 20,121 bp; IRB 20,115 bp) . The cp genome of C. burmanni encodes a total of 173 unique genes, which are 96 protein-coding genes, 19 rRNA genes, and 68 tRNA genes that can be utilized for advanced genetic and genomic studies of the species. READ ALL READ LESS Keywords Conservation, complete chloroplast genome, Lauraceae, phylogenetic Corresponding Author(s) Iskandar Z. Siregar ( [email protected] ) Close Corresponding author: Iskandar Z. Siregar Competing interests: No competing interests were disclosed. Grant information: This research was funded by the National Competitive Basic Research 2022-2023 Scheme No: 001/E5/PG.02.00PT/2022 and 001/E5/PG.02.00.PL/2023 awarded by the Ministry of Education, Culture, Research and Technology of the Republic of Indonesia entitled “Pilot Sequencing of 100 Native Forest Tree Genomes to Support Ecosystem Restoration (Rintisan Sekuensing 100 Genom Pohon Hutan Asli untuk Mendukung Restorasi Ekosistem)” granted to the corresponding author. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2025 Salindeho RA 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: Salindeho RA, Dwiyanti FG, Pratama R et al. Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.12688/f1000research.145790.3 ) First published: 20 Feb 2024, 13 :127 ( https://doi.org/10.12688/f1000research.145790.1 ) Latest published: 16 Dec 2025, 13 :127 ( https://doi.org/10.12688/f1000research.145790.3 ) Revised Amendments from Version 2 We updated the Introduction and Result sections according to reviewers suggestion. We updated the Introduction and Result sections according to reviewers suggestion. See the authors' detailed response to the review by Jakub Sawicki See the authors' detailed response to the review by Hoang Dang Khoa Do READ REVIEWER RESPONSES Introduction Cinnamomum burmanni (or cinnamon) is an endemic woody shrub belonging to the Lauraceae family, which is widely distributed in Indonesia, covering West Sumatra, North Sumatra, Jambi, Bengkulu, Java Island, and Maluku Islands ( Suwarto et al. , 2014 ). The species grows in altitudes between 0 and 2000 m above sea level. The tree can grow up to 15 m tall, and the wood is grey with a very distinctive aroma and sweet taste, so its wood is widely used for spices, cosmetics, and herbs. The active compounds contained in cinnamon wood are cinnamaldehyde, flavonoids, alkaloids, tannins, saponins, coumarins, steroids, eugenol, and phenols, which act as anti-bacterial, anti-tumor, antioxidant, anti-inflammatory, anti-cancer, and anti-diabetic agents ( Indarto et al. , 2022 ). The chloroplast (cp) genome sequence of C. burmanni from China was previously elucidated by Yang et al. (2019) utilizing 11 universal primer pairs for long-range PCR in next-generation sequencing. However, their study provided only a phylogenetic tree, and the corresponding sequence data and cp genome map are not readily accessible ( https://lcgdb.wordpress.com ). In the present study, we present genomic resources for C. burmanni from Indonesia, generated through the long-read sequencing method utilizing MinION technology from Oxford Nanopore Technologies. This study includes a comprehensive list of genes within the chloroplast genome of C. burmanni , which was not included in the previous study. Such information is of considerable significance as a foundation for further genetic investigations. Additionaly, the study of the cp genome C. burmanni from Indonesia using PCR-free library preparation method and long-read sequencing generated by MinION Oxford Nanopore Technologies (ONT) has not been carried out, whereas this information is needed to improve correct species identification and to optimize the sustainable use of genetic resources for this species. MinION is a third-generation sequencing technology with nanopore technology ( Oxford Nanopore Technologies (ONT), 2017 ). Furthermore, the present study aimed to re-sequence and assemble the complete cp genome C. burmanni from Indonesia using MinION Oxford Nanopore Technologies (ONT). Methods Fresh leaf samples were collected from one individual C. burmanni tree in Lembang Subdistrict, West Bandung Regency, West Java Province, Indonesia. The collected leaf sample was subsequently used for DNA extraction and sequencing in the field. The data analysis of the chloroplast genome was performed at the Laboratory of Forest Genetics and Molecular Forestry, Department of Silviculture, Faculty of Forestry and Environment, IPB University. C. burmanni genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit (cat. nos. 69104 and 69106) following the manufacturer’s protocol with slight modifications. Extraction was first done by grinding fresh leaf samples to which 400 μl of Buffer AP1 and 1 μl of mercaptoethanol had been added using a mortar and pestle. The disrupted sample was placed into a 1.5 ml microcentrifuge tube. The mixture was then incubated for 10 min at 65°C using Mini Heating Dry Bath Incubator MD-MINI (Major Science Co., Ltd). Afterward, 130 μl Buffer P3 was added into the microtube and then vortexed using Biosan V-32 Multi-Vortex and incubated for 5 min on ice. The mixture was centrifuged for 2 min at 8000 × g using a portable microcentrifuge on the Bento Lab device (Bento Bioworks Ltd). The lysate was pipetted into a QIAshredder spin column placed in a 2 ml collection tube. The lysate was centrifuged for 2 min at 8000 × g using a portable microcentrifuge on the Bento Lab device (Bento Bioworks Ltd). The flow-through was transferred into a new tube without disturbing the DNA pellet. 1.5 volumes of Buffer AW1 were then added and mixed by pipetting. 650 μl of the mixture was transferred into a DNeasy Mini spin column placed in a 2 ml collection tube and subsequently centrifuged for 1 min at 6000 × g. The flow-through was discarded, and the spin column was placed into a new 2 ml collection tube. 500 μl Buffer AW2 was added to the spin column and centrifuged for 1 min at 6000 × g. The flow-through was then discarded and the spin column was transferred to a new 1.5 ml microcentrifuge tube. 50 μl Buffer AE was added for elution and subsequently incubated for 5 min at room temperature (15–25°C) before centrifuging for 1 min at 6000 × g. The quantity of genomic DNA was measured by the Invitrogen Qubit 1.0 fluorometer with the Qubit dsDNA BR assay kit. The high molecular weight of 400 ng evaluated DNA proceeded to PCR-free library preparation, which followed the Nanopore protocol for Rapid sequencing gDNA – Field Sequencing Kit (SQK-LRK 001) version FSK_9049_v1_revR_14Aug2019. The prepared DNA library was sequenced using the MinION R9.4.1 flow cell (FLO-MIN106D) on a MinION Mk1B sequencer (Oxford Nanopore Technologies). The runs were visualized by MinKnow v3.6.5 software ( http://community.nanoporetech.com Oxford Nanopore Technologies). Basecalling with super accuracy mode (SUP) to translate Fast5 raw data into Fastq (DNA-Seq of Cinnamomum burmanni. NCBI Accession number SRX22198906) data was performed using the Guppy program (RRID:SCR_023196) v4.2.3+8aca2af8 ( Wick et al. , 2019 ). Quality control was done using NanoStat v1.5.0 and NanoPlot (RRID:SCR_024128) v1.28.2 ( De Coster et al. , 2018 ). Chloroplast genome assembly was performed using Galaxy Server (RRID:SCR_006281) version 23.1.1.dev0 ( Sloggett et al. , 2013 ). The assembly includes a filtering step to filter reads quality (Q>7) and length minimum of reads (>500 bp), using the Flye program (RRID:SCR_017016) v2.9 ( Kolmogorov et al. , 2020 ) and polishing the assembly results using the MEDAKA consensus program (RRID:SCR_005857) v1.4.4 ( Oosterbroek et al. , 2021 ). The cpDNA data was then annotated using the GeSeq (RRID:SCR_017336) on the CHLOROBOX platform ( Tillich et al. , 2017 ) to assign functions to the predicted genes and generate a map representation of the chloroplast genome. Results The sequencing resulted in a total of 59,589 reads, total bases of 140,909,220 bp, and read length N50 4,377 bp. The assembly resulted in 288 contigs, contig_246 annotated as cp genome with coverage of 37x. The cp genome showed a typical quadripartite structure ( Figure 1 ) with a length of 152,765 bp, consisting of small single copy (SSC 18,893 bp) and large single copy (LSC 93,636 bp) regions separated by a pair of inverted repeat A (IRA 20,121 bp) and inverted repeat B (IRB 20,115 bp) regions ( Figure 1 ). The C. burmanni chloroplast genome contained 173 unique genes, including 96 coding sequences, 68 transfer RNA (tRNA), and 19 ribosomal RNA (rRNA) genes ( Table 1 ). The C. burmanni sequence had a GC content of 39% (LSC 38%; SSC 34%; IR 44%) and a coverage depth 37x. The results of the typical quadripartite structure were similar to the C. burmanni reported by Yang et al. (2019) . The chloroplast genome assembly of C. burmanni has 10 bp less (152,765 bp) than previously reported by Yang et al. (2019) (152,775 bp). However, the general GC ratio of each region is comparable at 38% (LSC), 34% (SSC), and 44% (IR). Figure 1. The complete chloroplast genome of Cinnamomum burmanni . Genes shown inside and outside the circle are transcribed clockwise and counterclockwise, respectively. Annotated genes are colored according to the functional categories. Table 1. List of genes in the chloroplast genome of Cinnamomum burmanni. Functional category Group of genes Name of genes Self-replication Large subunit ribosomal proteins rpl32, rpl33, rpl20, rpl36, rpl14, rpl16 * (×2) , rpl22, rpl2 * (×2) , rpl23 DNA dependent RNA polymerase rpoC2, rpoC1 * (×2) , rpoB, rpoA Small subunit ribosomal proteins rps7, rps12 ** (×2) , rps15, rps7, rps16 * (×2) , rps2, rps14, rps4, rps18, rps11, rps8, rps3, rps19, rps12- fragment * rRNAs rrn16, rrn23, rrn5, rrn4.5 tRNAs trnL-CAA, trnV-GAC, trnE-UUC, trnA-UGC * (×2) , trnN-GUU, trnL-UAG, trnN-GUU, trnR-ACG, trnR-ACG, trnI-GAU * (×2) , trnV-GAC, trnL-CAA, trnH-GUG, trnK-UUU * (×2) , trnQ-UUG, trnG-UCC * (×2) , trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnT-GGU, trnS-UGA, trnG-GCC, trnM-CAU, trnfM-CAU, trnS-GGA, trnT-UGU, trnL-UAA * (×2) , trnF-GAA, trnV-UAC * (×2) , trnW-CCA, trnP-UGG, trnI-CAU, trnS-GCU Subunit of ATP synthase atpA, atpF * (×2) , atpH, atpI, atpE, atpB Subunit of NADH-dehydrogenase ndhB * (×2) , ndhH, ndhA * (×2) , ndhI, ndhG, ndhE, ndhD, ndhF, ndhJ, ndhK, ndhC Photosynthesis Subunits of cytochrome b/f complex petN, petA, petL, petG, petB * (×2) , petD * (×2) Subunits of photosystem I psaC, psaB, psaA, psaI, psaJ Subunits of photosystem II psbK, psbI, psbM, psbD, psbC, psbZ, psbJ, psbL, psbF, psbE, psbB, psbT, psbH, psbA Subunit rubisco rbcL Photosystem assembly factors pafI ** (×2) , pafII Photosystem biogenesis factor Pbf1 Subunit of acetyl-CoA-carboxylase accD C-type cytochrome synthesis gene ccsA Other functions Envelope membrane protein cemA ATP-dependent protease subunit P clpP1 ** (×2) Maturase matK Conserved open reading frames ycf1 (×2), ycf2 (×2) Transitional initiation factor infA * Gene containing single intron. ** Gene containing two introns. Data availability Underlying data NCBI’s Short Read Archive (SRA): DNA-Seq of Cinnamomum burmanni. Accession number SRX22198906; https://www.ncbi.nlm.nih.gov/sra/SRX22198906 ( IPB University, 2023 ). Acknowledgements The authors thank Mrs. Siska Nurfajri and Ms. Nabila Salsabila Salmah, the alumni of the Department of Silviculture, Faculty of Forestry and Environment, IPB University, for their valuable assistance in DNA extraction. References De Coster W, D’Hert S, Schultz DT, et al. : NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 2018; 34 (15): 2666–2669. PubMed Abstract | Publisher Full Text | Free Full Text Indarto, Isnanto T, Muyassaroh F, et al. : Efektivitas Kombinasi Ekstrak Kayu Manis ( Cinnamomum burmanni ) dan Mikroalga ( Haematococcus pluvialis ) sebagai Krim Tabir Surya: Formulasi, Uji In Vitro, dan In Vivo. Jurnal Kefarmasian Indonesia. 2022; 12 (1): 11–24. Publisher Full Text IPB University: DNA-Seq of Cinnamomum burmanni. Sequence Read Archive by NCBI. 2023. Reference Source Kolmogorov M, Bickhart DM, Behsaz B, et al. : metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods. 2020; 17 (11): 1103–1110. PubMed Abstract | Publisher Full Text | Free Full Text Oosterbroek S, Doorenspleet K, Nijland R, et al. : Decona: From demultiplexing to consensus for Nanopore amplicon data. ARPHA Conf. Abstr. 2021; 4 : e65029. Publisher Full Text Oxford Nanopore Technologies (ONT): Nanopore sequencing the advantages of long reads for genome assembly.2017. Reference Source Sloggett C, Goonasekera N, Afgan E: BioBlend: automating pipeline analyses within Galaxy and CloudMan. Bioinformatics. 2013; 29 (13): 1685–1686. PubMed Abstract | Publisher Full Text | Free Full Text Suwarto, Octavianty Y, Hermawati S: Top 15 tanaman perkebunan.2014. Reference Source Tillich M, Lehwark P, Pellizzer T, et al. : GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017; 45 (W1): W6–W11. PubMed Abstract | Publisher Full Text | Free Full Text Wick RR, Judd LM, Holt KE: Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol. 2019; 20 (1): 129. PubMed Abstract | Publisher Full Text | Free Full Text Yang Y, Song Y, Xin P: The chloroplast genome of aromatic plants Cinnamomum burmanni (Lauraceae). Mitochondrial DNA B Resour. 2019; 4 (2): 3616–3617. PubMed Abstract | Publisher Full Text | Free Full Text Comments on this article Comments (0) Version 3 VERSION 3 PUBLISHED 20 Feb 2024 ADD YOUR COMMENT Comment Author details Author details 1 Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, West Java, 16680, Indonesia 2 Molecular Science Research Group, Advanced Research Laboratory, IPB University, Bogor, West Java, 16680, Indonesia 3 Department of Biochemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, West Java, 16680, Indonesia 4 Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor, West Java, 16680, Indonesia Richard Andreas Salindeho Roles: Data Curation, Formal Analysis, Investigation, Visualization, Writing – Original Draft Preparation Fifi Gus Dwiyanti Roles: Project Administration, Resources, Validation, Writing – Review & Editing Rahadian Pratama Roles: Data Curation, Methodology, Validation, Writing – Review & Editing Deden Derajat Matra Roles: Methodology, Validation, Writing – Review & Editing Muhammad Majiidu Roles: Data Curation, Methodology Iskandar Z. Siregar Roles: Conceptualization, Funding Acquisition, Supervision, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information This research was funded by the National Competitive Basic Research 2022-2023 Scheme No: 001/E5/PG.02.00PT/2022 and 001/E5/PG.02.00.PL/2023 awarded by the Ministry of Education, Culture, Research and Technology of the Republic of Indonesia entitled “Pilot Sequencing of 100 Native Forest Tree Genomes to Support Ecosystem Restoration (Rintisan Sekuensing 100 Genom Pohon Hutan Asli untuk Mendukung Restorasi Ekosistem)” granted to the corresponding author. 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: 16 Dec 2025, 13:127 https://doi.org/10.12688/f1000research.145790.3 version 2 Revised Published: 21 May 2024, 13:127 https://doi.org/10.12688/f1000research.145790.2 version 1 Published: 20 Feb 2024, 13:127 https://doi.org/10.12688/f1000research.145790.1 Copyright © 2025 Salindeho RA 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. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Salindeho RA, Dwiyanti FG, Pratama R et al. Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.12688/f1000research.145790.3 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. 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 3 VERSION 3 PUBLISHED 16 Dec 2025 Revised Views 0 Cite How to cite this report: Quang MT. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441776 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v3#referee-response-441776 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 Minh Trong Quang , University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam Approved VIEWS 0 https://doi.org/10.5256/f1000research.193459.r441776 I have carefully reviewed the revised version of the manuscript as well as the authors’ responses to previous reviewer comments. The authors have addressed the major technical and presentation-related concerns raised during earlier review rounds, including improvements to the Introduction, ... Continue reading READ ALL I have carefully reviewed the revised version of the manuscript as well as the authors’ responses to previous reviewer comments. The authors have addressed the major technical and presentation-related concerns raised during earlier review rounds, including improvements to the Introduction, clarification of the sequencing and assembly workflow, correction of inconsistencies between Figure 1 and Table 1, and clearer reporting of chloroplast genome structure and gene content. The methodological description is now more focused, and the Results section more clearly reports key assembly statistics and genome features. While some limitations inherent to a Genome Note remain (e.g., limited comparative and evolutionary interpretation), these are now appropriately aligned with the scope and aims of the article. Overall, the revised manuscript represents a technically sound and useful genomic resource that adds geographic representation for Cinnamomum burmanni plastomes and should be of value to researchers working in plant genomics and chloroplast genome studies. I therefore have no further major comments to make on this revised version. Competing Interests: No competing interests were disclosed. Reviewer Expertise: Bioinformatics, Genetics, Biotechnology 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 Quang MT. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441776 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v3#referee-response-441776 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 Views 0 Cite How to cite this report: Sawicki J. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441775 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v3#referee-response-441775 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 10 Jan 2026 Jakub Sawicki , Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland Approved VIEWS 0 https://doi.org/10.5256/f1000research.193459.r441775 The authors resolved all ... Continue reading READ ALL The authors resolved all raised issues. I recommend acceptance. Competing Interests: No competing interests were disclosed. 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 Sawicki J. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441775 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v3#referee-response-441775 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 Views 0 Cite How to cite this report: Bashir NH. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441778 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v3#referee-response-441778 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 31 Dec 2025 Nawaz Haider Bashir , Qujing Normal University, Qujing, Yunnan, China Approved VIEWS 0 https://doi.org/10.5256/f1000research.193459.r441778 The authors have incorporated the ... Continue reading READ ALL The authors have incorporated the necessary changes in the revised version. Competing Interests: No competing interests were disclosed. Reviewer Expertise: Entomologist, Evolutionary Biology 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 Bashir NH. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441778 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v3#referee-response-441778 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 Views 0 Cite How to cite this report: Do HDK. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441779 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v3#referee-response-441779 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 16 Dec 2025 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.193459.r441779 Dear Authors, Thank you very much for revising the manuscript. However, many issues were not addressed, and the ... Continue reading READ ALL Dear Authors, Thank you very much for revising the manuscript. However, many issues were not addressed, and the text was the same as previous version without clear explanation. Therefore, I am not confident for further reviewing this manuscript. Best regards. Competing Interests: No competing interests were disclosed. Reviewer Expertise: Genomics, Chloroplast genome evolution, Phylogeny I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Do HDK. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441779 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v3#referee-response-441779 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 2 VERSION 2 PUBLISHED 21 May 2024 Revised Views 0 Cite How to cite this report: WU Z. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r424130 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-424130 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 20 Nov 2025 Zinian WU , Chinese Academy of Agricultural Sciences, Beijing, Beijing, China Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.166509.r424130 1. The description of sequencing in the Methods section is excessively detailed, and most content pertains to routine operations performed by the sequencing company. It is recommended to condense this part: briefly state the sequencing method, data volume, and ... Continue reading READ ALL 1. The description of sequencing in the Methods section is excessively detailed, and most content pertains to routine operations performed by the sequencing company. It is recommended to condense this part: briefly state the sequencing method, data volume, and other core information in one sentence, and focus on the analysis and discussion of the results. 2. The chloroplast genome typically has a quadripartite structure, consisting of four regions (LSC, SSC, IRa, and IRb), where IRa and IRb are equal in length and inverted in direction. However, the lengths of the two IR regions assembled by the authors are 20,121 bp and 20,115 bp, respectively, which is obviously incorrect. Consequently, the annotation results are inevitably inaccurate, and the authors are advised to further verify and correct them. In summary, it is recommended to reject the manuscript and invite resubmission after revisions. Are the rationale for sequencing the genome and the species significance clearly described? No 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: genome I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT WU Z. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r424130 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-424130 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 Views 0 Cite How to cite this report: Bashir NH. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r421284 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-421284 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 Nov 2025 Nawaz Haider Bashir , Qujing Normal University, Qujing, Yunnan, China Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.166509.r421284 This Genome Note describes the re-sequencing and assembly of the chloroplast genome of Cinnamomum burmanni from Indonesia. The topic has significant relevance and potential value, particularly since it adds geographic representation to existing plastome data. The authors have already ... Continue reading READ ALL This Genome Note describes the re-sequencing and assembly of the chloroplast genome of Cinnamomum burmanni from Indonesia. The topic has significant relevance and potential value, particularly since it adds geographic representation to existing plastome data. The authors have already revised and improved the manuscript in accordance with the reviewers’ comments. However, the manuscript still requires substantial improvements, such as: In the introduction, it is not clear why resequencing the plastome is necessary since there is already a complete C. burmanni plastome (China accession). Remove repeated sentences in the introduction, like "MinION, one of the ONT devices." Differences between Indonesian and Chinese accessions and their biological significance need to be explained. Figure 1: ycf1 appears in Figure 1 but is missing in Table 1. Results of sequencing can be made clear with total reads, average read length, longest read, percentage of reads used for cp assembly, and chloroplast vs. nuclear read percentages. 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? Partly 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: Entomologist, Evolutionary Biology 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 Bashir NH. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r421284 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-421284 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 Views 0 Cite How to cite this report: Quang MT. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r417958 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-417958 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 11 Oct 2025 Minh Trong Quang , University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.166509.r417958 Your Genome Note is a useful contribution that documents a MinION-based chloroplast assembly for Indonesian Cinnamomum burmanni , but to make it scientifically sound and maximally reusable, please (i) strengthen the rationale by stating explicitly what ONT long ... Continue reading READ ALL Your Genome Note is a useful contribution that documents a MinION-based chloroplast assembly for Indonesian Cinnamomum burmanni , but to make it scientifically sound and maximally reusable, please (i) strengthen the rationale by stating explicitly what ONT long reads add beyond the existing Chinese plastome (e.g., resolving repeats, verifying IR junctions, detecting structural/indel differences) and include a concise, tabulated comparison (genome size, GC%, LSC/SSC/IR lengths, IR junction coordinates, gene content); (ii) deposit the assembled plastome (FASTA) and its annotation (GenBank flatfile and/or GFF3) in a subject-specific repository (GenBank/ENA/DDBJ) and cite the accession(s) in the Data Availability section, alongside a clear list of all deposited file types (FASTQ and, if possible, FAST5/POD5; assembly FASTA; GFF3/GBK; circular genome map) with checksums/DOIs; (iii) resolve the IR asymmetry (IRa vs IRb lengths) by validating junctions with read-depth plots and alignment/dot-plots—either justify true asymmetry or correct the assembly—and report the outcome briefly in Results/Discussion; (iv) improve reproducibility by providing key commands/parameters for each step (Guppy model and thresholds; read filtering; Flye options including genome size/plasmid mode; number of polishing iterations and Medaka model; circularization/rotation procedure; GeSeq reference sets and identity thresholds; any manual curation of starts/stops and introns), plus a simple pipeline schematic; (v) add minimal HMW DNA QC evidence (method and metrics, image or table) to support the reported read N50 and correct the MinKNOW wording to reflect its role during acquisition rather than post-run visualization; (vi) ensure internal consistency between Figure 1 and Table 1 (e.g., presence of ycf1; remove “fragment” labels), standardize numerical formatting (e.g., 152,765 bp), and trim repeated sentences in the Introduction; and (vii) enrich the Results with mapping proportion to chloroplast, percent reads retained after filtering, basic assembly stats, and a coverage-depth plot across the plastome. These revisions will clarify the manuscript’s added value, secure data accessibility, and substantially improve technical rigor and reproducibility. 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? Partly 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: Bioinformatics, Genetics, Biotechnology I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Quang MT. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r417958 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-417958 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 Views 0 Cite How to cite this report: Do HDK. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r280927 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-280927 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 11 Jun 2024 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.166509.r280927 Dear Authors, Thank you very much for your revised manuscript. The manuscript was revised based on the reviewer's comments. However, some issues have not been resolved. 1) The d 152.775 bp in the text. unequal length ... Continue reading READ ALL Dear Authors, Thank you very much for your revised manuscript. The manuscript was revised based on the reviewer's comments. However, some issues have not been resolved. 1) The d 152.775 bp in the text. unequal length of IR regions was not discussed with the reason. 2) Comparison between the China and Indonesia Cinnamomum burmanni is too simple. Please add more details. 3) Figure 1 was not revised (please delete "fragment" in the gene names). Other comments for minor issues. 1) ycf1 gene was shown in Figure 1, but it is absent in Table 1. 2) Please use the format of 152,765 bp and 152,775 bp for 152.765 bp an Thank you. Competing Interests: No competing interests were disclosed. Reviewer Expertise: Genomics, Chloroplast genome evolution, Phylogeny 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 Do HDK. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r280927 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-280927 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 Views 0 Cite How to cite this report: Sawicki J. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r280926 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-280926 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 11 Jun 2024 Jakub Sawicki , Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.166509.r280926 The revised version has improved, but it still requires some corrections. Introduction: The last two sentences should be removed because they repeat previous statements. Methods Section: 1. MinKnow is not intended for ... Continue reading READ ALL The revised version has improved, but it still requires some corrections. Introduction: The last two sentences should be removed because they repeat previous statements. Methods Section: 1. MinKnow is not intended for post-run visualization. 2. The authors did not assess HMW DNA fragment distribution, which raises questions about how they determined the N50 value and whether their results accurately reflect this metric. Competing Interests: No competing interests were disclosed. Reviewer Expertise: Chloroplast genomics, nanopore sequencing 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 Sawicki J. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r280926 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v2#referee-response-280926 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 20 Feb 2024 Views 0 Cite How to cite this report: Sawicki J. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.159786.r262304 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v1#referee-response-262304 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 25 Apr 2024 Jakub Sawicki , Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland Not Approved VIEWS 0 https://doi.org/10.5256/f1000research.159786.r262304 This paper presents a clear and well-structured investigation into the chloroplast genome of Indonesian Cinnamomum burmanni. The authors effectively introduce the plant's significance and the rationale for studying its genome, highlighting the knowledge gap regarding this specific Indonesian variety. Authors ... Continue reading READ ALL This paper presents a clear and well-structured investigation into the chloroplast genome of Indonesian Cinnamomum burmanni. The authors effectively introduce the plant's significance and the rationale for studying its genome, highlighting the knowledge gap regarding this specific Indonesian variety. Authors propose the use of MinION Oxford Nanopore Technologies for sequencing and provide a detailed, step-by-step methodological outline. This includes sample collection, DNA extraction techniques, sequencing hardware, and a comprehensive list of software used for analysis. While a bit more context on chloroplast genome research and the reasoning behind specific methodological choices would be beneficial, the paper overall offers a solid foundation for understanding their research aims and procedures. However the reviewed Genome Note has some issues that should be solved before acceptance: 1. The justification of study is unclear since the reference genome was previously sequenced. Why the ONT sequencing was used and what are possible pros of using this approach 2. Meanwhile the second genome is reported, the paper lacks of any comparison between Chinese and Indonesian accessions. 3. The described DNA extraction protocol is not suitable for HMW DNA. There's no size distribution or validation at this point. 4. The results section lack of any details on sequencing results including total output, percentage of read used for assembly, N50 reads and assembly coverage. 5. How the authors handle heteroplasmy? 6. An the least but not last, the SRA accesssion data do not contain fastq/fast5/pod5/ reads. 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? Partly 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: Chloroplast genomics, nanopore sequencing I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Sawicki J. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.159786.r262304 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v1#referee-response-262304 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 26 Jun 2024 Richard Salindeho , Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, 16680, Indonesia 26 Jun 2024 Author Response Dear Editor and Reviewer, Thank you for your comment and suggestion. We have responded to all reviewer's comment's as you may find in the following link Response to ... Continue reading Dear Editor and Reviewer, Thank you for your comment and suggestion. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Sincerely yours, Corresponding author Dear Editor and Reviewer, Thank you for your comment and suggestion. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Sincerely yours, Corresponding author Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 26 Jun 2024 Richard Salindeho , Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, 16680, Indonesia 26 Jun 2024 Author Response Dear Editor and Reviewer, Thank you for your comment and suggestion. We have responded to all reviewer's comment's as you may find in the following link Response to ... Continue reading Dear Editor and Reviewer, Thank you for your comment and suggestion. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Sincerely yours, Corresponding author Dear Editor and Reviewer, Thank you for your comment and suggestion. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Sincerely yours, Corresponding author Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Do HDK. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.159786.r255270 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v1#referee-response-255270 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 18 Mar 2024 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.159786.r255270 1/ "MinION is a third-generation sequencing technology with nanopore technology (Oxford Nanopore Technologies (ONT), 2017)". MinION is one of the devices of ONT for performing sequencing. Therefore, please revise the sentence. 2/ Please revise the Figure 1. There are ... Continue reading READ ALL 1/ "MinION is a third-generation sequencing technology with nanopore technology (Oxford Nanopore Technologies (ONT), 2017)". MinION is one of the devices of ONT for performing sequencing. Therefore, please revise the sentence. 2/ Please revise the Figure 1. There are several errors in gene names such as three ndhK, rrn16 fragment, rps12 absence, etc... 3/ Also, please revise the Figure 1 legend with more detail about Figure 1. 4/ The protocol for DNA extraction can be found in the kit. Therefore, mentioning it again in the method part is unnecessary. The authors should add more details about the results and comparison between the new and old chloroplast genomes of Cinnamomum burmanni. 5/ Please add the coverage depth of the new chloroplast genome. 6/ The IR regions do not have the same length. Please add the reason for this uncommon in chloroplast genome. Are the rationale for sequencing the genome and the species significance clearly described? Partly 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: Genomics, Chloroplast genome evolution, Phylogeny 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 Do HDK. Reviewer Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.159786.r255270 ) The direct URL for this report is: https://f1000research.com/articles/13-127/v1#referee-response-255270 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 Jun 2024 Richard Salindeho , Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, 16680, Indonesia 20 Jun 2024 Author Response Dear Reviewer, Thank you for the constructive inputs to our manuscript. We have responded to all reviewer's comment's as you may find in the following link Response to ... Continue reading Dear Reviewer, Thank you for the constructive inputs to our manuscript. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Please note that the revised Figure 1 is presented in this link Best Regards. Richard Andreas Salindeho Dear Reviewer, Thank you for the constructive inputs to our manuscript. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Please note that the revised Figure 1 is presented in this link Best Regards. Richard Andreas Salindeho Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 20 Jun 2024 Richard Salindeho , Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, 16680, Indonesia 20 Jun 2024 Author Response Dear Reviewer, Thank you for the constructive inputs to our manuscript. We have responded to all reviewer's comment's as you may find in the following link Response to ... Continue reading Dear Reviewer, Thank you for the constructive inputs to our manuscript. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Please note that the revised Figure 1 is presented in this link Best Regards. Richard Andreas Salindeho Dear Reviewer, Thank you for the constructive inputs to our manuscript. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Please note that the revised Figure 1 is presented in this link Best Regards. Richard Andreas Salindeho 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 20 Feb 2024 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 3 4 5 Version 3 (revision) 16 Dec 25 read read read read Version 2 (revision) 21 May 24 read read read read read Version 1 20 Feb 24 read read Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam Jakub Sawicki , University of Warmia and Mazury in Olsztyn, Olsztyn, Poland Minh Trong Quang , University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam Nawaz Haider Bashir , Qujing Normal University, Qujing, China Zinian WU , Chinese Academy of Agricultural Sciences, Beijing, China 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 Quang 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 3 Minh Trong Quang , University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam 0 Views copyright © 2026 Quang 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 (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 have carefully reviewed the revised version of the manuscript as well as the authors’ responses to previous reviewer comments. The authors have addressed the major technical and presentation-related concerns raised during earlier review rounds, including improvements to the Introduction, clarification of the sequencing and assembly workflow, correction of inconsistencies between Figure 1 and Table 1, and clearer reporting of chloroplast genome structure and gene content. The methodological description is now more focused, and the Results section more clearly reports key assembly statistics and genome features. While some limitations inherent to a Genome Note remain (e.g., limited comparative and evolutionary interpretation), these are now appropriately aligned with the scope and aims of the article. Overall, the revised manuscript represents a technically sound and useful genomic resource that adds geographic representation for Cinnamomum burmanni plastomes and should be of value to researchers working in plant genomics and chloroplast genome studies. I therefore have no further major comments to make on this revised version. Competing Interests No competing interests were disclosed. Reviewer Expertise Bioinformatics, Genetics, Biotechnology 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) Quang MT. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441776) 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/13-127/v3#referee-response-441776 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2026 Sawicki J. 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. 10 Jan 2026 | for Version 3 Jakub Sawicki , Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland 0 Views copyright © 2026 Sawicki J. 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 The authors resolved all raised issues. I recommend acceptance. Competing Interests No competing interests were disclosed. 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) Sawicki J. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441775) 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/13-127/v3#referee-response-441775 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2026 Bashir N. 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. 31 Dec 2025 | for Version 3 Nawaz Haider Bashir , Qujing Normal University, Qujing, Yunnan, China 0 Views copyright © 2026 Bashir N. 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 The authors have incorporated the necessary changes in the revised version. Competing Interests No competing interests were disclosed. Reviewer Expertise Entomologist, Evolutionary Biology 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) Bashir NH. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441778) 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/13-127/v3#referee-response-441778 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Do H. 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. 16 Dec 2025 | for Version 3 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam 0 Views copyright © 2025 Do H. 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) Not 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 Dear Authors, Thank you very much for revising the manuscript. However, many issues were not addressed, and the text was the same as previous version without clear explanation. Therefore, I am not confident for further reviewing this manuscript. Best regards. Competing Interests No competing interests were disclosed. Reviewer Expertise Genomics, Chloroplast genome evolution, Phylogeny I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (0) Do HDK. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.193459.r441779) 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/13-127/v3#referee-response-441779 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 WU Z. 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. 20 Nov 2025 | for Version 2 Zinian WU , Chinese Academy of Agricultural Sciences, Beijing, Beijing, China 0 Views copyright © 2025 WU Z. 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) Not 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 1. The description of sequencing in the Methods section is excessively detailed, and most content pertains to routine operations performed by the sequencing company. It is recommended to condense this part: briefly state the sequencing method, data volume, and other core information in one sentence, and focus on the analysis and discussion of the results. 2. The chloroplast genome typically has a quadripartite structure, consisting of four regions (LSC, SSC, IRa, and IRb), where IRa and IRb are equal in length and inverted in direction. However, the lengths of the two IR regions assembled by the authors are 20,121 bp and 20,115 bp, respectively, which is obviously incorrect. Consequently, the annotation results are inevitably inaccurate, and the authors are advised to further verify and correct them. In summary, it is recommended to reject the manuscript and invite resubmission after revisions. Are the rationale for sequencing the genome and the species significance clearly described? No 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 genome I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (0) WU Z. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r424130) 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/13-127/v2#referee-response-424130 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Bashir N. 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 Nov 2025 | for Version 2 Nawaz Haider Bashir , Qujing Normal University, Qujing, Yunnan, China 0 Views copyright © 2025 Bashir N. 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 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 This Genome Note describes the re-sequencing and assembly of the chloroplast genome of Cinnamomum burmanni from Indonesia. The topic has significant relevance and potential value, particularly since it adds geographic representation to existing plastome data. The authors have already revised and improved the manuscript in accordance with the reviewers’ comments. However, the manuscript still requires substantial improvements, such as: In the introduction, it is not clear why resequencing the plastome is necessary since there is already a complete C. burmanni plastome (China accession). Remove repeated sentences in the introduction, like "MinION, one of the ONT devices." Differences between Indonesian and Chinese accessions and their biological significance need to be explained. Figure 1: ycf1 appears in Figure 1 but is missing in Table 1. Results of sequencing can be made clear with total reads, average read length, longest read, percentage of reads used for cp assembly, and chloroplast vs. nuclear read percentages. 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? Partly 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 Entomologist, Evolutionary Biology 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 (0) Bashir NH. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r421284) 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/13-127/v2#referee-response-421284 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Quang 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. 11 Oct 2025 | for Version 2 Minh Trong Quang , University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam 0 Views copyright © 2025 Quang 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 (0) Not 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 Your Genome Note is a useful contribution that documents a MinION-based chloroplast assembly for Indonesian Cinnamomum burmanni , but to make it scientifically sound and maximally reusable, please (i) strengthen the rationale by stating explicitly what ONT long reads add beyond the existing Chinese plastome (e.g., resolving repeats, verifying IR junctions, detecting structural/indel differences) and include a concise, tabulated comparison (genome size, GC%, LSC/SSC/IR lengths, IR junction coordinates, gene content); (ii) deposit the assembled plastome (FASTA) and its annotation (GenBank flatfile and/or GFF3) in a subject-specific repository (GenBank/ENA/DDBJ) and cite the accession(s) in the Data Availability section, alongside a clear list of all deposited file types (FASTQ and, if possible, FAST5/POD5; assembly FASTA; GFF3/GBK; circular genome map) with checksums/DOIs; (iii) resolve the IR asymmetry (IRa vs IRb lengths) by validating junctions with read-depth plots and alignment/dot-plots—either justify true asymmetry or correct the assembly—and report the outcome briefly in Results/Discussion; (iv) improve reproducibility by providing key commands/parameters for each step (Guppy model and thresholds; read filtering; Flye options including genome size/plasmid mode; number of polishing iterations and Medaka model; circularization/rotation procedure; GeSeq reference sets and identity thresholds; any manual curation of starts/stops and introns), plus a simple pipeline schematic; (v) add minimal HMW DNA QC evidence (method and metrics, image or table) to support the reported read N50 and correct the MinKNOW wording to reflect its role during acquisition rather than post-run visualization; (vi) ensure internal consistency between Figure 1 and Table 1 (e.g., presence of ycf1; remove “fragment” labels), standardize numerical formatting (e.g., 152,765 bp), and trim repeated sentences in the Introduction; and (vii) enrich the Results with mapping proportion to chloroplast, percent reads retained after filtering, basic assembly stats, and a coverage-depth plot across the plastome. These revisions will clarify the manuscript’s added value, secure data accessibility, and substantially improve technical rigor and reproducibility. 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? Partly 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 Bioinformatics, Genetics, Biotechnology I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (0) Quang MT. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r417958) 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/13-127/v2#referee-response-417958 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Do H. 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. 11 Jun 2024 | for Version 2 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam 0 Views copyright © 2024 Do H. 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 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 Dear Authors, Thank you very much for your revised manuscript. The manuscript was revised based on the reviewer's comments. However, some issues have not been resolved. 1) The d 152.775 bp in the text. unequal length of IR regions was not discussed with the reason. 2) Comparison between the China and Indonesia Cinnamomum burmanni is too simple. Please add more details. 3) Figure 1 was not revised (please delete "fragment" in the gene names). Other comments for minor issues. 1) ycf1 gene was shown in Figure 1, but it is absent in Table 1. 2) Please use the format of 152,765 bp and 152,775 bp for 152.765 bp an Thank you. Competing Interests No competing interests were disclosed. Reviewer Expertise Genomics, Chloroplast genome evolution, Phylogeny 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 (0) Do HDK. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r280927) 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/13-127/v2#referee-response-280927 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Sawicki J. 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. 11 Jun 2024 | for Version 2 Jakub Sawicki , Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland 0 Views copyright © 2024 Sawicki J. 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 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 The revised version has improved, but it still requires some corrections. Introduction: The last two sentences should be removed because they repeat previous statements. Methods Section: 1. MinKnow is not intended for post-run visualization. 2. The authors did not assess HMW DNA fragment distribution, which raises questions about how they determined the N50 value and whether their results accurately reflect this metric. Competing Interests No competing interests were disclosed. Reviewer Expertise Chloroplast genomics, nanopore sequencing 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 (0) Sawicki J. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.166509.r280926) 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/13-127/v2#referee-response-280926 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Sawicki J. 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. 25 Apr 2024 | for Version 1 Jakub Sawicki , Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland 0 Views copyright © 2024 Sawicki J. 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) Not 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 paper presents a clear and well-structured investigation into the chloroplast genome of Indonesian Cinnamomum burmanni. The authors effectively introduce the plant's significance and the rationale for studying its genome, highlighting the knowledge gap regarding this specific Indonesian variety. Authors propose the use of MinION Oxford Nanopore Technologies for sequencing and provide a detailed, step-by-step methodological outline. This includes sample collection, DNA extraction techniques, sequencing hardware, and a comprehensive list of software used for analysis. While a bit more context on chloroplast genome research and the reasoning behind specific methodological choices would be beneficial, the paper overall offers a solid foundation for understanding their research aims and procedures. However the reviewed Genome Note has some issues that should be solved before acceptance: 1. The justification of study is unclear since the reference genome was previously sequenced. Why the ONT sequencing was used and what are possible pros of using this approach 2. Meanwhile the second genome is reported, the paper lacks of any comparison between Chinese and Indonesian accessions. 3. The described DNA extraction protocol is not suitable for HMW DNA. There's no size distribution or validation at this point. 4. The results section lack of any details on sequencing results including total output, percentage of read used for assembly, N50 reads and assembly coverage. 5. How the authors handle heteroplasmy? 6. An the least but not last, the SRA accesssion data do not contain fastq/fast5/pod5/ reads. 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? Partly 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 Chloroplast genomics, nanopore sequencing I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above. reply Respond to this report Responses (1) Author Response 26 Jun 2024 Richard Salindeho, Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, 16680, Indonesia Dear Editor and Reviewer, Thank you for your comment and suggestion. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Sincerely yours, Corresponding author View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Sawicki J. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.159786.r262304) 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/13-127/v1#referee-response-262304 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Do H. 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. 18 Mar 2024 | for Version 1 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam 0 Views copyright © 2024 Do H. 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 1/ "MinION is a third-generation sequencing technology with nanopore technology (Oxford Nanopore Technologies (ONT), 2017)". MinION is one of the devices of ONT for performing sequencing. Therefore, please revise the sentence. 2/ Please revise the Figure 1. There are several errors in gene names such as three ndhK, rrn16 fragment, rps12 absence, etc... 3/ Also, please revise the Figure 1 legend with more detail about Figure 1. 4/ The protocol for DNA extraction can be found in the kit. Therefore, mentioning it again in the method part is unnecessary. The authors should add more details about the results and comparison between the new and old chloroplast genomes of Cinnamomum burmanni. 5/ Please add the coverage depth of the new chloroplast genome. 6/ The IR regions do not have the same length. Please add the reason for this uncommon in chloroplast genome. Are the rationale for sequencing the genome and the species significance clearly described? Partly 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 Genomics, Chloroplast genome evolution, Phylogeny 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 Jun 2024 Richard Salindeho, Department of Silviculture, Faculty of Forestry and Environment, IPB University, Bogor, 16680, Indonesia Dear Reviewer, Thank you for the constructive inputs to our manuscript. We have responded to all reviewer's comment's as you may find in the following link Response to Reviewer's comments Please note that the revised Figure 1 is presented in this link Best Regards. Richard Andreas Salindeho View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Do HDK. Peer Review Report For: Re-sequencing of the complete chloroplast genome of Cinnamomum burmanni (Nees & T.Nees) Blume (Lauraceae) from Indonesia using MinION Oxford Nanopore Technologies [version 3; peer review: 3 approved, 2 not approved] . F1000Research 2025, 13 :127 ( https://doi.org/10.5256/f1000research.159786.r255270) 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/13-127/v1#referee-response-255270 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 Adjust parameters to alter display View on desktop for interactive features Includes Interactive Elements View on desktop for interactive features Competing Interests Policy Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. 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