The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae)

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Skeels (Phyllanthaceae)", "datePublished": "2023-08-31T10:13:44", "dateModified": "2025-11-21T10:39:01", "author": [ { "@type": "Person", "name": "Hoang Danh Nguyen" }, { "@type": "Person", "name": "Thi Diem Quynh Nguyen" }, { "@type": "Person", "name": "Minh Thiet Vu" }, { "@type": "Person", "name": "Hoang Dang Khoa Do" } ], "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": " Phyllanthus acidus (L.) Skeels (Phyllanthaceae) is a potential medicinal plant recognized for its sour and tart-tasting fruits. In this study, the chloroplast genome of P. acidus was sequenced, assembled, and characterized. The chloroplast genome size was 156,331 bp, and the overall GC content was 36.9%. Additionally, the chloroplast genome had a quadripartite structure consisting of a large single copy (LSC; 85,807 bp in length; GC content: 34.6%), a small single copy (SSC; 19,262 bp in length; GC content: 30.6%), and two inverted repeat regions (IR; 25,631 bp in length; GC content: 43.1%). A total of 113 unique genes were annotated in the chloroplast genome, including 79 protein-coding genes, 30 tRNAs, and four rRNAs. The phylogenetic analysis based on 79 protein-coding genes revealed the paraphyly of the Phyllanthus genus. These findings provided additional genetic information for further research on P. acidus and the cp genome in the Phyllanthaceae family." } { "@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/12-1059", "name": "The complete chloroplast genome of Phyllanthus acidus (L.) Skeels..." } } ] } Home Browse The complete chloroplast genome of Phyllanthus acidus (L.) Skeels... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Nguyen HD, Nguyen TDQ, Vu MT and Do HDK. The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.12688/f1000research.140134.3 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Genome Note Revised The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] Hoang Danh Nguyen 1 , Thi Diem Quynh Nguyen 2 , Minh Thiet Vu 1 , Hoang Dang Khoa Do https://orcid.org/0000-0002-7970-9359 1 Hoang Danh Nguyen 1 , Thi Diem Quynh Nguyen 2 , Minh Thiet Vu 1 , Hoang Dang Khoa Do https://orcid.org/0000-0002-7970-9359 1 PUBLISHED 21 Nov 2025 Author details Author details 1 NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam 2 Faculty of Nursing and Medical Technology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam Hoang Danh Nguyen Roles: Data Curation, Formal Analysis, Funding Acquisition, Writing – Original Draft Preparation Thi Diem Quynh Nguyen Roles: Formal Analysis, Investigation, Methodology, Writing – Original Draft Preparation Minh Thiet Vu Roles: Conceptualization, Investigation, Methodology, Supervision, Writing – Review & Editing Hoang Dang Khoa Do Roles: Conceptualization, Methodology, Supervision, Validation, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Plant Science gateway. This article is included in the Genomics and Genetics gateway. Abstract Phyllanthus acidus (L.) Skeels (Phyllanthaceae) is a potential medicinal plant recognized for its sour and tart-tasting fruits. In this study, the chloroplast genome of P. acidus was sequenced, assembled, and characterized. The chloroplast genome size was 156,331 bp, and the overall GC content was 36.9%. Additionally, the chloroplast genome had a quadripartite structure consisting of a large single copy (LSC; 85,807 bp in length; GC content: 34.6%), a small single copy (SSC; 19,262 bp in length; GC content: 30.6%), and two inverted repeat regions (IR; 25,631 bp in length; GC content: 43.1%). A total of 113 unique genes were annotated in the chloroplast genome, including 79 protein-coding genes, 30 tRNAs, and four rRNAs. The phylogenetic analysis based on 79 protein-coding genes revealed the paraphyly of the Phyllanthus genus. These findings provided additional genetic information for further research on P. acidus and the cp genome in the Phyllanthaceae family. READ ALL READ LESS Keywords Malpighiales, Phyllanthaceae, phylogenetic relationships, plastome, star gooseberry Corresponding Author(s) Hoang Dang Khoa Do ( [email protected] ) Close Corresponding author: Hoang Dang Khoa Do Competing interests: No competing interests were disclosed. Grant information: This research is funded by Nguyen Tat Thanh University, Ho Chi Minh city, Vietnam to Nguyen Hoang Danh. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2025 Nguyen HD 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: Nguyen HD, Nguyen TDQ, Vu MT and Do HDK. The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.12688/f1000research.140134.3 ) First published: 31 Aug 2023, 12 :1059 ( https://doi.org/10.12688/f1000research.140134.1 ) Latest published: 21 Nov 2025, 12 :1059 ( https://doi.org/10.12688/f1000research.140134.3 ) Revised Amendments from Version 2 The revised manuscript was modified based on the comments of two new reviewers about the content of version 2 related to the aim of the study, the tool (OrgabellgenomeDRAW which is for illustrating the genome map) for annotating chloroplast genome, and the method to extract protein-coding genes for phylogenetic analysis. We revised the aim of the study and added more details about the methods of our manuscript (e.g., annotating, illustrating, and extracting sequences from chloroplast genomes). For the comment about phylogenetic analysis, we added an additonal description about the phylogenetic result and refused to add discussion because of the regulation of Genome Note regulation. There is no change in title, figure, table, and authors of the manuscript. The revised manuscript was modified based on the comments of two new reviewers about the content of version 2 related to the aim of the study, the tool (OrgabellgenomeDRAW which is for illustrating the genome map) for annotating chloroplast genome, and the method to extract protein-coding genes for phylogenetic analysis. We revised the aim of the study and added more details about the methods of our manuscript (e.g., annotating, illustrating, and extracting sequences from chloroplast genomes). For the comment about phylogenetic analysis, we added an additonal description about the phylogenetic result and refused to add discussion because of the regulation of Genome Note regulation. There is no change in title, figure, table, and authors of the manuscript. See the authors' detailed response to the review by Jessica D. Rey See the authors' detailed response to the review by Qiang Li See the authors' detailed response to the review by Shiou Yih Lee READ REVIEWER RESPONSES Introduction Phyllanthus acidus (L.) Skeels, also known as star gooseberry, belongs to the Phyllanthaceae family and is commonly distributed in the wet tropical regions, including South Asia, Southeast Asia, Central Africa, the Caribbean region, Central America, and South America ( POWO 2022 ). P. acidus has been traditionally used to treat various diseases, including inflammation, gastrointestinal problems, rheumatism, bronchitis, Alzheimer’s, and hepatic diseases ( Jain et al . 2011 ; Chakraborty et al . 2012 ; Srirama et al . 2012 ; Uddin et al . 2016 ). The leaves and roots of P. acidus also possess antidotal properties against viper venom ( Jayvir 1998 ). Moreover, P. acidus could potentially alleviate hypertension ( Leeya et al . 2010 ). The chloroplast (cp) genome is highly effective at inferring phylogeny since it is predominantly maternally inherited, has a conversed structure and gene content, and has slow mutation frequency ( Palmer et al . 1988 ). Additionally, the cp genomes provide essential data for examining population genetics, molecular identification, and genetic engineering ( Powell et al . 1995 ; Daniell et al . 2016 ; Cao et al . 2022 ). Previously, a comparative chloroplast genomic study revealed the features of Phyllanthus chloroplast genomes and the non-monophyletic status of Phyllanthus species ( Fang et al. 2023 ). Therefore, in the current study, we explored the characteristics of the P. acidus cp genome and its phylogenetic implication to gain more genomic information about the chloroplast genome evolution and to provide more data to resolve controversy of phylogenetic relationships within the Phyllanthus genus and closely related taxa in Phyllanthaceae. Methods Sample collection The P. acidus sample (young branches with leaves) was collected from Can Tho, Viet Nam (9°56′55.7″N, 105°30′16.0″E) and labeled with voucher number: NTT-2022.12.CR (contact person: Dr. Do Hoang Dang Khoa, [email protected] ). It was deposited at the NTT Hi-tech Institute, Nguyen Tat Thanh University. No specific permit was required to collect and study the species in Vietnam. The leaf sample was dried with silica gel and stored in a -80°C freezer until DNA extraction was conducted. Data collection and analysis The total genomic DNA extraction from the dried leaves was carried out using the Cetyltrimethylammonium bromide (CTAB) protocol ( Doyle & Doyle 1987 ). The quality of genomic DNA samples was checked using gel electrophoresis and the NanoDrop One C Spectrophotometer. The DNA samples that showed a clear band on agarose gel and had a 260/280 ratio between 1,8-2 and a 260/230 ratio between 2.0-2.2 were selected for conducting the next-generation sequencing step. Subsequently, the library was prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, USA). The library was sequenced using the Illumina MiSeq platform to generate paired-end reads of 150 bp (Ktest Science Co. Ltd., Vietnam). The raw reads were qualified and filtered for low-quality reads (Q score < 20 and length < 100 bp) and reads containing primers or adapters using FastQC v0.12.1 and Trimmomatic v0.39 programs ( Andrews 2010 ; Bolger et al . 2014 ). For the assembly of the cp genome, the NOVOPlasty v4.3.1 program was used ( Dierckxsens et al . 2017 ). Preliminary annotation was conducted by Geseq with default parameters for land plant plastid and chloroplast land plant reference set (MPI-MP Reference Set) ( Tillich et al . 2017 ). The complete annotation genome was illustrated using OrganellarGenomeDRAW v1.3.1 with default settings for circular plastid genome ( Greiner et al . 2019 ). All 79 protein-coding regions in the cp genomes of P. acidus and 16 related taxa from the Phyllanthaceae were extracted and aligned for phylogenetic analysis using MUSCLE v5 program ( Edgar 2004 ). The chloroplast genome of Acalypha hispida (Euphorbiaceae; Genbank accession no. NC_070339) was selected as an outgroup. A maximum likelihood phylogenetic tree was reconstructed using IQTREE with 1000 bootstrap replicates and GTRGAMMA substitution model ( Nguyen et al . 2015 ). In addition, Bayesian inference method was applied to the aligned sequnces under GTRGAMMA substitution model using MrBayes v3.2.7a with 1,000,000 generations and a discard of 25% sample ( Ronquist et al. 2012 ). Results Approximately 349.8 MB of clean reads were obtained and used for completing the cp genome of P. acidus. The assembly process utilized 1,166,034 paired-end reads, resulting in an average coverage depth of 2,234.3X ( Nguyen, Nguyen, Do, and Vu, 2023 ; Nguyen, Do, and Vu, 2023 ) (Supplementary Figure S1, Do 2025 ). The quadripartite cp genome of P. acidus (GenBank accession number OR050568) had a length of 156,331 bp and consisted of an LSC region of 85,807 bp, a SSC region of 19,262 bp, and a pair of IR regions of 25,631 bp ( Figure 1 ). The overall GC contents of the genome was 36.9%, and the GC content of the LSC, SSC, and IR regions were 34.6%, 30.6%, and 43.1%, respectively. The cp genome of P. acidus contained a total of 130 genes, including 85 protein-coding regions, 37 tRNA genes, and eight rRNA genes ( Table 1 ). Among 85 protein-coding genes, 17 genes contained introns, of which ycf3 and clpP contained two introns (Supplementary Figure S2, Do 2025 ). In IR regions, a total of 19 genes were duplicated, including eight protein-coding regions (i.e., rps19, rpl2, rpl23, ycf1, ycf2, ndhB , rps12 , and rps7 ), seven tRNAs ( trnI_CAU, trnL_CAA, trnV_GAC, trnI_GAU, trnA_UGC, trnR_ACG , and trnN_GUU ), and four rRNAs ( rrn16S, rrn23S, rrn4.5S , and rrn5S ). Notably, rps19 and ycf1 duplications were incomplete. The phylogenetic analysis revealed a paraphyly of Phyllanthus species, in which Breynia futicosa and Glochidion chodoense formed a clade with Phyllanthus amarus ( Figure 2 ). Therefore, more genomic data and samples of Phyllanthaceae species are required for further phylogenetic studies. Figure 1. Map of the cp genome of Phyllanthus acidus. Genes located inside the circle are transcribed in a clockwise direction, while genes outside the circle are transcribed counterclockwise. The inner circle depicted in dark gray represents the GC content, while the light-gray circle represents the AT content of the genome. LSC: large single copy; SSC: small single copy; IRA/IRB: inverted repeat regions. Table 1. List of genes in the chloroplast genome of Phyllanthus acidus. Groups of genes Name of genes Ribosomal RNAs rrn4.5(2x), rrn5(2x), rrn16(2x), rrn23(2x) Transfer RNAs trnA_UGC * (2x), trnC_GCA, trnD_GUC, trnE_UUC, trnF_GAA, trnG_UCC * , trnG_GCC, trnH_GUG, trnI_GAU * (2x), trnK_UUU * , trnL_CAA(2x), trnL_UAA * , trnL_UAG, trnfM_CAU, trnM_CAU(2x), trnM_CAU, trnN_GUU(2x), trnP_UGG, trnQ_UUG, trnR_ACG(2x), trnR_UCU, trnS_GCU, trnS_GGA, trnS_UGA, trnT_GGU, trnT_UGU, trnV_GAC(2x), trnV_UAC * , trnW_CCA, trnY_GUA Photosystem I psaA, psaB, psaC, psaI, psaJ Photosystem II psbA, psbB, psbC, psbD, psbE, psbF, psbH, psbI, psbJ, psbK, psbL, psbM, psbN, psbT, psbZ Cytochrome petA, petB * , petD * , petG, petL, petN ATP synthases atpA, atpB, atpE, atpF * , atpH, atpI Large unit of Rubisco rbcL NADH dehydrogenase ndhA * , ndhB * (2x), ndhC, ndhD, ndhE, ndhF, ndhG, ndhH, ndhI, ndhJ, ndhK ATP-dependent protease subunit P clpP * Envelop membrane protein cemA Large units of ribosome rpl2 * (2x), rpl14, rpl16 * , rpl20, rpl22, rpl23(2x), rpl32, rpl33, rpl36 Small units of ribosome rps2, rps3, rps4, rps7(2x), rps8, rps11, rps12 * (2x), rps14, rps15, rps16 * , rps18, rps19(2xa) RNA polymerase rpoA, rpoB, rpoC1 * , rpoC2 Initiation factor infA Other genes accD, ccsA, matK Hypothetical proteins and conserved reading frames ycf1(2xa), ycf2(2x), ycf3 * , ycf4 * Gene with introns; 2x – duplicated gene in IR region; 2xa – incomplete duplicated gene in IR region. Figure 2. The phylogenetic tree of Phyllanthus acidus and related species based on the 79 protein-coding sequences of cp genome. The asterisk indicates P. acidus sequenced in this study. The numbers next to each node are bootstrap values and posterior probability inferred from maximum likelihood and Bayesian inference methods. Data availability NCBI Short Read Archive (SRA): DNA-seq of Phyllanthus acidus. Accession number SRR24772537; https://www.ncbi.nlm.nih.gov/sra/SRR24772537 ( Nguyen, Nguyen, Do, and Vu, 2023 ). NCBI Assembly database: Phyllanthus acidus chloroplast, complete genome. Accession number OR050568; https://www.ncbi.nlm.nih.gov/nuccore/OR050568 ( Nguyen, Do, and Vu, 2023 ). Extended data Figshare: Supplementary Files. https://doi.org/10.6084/m9.figshare.30354073 ( Do 2025 ). Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0) Acknowledgements The authors thank to anonymous reviewers for their helpful comments to improve the quality of this manuscript. References Andrews S: FastQC: A Quality Control Tool for High Throughput Sequence Data.2010. Bolger AM, Lohse M, Usadel B: Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30 (15): 2114–2120. PubMed Abstract | Publisher Full Text | Free Full Text Cao D-L, et al. : Application of chloroplast genome in the identification of Traditional Chinese Medicine Viola philippica. BMC Genomics. 2022; 23 (1): 540. Publisher Full Text Chakraborty R, et al. : Antiinflammatory, antinociceptive and antioxidant activities of Phyllanthus acidus L. extracts. Asian Pac. J. Trop. Biomed. 2012; 2 (2): S953–S961. Publisher Full Text Daniell H, et al. : Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol. 2016; 17 (1): 134. PubMed Abstract | Publisher Full Text | Free Full Text Dierckxsens N, Mardulyn P, Smits G: NOVOPlasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2017; 45 (4): gkw955. Publisher Full Text Do KHD: Supplementary Files. [Dataset]. figshare. 2025. Publisher Full Text Doyle JJ, Doyle JL: A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 1987; 19 : 11–15. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004; 32 (5): 1792–1797. PubMed Abstract | Publisher Full Text | Free Full Text Fang H, et al. : Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants. Front. Plant Sci. 2023; 13 : 1099856. Publisher Full Text Greiner S, Lehwark P, Bock R: OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 2019; 47 (W1): W59–W64. PubMed Abstract | Publisher Full Text | Free Full Text Jain NK, et al. : Effects of Phyllanthus acidus (L.) Skeels fruit on carbon tetrachloride-induced acute oxidative damage in livers of rats and mice. Zhong Xi Yi Jie He Xue Bao = Journal of Chinese Integrative Medicine. 2011; 9 (1): 49–56. PubMed Abstract | Publisher Full Text Jayvir A: Nature heals, a glossary of selected indigenous medicinal plants of India. Indian J. Pharm. 1998; 30 (2): 126. Leeya Y, et al. : Hypotensive activity of an n-butanol extract and their purified compounds from leaves of Phyllanthus acidus (L.) Skeels in rats. Eur. J. Pharmacol. 2010; 649 (1–3): 301–313. PubMed Abstract | Publisher Full Text Nguyen L-T, et al. : IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015; 32 (1): 268–274. PubMed Abstract | Publisher Full Text | Free Full Text Nguyen DH, Nguyen TDQ, Do KHD, et al. : DNA-seq of Phyllanthus acidus. NCBI Short Read Archive. [Dataset]. 2023. Reference Source Nguyen DH, Do KHD, Vu TM: Phyllanthus acidus chloroplast, complete genome. [Dataset]. GenBank. 2023. Reference Source Palmer JD, et al. : Chloroplast DNA variation and plant phylogeny. Ann. Mo. Bot. Gard. 1988; 75 : 1180–1206. Publisher Full Text Powell W, et al. : Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc. Natl. Acad. Sci. 1995; 92 (17): 7759–7763. PubMed Abstract | Publisher Full Text | Free Full Text POWO: Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew.2022. Ronquist F, et al. : MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Syst. Biol. 2012; 61 (3):539–542. PubMed Abstract | Publisher Full Text | Free Full Text Srirama R, et al. : Hepatoprotective activity of Indian phyllanthus. Pharm. Biol. 2012; 50 (8): 948–953. Publisher Full Text Tillich M, 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 Uddin MS, et al. : Neuroprotective Effect of Phyllanthus acidus L. on Learning and Memory Impairment in Scopolamine-Induced Animal Model of Dementia and Oxidative Stress: Natural Wonder for Regulating the Development and Progression of Alz. Adv. Alzheimer’s Dis. 2016; 05 (02): 53–72. Publisher Full Text Comments on this article Comments (0) Version 3 VERSION 3 PUBLISHED 31 Aug 2023 ADD YOUR COMMENT Comment Author details Author details 1 NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam 2 Faculty of Nursing and Medical Technology, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam Hoang Danh Nguyen Roles: Data Curation, Formal Analysis, Funding Acquisition, Writing – Original Draft Preparation Thi Diem Quynh Nguyen Roles: Formal Analysis, Investigation, Methodology, Writing – Original Draft Preparation Minh Thiet Vu Roles: Conceptualization, Investigation, Methodology, Supervision, Writing – Review & Editing Hoang Dang Khoa Do Roles: Conceptualization, Methodology, Supervision, Validation, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information This research is funded by Nguyen Tat Thanh University, Ho Chi Minh city, Vietnam to Nguyen Hoang Danh. 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: 21 Nov 2025, 12:1059 https://doi.org/10.12688/f1000research.140134.3 version 2 Revised Published: 16 Oct 2025, 12:1059 https://doi.org/10.12688/f1000research.140134.2 version 1 Published: 31 Aug 2023, 12:1059 https://doi.org/10.12688/f1000research.140134.1 Copyright © 2025 Nguyen HD 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 Nguyen HD, Nguyen TDQ, Vu MT and Do HDK. The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.12688/f1000research.140134.3 ) 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 21 Nov 2025 Revised Views 0 Cite How to cite this report: Sahu SK. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r439860 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v3#referee-response-439860 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 07 Jan 2026 Sunil Kumar Sahu , BGI-Shenzhen, Shenzhen, China Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.190830.r439860 This Genome Note is technically sound and presents a well-covered Phyllanthus acidus plastome, accompanied by open data and a straightforward phylogenetic analysis that agrees with previous plastome-based inferences for Phyllanthaceae. The study has clear potential value, both because P. acidus ... Continue reading READ ALL This Genome Note is technically sound and presents a well-covered Phyllanthus acidus plastome, accompanied by open data and a straightforward phylogenetic analysis that agrees with previous plastome-based inferences for Phyllanthaceae. The study has clear potential value, both because P. acidus is medicinally important and because the clade itself is taxonomically challenging. That said, several aspects still need clarification or correction before the manuscript can be considered fully robust. In particular, the rationale for generating a new plastome despite the existence of an earlier P. acidus assembly needs to be explicitly stated, along with any improvements your dataset contributes. My specific comments and questions are below: • What is the explicit justification for re-sequencing P. acidus given the available GenBank plastome (N C_070169)? Please indicate whether your assembly provides concrete improvements or corrections (for example, IR boundary resolution, the extent of ycf1 / rps19 pseudogenization, or annotation differences). • The manuscript reports inconsistent gene counts: the Abstract lists 113 unique genes (79 PCGs, 30 tRNAs, 4 rRNAs) whereas the Results and Table 1 suggest 130 total genes (85 PCGs, 37 tRNAs, 8 rRNAs). Please clarify which numbers refer to unique genes versus totals including IR duplicates, and ensure Table 1 reflects accurate gene names and counts. • Table 1 contains several typographical issues (for example, Cyrillic characters in rpo -genes, duplicated trnM-CAU , and the inclusion of “ rps1 ”). Please correct these using your GeSeq output, and explicitly indicate that rps12 is a trans‑spliced gene. • Please specify the seed sequence and parameters used in NOVOPlasty, and describe how you validated genome circularization and IR/SC junction accuracy (for example, via read‑mapping coverage, junction‑spanning reads, or targeted PCR). • For the phylogenetic analyses, please report the exact models used in IQ‑TREE and MrBayes, using each program’s proper nomenclature. Indicate whether you performed model selection (e.g., ModelFinder), partitioning (gene or codon level), alignment trimming or masking, or any saturation testing. • If you have compared your plastome directly to NC_070169 (e.g., pairwise divergence, structural differences, annotation discrepancies), please summarize the key findings. If not, a brief comparison would strengthen the manuscript. Overall, the work is promising and close to solid, but addressing these issues will substantially improve clarity, reproducibility, and the manuscript’s contribution to plastome resources for Phyllanthus . Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Plant genomics and evolution 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 Sahu SK. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r439860 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v3#referee-response-439860 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: Fukasawa Y. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r435864 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v3#referee-response-435864 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 Dec 2025 Yoshinori Fukasawa , Center for Bioscience Research and Education Utsunomiya University, Tochigi, Japan Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.190830.r435864 I agree with the other reviewers. The manuscript clearly describes the importance of P. acidus as a species and provides a technically sound chloroplast assembly with appropriate sequencing and annotation procedures. These strengths are appreciated. However, there ... Continue reading READ ALL I agree with the other reviewers. The manuscript clearly describes the importance of P. acidus as a species and provides a technically sound chloroplast assembly with appropriate sequencing and annotation procedures. These strengths are appreciated. However, there is already an existing P. acidus chloroplast genome available in NCBI, and the Genome Note guidelines require authors to explain “ why and how the genomes were sequenced .” Simply removing the earlier incorrect statement (“has not been studied”) or adding comments on the species’ economic or medicinal value does not address the core issue raised by the reviewer. The manuscript should explicitly clarify the rationale for resequencing the chloroplast genome despite the presence of a previously published assembly—e.g., whether the new (meta)data provide validation, improved quality, structural corrections, or broader comparative relevance. Minor technical corrections Additionally, several tool names should be standardized (e.g., GeSeq, IQ-TREE), and the substitution model should match the nomenclature actually used in IQ-TREE or MrBayes, as “GTRGAMMA” is not a conventional model designation in those programs. 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? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Bioinformatics, genome assembly, and computational genomics. 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 Fukasawa Y. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r435864 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v3#referee-response-435864 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: Li Q. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r434949 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v3#referee-response-434949 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 08 Dec 2025 Qiang Li , Nanjing Forestry University, Nanjing, China; Anhui Normal University, Wuhu, Anhui, China Approved VIEWS 0 https://doi.org/10.5256/f1000research.190830.r434949 I have finished reading the revised manuscript. The article ... Continue reading READ ALL I have finished reading the revised manuscript. The article reads very well, and I have no further comments. 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 Li Q. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r434949 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v3#referee-response-434949 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 16 Oct 2025 Revised Views 0 Cite How to cite this report: Lee SY. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.189635.r426288 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v2#referee-response-426288 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 03 Nov 2025 Shiou Yih Lee , INTI International University, Nilai, Malaysia Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.189635.r426288 The manuscript describes on the characterisation of the chloroplast genome sequence of Phyllanthus acidus. My comments are as follows: 1. There is one chloroplast genome sequence of P. acidus in NCBI. The problem statement and objective of this study ... Continue reading READ ALL The manuscript describes on the characterisation of the chloroplast genome sequence of Phyllanthus acidus. My comments are as follows: 1. There is one chloroplast genome sequence of P. acidus in NCBI. The problem statement and objective of this study are not very relevant. 2. How did the authors extract the protein-coding sequences from the chloroplast genome sequence for phylogenetic analysis? 3. As there is another record of P. acidus in NCBI GenBank, no discussion or comparison was conducted between that and the one from this study. The placement of P. acidus of this study in the phylogenetic tree was not described in the Results. There is no discussion on the findings from the phylogenetic analysis. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: forestry, molecular phylogenetics and evolutionary 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 Lee SY. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.189635.r426288 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v2#referee-response-426288 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 21 Nov 2025 Hoang Dang Khoa Do , NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam 21 Nov 2025 Author Response Dear Reviewer, Thank you very much for your comments and suggestions. We revised the manuscript based on your suggestions. Please check our responses as mentioned below. The manuscript describes ... Continue reading Dear Reviewer, Thank you very much for your comments and suggestions. We revised the manuscript based on your suggestions. Please check our responses as mentioned below. The manuscript describes on the characterisation of the chloroplast genome sequence of Phyllanthus acidus . My comments are as follows: 1. There is one chloroplast genome sequence of P. acidus in NCBI. The problem statement and objective of this study are not very relevant. Response: Thank you very much for your comment. In the original version, we did not mention as "The current study explored the characteristics of the P. acidus cp genome which has not been studied" which was added in the revised version. We are so sorry for the wrong information. We revised this information in the newest version of our manuscript. 2. How did the authors extract the protein-coding sequences from the chloroplast genome sequence for phylogenetic analysis? Response: Thank you very much for your question. We added the program for extracting protein-coding genes which is Geneious Prime v2023.0 in the revised manuscript. 3. As there is another record of P. acidus in NCBI GenBank, no discussion or comparison was conducted between that and the one from this study. The placement of P. acidus of this study in the phylogenetic tree was not described in the Results. There is no discussion on the findings from the phylogenetic analysis. Response: Thank you very much for your comment. We submitted our manuscript as a Genome Note type which requires "brief descriptions of genome sequences that include details of why and how the genomes were sequenced; they do not include any analyses or conclusions.". Therefore, we focused on description of our target genome and did not do comparative genomic analyses. In addition, in Genome Note type, the regulation does not allow a Discussion part in the manuscript ( https://f1000research.com/for-authors/article-guidelines/genome-notes ). Therefore, we did not discuss in depth about phylogenetic analysis in our manuscript. We added more details about phylogenetic relationship between Phyllanthus acidus in the main text. Thank you. Dear Reviewer, Thank you very much for your comments and suggestions. We revised the manuscript based on your suggestions. Please check our responses as mentioned below. The manuscript describes on the characterisation of the chloroplast genome sequence of Phyllanthus acidus . My comments are as follows: 1. There is one chloroplast genome sequence of P. acidus in NCBI. The problem statement and objective of this study are not very relevant. Response: Thank you very much for your comment. In the original version, we did not mention as "The current study explored the characteristics of the P. acidus cp genome which has not been studied" which was added in the revised version. We are so sorry for the wrong information. We revised this information in the newest version of our manuscript. 2. How did the authors extract the protein-coding sequences from the chloroplast genome sequence for phylogenetic analysis? Response: Thank you very much for your question. We added the program for extracting protein-coding genes which is Geneious Prime v2023.0 in the revised manuscript. 3. As there is another record of P. acidus in NCBI GenBank, no discussion or comparison was conducted between that and the one from this study. The placement of P. acidus of this study in the phylogenetic tree was not described in the Results. There is no discussion on the findings from the phylogenetic analysis. Response: Thank you very much for your comment. We submitted our manuscript as a Genome Note type which requires "brief descriptions of genome sequences that include details of why and how the genomes were sequenced; they do not include any analyses or conclusions.". Therefore, we focused on description of our target genome and did not do comparative genomic analyses. In addition, in Genome Note type, the regulation does not allow a Discussion part in the manuscript ( https://f1000research.com/for-authors/article-guidelines/genome-notes ). Therefore, we did not discuss in depth about phylogenetic analysis in our manuscript. We added more details about phylogenetic relationship between Phyllanthus acidus in the main text. Thank you. Competing Interests: We do not have any conflicts of interest. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 21 Nov 2025 Hoang Dang Khoa Do , NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam 21 Nov 2025 Author Response Dear Reviewer, Thank you very much for your comments and suggestions. We revised the manuscript based on your suggestions. Please check our responses as mentioned below. The manuscript describes ... Continue reading Dear Reviewer, Thank you very much for your comments and suggestions. We revised the manuscript based on your suggestions. Please check our responses as mentioned below. The manuscript describes on the characterisation of the chloroplast genome sequence of Phyllanthus acidus . My comments are as follows: 1. There is one chloroplast genome sequence of P. acidus in NCBI. The problem statement and objective of this study are not very relevant. Response: Thank you very much for your comment. In the original version, we did not mention as "The current study explored the characteristics of the P. acidus cp genome which has not been studied" which was added in the revised version. We are so sorry for the wrong information. We revised this information in the newest version of our manuscript. 2. How did the authors extract the protein-coding sequences from the chloroplast genome sequence for phylogenetic analysis? Response: Thank you very much for your question. We added the program for extracting protein-coding genes which is Geneious Prime v2023.0 in the revised manuscript. 3. As there is another record of P. acidus in NCBI GenBank, no discussion or comparison was conducted between that and the one from this study. The placement of P. acidus of this study in the phylogenetic tree was not described in the Results. There is no discussion on the findings from the phylogenetic analysis. Response: Thank you very much for your comment. We submitted our manuscript as a Genome Note type which requires "brief descriptions of genome sequences that include details of why and how the genomes were sequenced; they do not include any analyses or conclusions.". Therefore, we focused on description of our target genome and did not do comparative genomic analyses. In addition, in Genome Note type, the regulation does not allow a Discussion part in the manuscript ( https://f1000research.com/for-authors/article-guidelines/genome-notes ). Therefore, we did not discuss in depth about phylogenetic analysis in our manuscript. We added more details about phylogenetic relationship between Phyllanthus acidus in the main text. Thank you. Dear Reviewer, Thank you very much for your comments and suggestions. We revised the manuscript based on your suggestions. Please check our responses as mentioned below. The manuscript describes on the characterisation of the chloroplast genome sequence of Phyllanthus acidus . My comments are as follows: 1. There is one chloroplast genome sequence of P. acidus in NCBI. The problem statement and objective of this study are not very relevant. Response: Thank you very much for your comment. In the original version, we did not mention as "The current study explored the characteristics of the P. acidus cp genome which has not been studied" which was added in the revised version. We are so sorry for the wrong information. We revised this information in the newest version of our manuscript. 2. How did the authors extract the protein-coding sequences from the chloroplast genome sequence for phylogenetic analysis? Response: Thank you very much for your question. We added the program for extracting protein-coding genes which is Geneious Prime v2023.0 in the revised manuscript. 3. As there is another record of P. acidus in NCBI GenBank, no discussion or comparison was conducted between that and the one from this study. The placement of P. acidus of this study in the phylogenetic tree was not described in the Results. There is no discussion on the findings from the phylogenetic analysis. Response: Thank you very much for your comment. We submitted our manuscript as a Genome Note type which requires "brief descriptions of genome sequences that include details of why and how the genomes were sequenced; they do not include any analyses or conclusions.". Therefore, we focused on description of our target genome and did not do comparative genomic analyses. In addition, in Genome Note type, the regulation does not allow a Discussion part in the manuscript ( https://f1000research.com/for-authors/article-guidelines/genome-notes ). Therefore, we did not discuss in depth about phylogenetic analysis in our manuscript. We added more details about phylogenetic relationship between Phyllanthus acidus in the main text. Thank you. Competing Interests: We do not have any conflicts of interest. Close Report a concern COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Li Q. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.189635.r426285 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v2#referee-response-426285 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 03 Nov 2025 Qiang Li , Nanjing Forestry University, Nanjing, China; Anhui Normal University, Wuhu, Anhui, China Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.189635.r426285 Phyllanthus is one of the taxonomic difficulties genera of Phyllanthaceae. It contains approximately 800 species, mainly distributed in the tropical and subtropical regions of the world, and a few are in the northern temperate zone. Previous studies have demonstrated that ... Continue reading READ ALL Phyllanthus is one of the taxonomic difficulties genera of Phyllanthaceae. It contains approximately 800 species, mainly distributed in the tropical and subtropical regions of the world, and a few are in the northern temperate zone. Previous studies have demonstrated that Phyllanthus is a paraphyletic group. Several solutions have been proposed for dividing Phyllanthus species. Some researchers classified previously established classifications into Phyllanthus sensu lato, such as (Kathriarachchi et al. 2006), who placed Breynia, Glochidion and Synostemon into Phyllanthus . Others split Phyllanthus into several monophyletic genera. However, these taxonomic evidence lack support from genomics. Therefore, we need to obtain more genomic data of this genus to better resolve the taxonomic controversies within it. I believe this is also the most important significance of this manuscript reporting the chloroplast genome of Phyllanthus acidus . The primary objective of this manuscript is to assemble and provide a basic description of the Phyllanthus acidus genome. The methods and content are straightforward and easy to follow. I have two main concerns that I hope the authors will address to enhance the quality of the manuscript. [1] I agree with the previous reviewer's opinion that the introduction lacks the significance of studying the chloroplast genome of this species. I suggest that the authors could add a concise introduction. For example, there is controversy over the broad and narrow senses of the genus Phyllanthus , and this molecular phylogenetic debate lacks evidence from genomics. Therefore, the genome sequenced in this study lays the foundation for resolving the taxonomic controversy of the genus Phyllanthus in the future. [2] OrganellarGenomeDRAW requires a reference genome for annotating chloroplast genomes, and the authors should specify which species' chloroplast genome was used as the reference. 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? Yes References 1. Nguyen H, Nguyen T, Vu M, Do H: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae). F1000Research . 2025; 12 . Publisher Full Text Competing Interests: No competing interests were disclosed. Reviewer Expertise: My research areas primarily encompass speciation, phylogenetics, and the conservation of endangered plants. Currently, I mainly utilize chloroplast genomes, mitochondrial genomes, and nuclear genomes to address evolutionary questions. 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 Li Q. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.189635.r426285 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v2#referee-response-426285 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 21 Nov 2025 Hoang Dang Khoa Do , NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam 21 Nov 2025 Author Response Dear Reviewer, Thank you very much for your helpful comments. We revised the manuscript based on your comments. Please check our response as mentioned below. The primary objective of ... Continue reading Dear Reviewer, Thank you very much for your helpful comments. We revised the manuscript based on your comments. Please check our response as mentioned below. The primary objective of this manuscript is to assemble and provide a basic description of the Phyllanthus acidus genome. The methods and content are straightforward and easy to follow. I have two main concerns that I hope the authors will address to enhance the quality of the manuscript. [1] I agree with the previous reviewer's opinion that the introduction lacks the significance of studying the chloroplast genome of this species. I suggest that the authors could add a concise introduction. For example, there is controversy over the broad and narrow senses of the genus Phyllanthus, and this molecular phylogenetic debate lacks evidence from genomics. Therefore, the genome sequenced in this study lays the foundation for resolving the taxonomic controversy of the genus Phyllanthus in the future. Response: Thank you very much for your suggestion. We revised the second part of the Introduction with an adding of a previous comparative genomic analysis based on complete chloroplast genomes of Phyllanthus which indicated a non-monophyletic status of Phyllanthus species. In addition, we modified the aims of the current study as "Therefore, in the current study, we explored the characteristics of the P. acidus cp genome and its phylogenetic implication to gain more genomic information about the chloroplast genome evolution and to provide more data to resolve controversy of phylogenetic relationships within the Phyllanthus genus and closely related taxa in Phyllanthaceae .". [2] OrganellarGenomeDRAW requires a reference genome for annotating chloroplast genomes, and the authors should specify which species' chloroplast genome was used as the reference. Response: Thank you very much for your suggestion. We checked the paper ( https://doi.org/10.1093/nar/gkz238 ) and the website ( https://chlorobox.mpimp-golm.mpg.de/OGDraw.html ) of OGDRAW and we did not find any regulation to select a reference genome for annotation chloroplast genome before drawing the chloroplast genome map. The input of OGDRAW is an annotated file (a GenBank flat file) of chloroplast genome which included all information of genes. Then OGDRAW will converts annotations in GenBank format to graphical maps. For annotating chloroplast genome using GESEQ, there is an option for selecting the reference genome. We selected the default reference set of the Geseq which is "MPI-MP Reference Set chloroplast land plants (CDS + rRNA)". We did not use a reference genome from Phyllanthus species because we would like to compare our sequence to the land plant database. The more annotation information we compare, the more accuracy of chloroplast genome annotation we get. Thank you. Dear Reviewer, Thank you very much for your helpful comments. We revised the manuscript based on your comments. Please check our response as mentioned below. The primary objective of this manuscript is to assemble and provide a basic description of the Phyllanthus acidus genome. The methods and content are straightforward and easy to follow. I have two main concerns that I hope the authors will address to enhance the quality of the manuscript. [1] I agree with the previous reviewer's opinion that the introduction lacks the significance of studying the chloroplast genome of this species. I suggest that the authors could add a concise introduction. For example, there is controversy over the broad and narrow senses of the genus Phyllanthus, and this molecular phylogenetic debate lacks evidence from genomics. Therefore, the genome sequenced in this study lays the foundation for resolving the taxonomic controversy of the genus Phyllanthus in the future. Response: Thank you very much for your suggestion. We revised the second part of the Introduction with an adding of a previous comparative genomic analysis based on complete chloroplast genomes of Phyllanthus which indicated a non-monophyletic status of Phyllanthus species. In addition, we modified the aims of the current study as "Therefore, in the current study, we explored the characteristics of the P. acidus cp genome and its phylogenetic implication to gain more genomic information about the chloroplast genome evolution and to provide more data to resolve controversy of phylogenetic relationships within the Phyllanthus genus and closely related taxa in Phyllanthaceae .". [2] OrganellarGenomeDRAW requires a reference genome for annotating chloroplast genomes, and the authors should specify which species' chloroplast genome was used as the reference. Response: Thank you very much for your suggestion. We checked the paper ( https://doi.org/10.1093/nar/gkz238 ) and the website ( https://chlorobox.mpimp-golm.mpg.de/OGDraw.html ) of OGDRAW and we did not find any regulation to select a reference genome for annotation chloroplast genome before drawing the chloroplast genome map. The input of OGDRAW is an annotated file (a GenBank flat file) of chloroplast genome which included all information of genes. Then OGDRAW will converts annotations in GenBank format to graphical maps. For annotating chloroplast genome using GESEQ, there is an option for selecting the reference genome. We selected the default reference set of the Geseq which is "MPI-MP Reference Set chloroplast land plants (CDS + rRNA)". We did not use a reference genome from Phyllanthus species because we would like to compare our sequence to the land plant database. The more annotation information we compare, the more accuracy of chloroplast genome annotation we get. Thank you. Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 21 Nov 2025 Hoang Dang Khoa Do , NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam 21 Nov 2025 Author Response Dear Reviewer, Thank you very much for your helpful comments. We revised the manuscript based on your comments. Please check our response as mentioned below. The primary objective of ... Continue reading Dear Reviewer, Thank you very much for your helpful comments. We revised the manuscript based on your comments. Please check our response as mentioned below. The primary objective of this manuscript is to assemble and provide a basic description of the Phyllanthus acidus genome. The methods and content are straightforward and easy to follow. I have two main concerns that I hope the authors will address to enhance the quality of the manuscript. [1] I agree with the previous reviewer's opinion that the introduction lacks the significance of studying the chloroplast genome of this species. I suggest that the authors could add a concise introduction. For example, there is controversy over the broad and narrow senses of the genus Phyllanthus, and this molecular phylogenetic debate lacks evidence from genomics. Therefore, the genome sequenced in this study lays the foundation for resolving the taxonomic controversy of the genus Phyllanthus in the future. Response: Thank you very much for your suggestion. We revised the second part of the Introduction with an adding of a previous comparative genomic analysis based on complete chloroplast genomes of Phyllanthus which indicated a non-monophyletic status of Phyllanthus species. In addition, we modified the aims of the current study as "Therefore, in the current study, we explored the characteristics of the P. acidus cp genome and its phylogenetic implication to gain more genomic information about the chloroplast genome evolution and to provide more data to resolve controversy of phylogenetic relationships within the Phyllanthus genus and closely related taxa in Phyllanthaceae .". [2] OrganellarGenomeDRAW requires a reference genome for annotating chloroplast genomes, and the authors should specify which species' chloroplast genome was used as the reference. Response: Thank you very much for your suggestion. We checked the paper ( https://doi.org/10.1093/nar/gkz238 ) and the website ( https://chlorobox.mpimp-golm.mpg.de/OGDraw.html ) of OGDRAW and we did not find any regulation to select a reference genome for annotation chloroplast genome before drawing the chloroplast genome map. The input of OGDRAW is an annotated file (a GenBank flat file) of chloroplast genome which included all information of genes. Then OGDRAW will converts annotations in GenBank format to graphical maps. For annotating chloroplast genome using GESEQ, there is an option for selecting the reference genome. We selected the default reference set of the Geseq which is "MPI-MP Reference Set chloroplast land plants (CDS + rRNA)". We did not use a reference genome from Phyllanthus species because we would like to compare our sequence to the land plant database. The more annotation information we compare, the more accuracy of chloroplast genome annotation we get. Thank you. Dear Reviewer, Thank you very much for your helpful comments. We revised the manuscript based on your comments. Please check our response as mentioned below. The primary objective of this manuscript is to assemble and provide a basic description of the Phyllanthus acidus genome. The methods and content are straightforward and easy to follow. I have two main concerns that I hope the authors will address to enhance the quality of the manuscript. [1] I agree with the previous reviewer's opinion that the introduction lacks the significance of studying the chloroplast genome of this species. I suggest that the authors could add a concise introduction. For example, there is controversy over the broad and narrow senses of the genus Phyllanthus, and this molecular phylogenetic debate lacks evidence from genomics. Therefore, the genome sequenced in this study lays the foundation for resolving the taxonomic controversy of the genus Phyllanthus in the future. Response: Thank you very much for your suggestion. We revised the second part of the Introduction with an adding of a previous comparative genomic analysis based on complete chloroplast genomes of Phyllanthus which indicated a non-monophyletic status of Phyllanthus species. In addition, we modified the aims of the current study as "Therefore, in the current study, we explored the characteristics of the P. acidus cp genome and its phylogenetic implication to gain more genomic information about the chloroplast genome evolution and to provide more data to resolve controversy of phylogenetic relationships within the Phyllanthus genus and closely related taxa in Phyllanthaceae .". [2] OrganellarGenomeDRAW requires a reference genome for annotating chloroplast genomes, and the authors should specify which species' chloroplast genome was used as the reference. Response: Thank you very much for your suggestion. We checked the paper ( https://doi.org/10.1093/nar/gkz238 ) and the website ( https://chlorobox.mpimp-golm.mpg.de/OGDraw.html ) of OGDRAW and we did not find any regulation to select a reference genome for annotation chloroplast genome before drawing the chloroplast genome map. The input of OGDRAW is an annotated file (a GenBank flat file) of chloroplast genome which included all information of genes. Then OGDRAW will converts annotations in GenBank format to graphical maps. For annotating chloroplast genome using GESEQ, there is an option for selecting the reference genome. We selected the default reference set of the Geseq which is "MPI-MP Reference Set chloroplast land plants (CDS + rRNA)". We did not use a reference genome from Phyllanthus species because we would like to compare our sequence to the land plant database. The more annotation information we compare, the more accuracy of chloroplast genome annotation we get. Thank you. Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Version 1 VERSION 1 PUBLISHED 31 Aug 2023 Views 0 Cite How to cite this report: Rey JD. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.153464.r202362 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v1#referee-response-202362 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 22 Jan 2024 Jessica D. Rey , Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines Manila, Manila, Metro Manila, Philippines Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.153464.r202362 This is a good genome note on the sequencing and assembly of the plastome of Phyllanthus acidus . However, the paper lacks enough details on the reasons behind investigating the species (i.e., limited genetic and genomic resources? problems with identification?). ... Continue reading READ ALL This is a good genome note on the sequencing and assembly of the plastome of Phyllanthus acidus . However, the paper lacks enough details on the reasons behind investigating the species (i.e., limited genetic and genomic resources? problems with identification?). The protocol on sequencing and assembly is appropriate and is clearly described in the paper. To improve data transparency, I suggest including supplementary data such as depth of coverage/read mapping depth and the list of genes which are hard to annotate (i.e., cis-splicing/trans-splicing genes). In addition, I would also like to suggest the use of at least two different methods of phylogenetic analyses (e.g., Maximum likelihood and Bayesian inference) and to indicate the statistical support values [of the two methods] in the tree. Lastly, to improve readability of the paper I would like to recommend checking for grammatical errors. 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? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Molecular characterization of different plant species i.e. Philippine endemic medicinal plants, strawberry varieties planted in the Philippines, genetics of disease resistance cultivated rice, soilless culture of leafy and fruiting vegetables 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 Rey JD. Reviewer Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.153464.r202362 ) The direct URL for this report is: https://f1000research.com/articles/12-1059/v1#referee-response-202362 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 15 Oct 2025 Hoang Dang Khoa Do , NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam 15 Oct 2025 Author Response Dear Reviewers, Thank you very much for your helpful comments. 1/ We added the reason for conducting genomic research about Phyllanthus acidus in the Introduction as “which has ... Continue reading Dear Reviewers, Thank you very much for your helpful comments. 1/ We added the reason for conducting genomic research about Phyllanthus acidus in the Introduction as “which has not been studied”. 2/ We added the information of depth of coverage/read mapping depth and cis-splicing/trans-splicing genes as supplementary files. 3/ We revised the phylogenetic tree with the Bayesian inference method. Best regards. Dear Reviewers, Thank you very much for your helpful comments. 1/ We added the reason for conducting genomic research about Phyllanthus acidus in the Introduction as “which has not been studied”. 2/ We added the information of depth of coverage/read mapping depth and cis-splicing/trans-splicing genes as supplementary files. 3/ We revised the phylogenetic tree with the Bayesian inference method. Best regards. Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 15 Oct 2025 Hoang Dang Khoa Do , NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam 15 Oct 2025 Author Response Dear Reviewers, Thank you very much for your helpful comments. 1/ We added the reason for conducting genomic research about Phyllanthus acidus in the Introduction as “which has ... Continue reading Dear Reviewers, Thank you very much for your helpful comments. 1/ We added the reason for conducting genomic research about Phyllanthus acidus in the Introduction as “which has not been studied”. 2/ We added the information of depth of coverage/read mapping depth and cis-splicing/trans-splicing genes as supplementary files. 3/ We revised the phylogenetic tree with the Bayesian inference method. Best regards. Dear Reviewers, Thank you very much for your helpful comments. 1/ We added the reason for conducting genomic research about Phyllanthus acidus in the Introduction as “which has not been studied”. 2/ We added the information of depth of coverage/read mapping depth and cis-splicing/trans-splicing genes as supplementary files. 3/ We revised the phylogenetic tree with the Bayesian inference method. Best regards. 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 31 Aug 2023 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) 21 Nov 25 read read read Version 2 (revision) 16 Oct 25 read read Version 1 31 Aug 23 read Jessica D. Rey , University of the Philippines Manila, Manila, Philippines Qiang Li , Nanjing Forestry University, Nanjing, China; Anhui Normal University, Wuhu, China Shiou Yih Lee , INTI International University, Nilai, Malaysia Yoshinori Fukasawa , Center for Bioscience Research and Education Utsunomiya University, Tochigi, Japan Sunil Kumar Sahu , BGI-Shenzhen, Shenzhen, 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 Sahu S. 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. 07 Jan 2026 | for Version 3 Sunil Kumar Sahu , BGI-Shenzhen, Shenzhen, China 0 Views copyright © 2026 Sahu S. 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 is technically sound and presents a well-covered Phyllanthus acidus plastome, accompanied by open data and a straightforward phylogenetic analysis that agrees with previous plastome-based inferences for Phyllanthaceae. The study has clear potential value, both because P. acidus is medicinally important and because the clade itself is taxonomically challenging. That said, several aspects still need clarification or correction before the manuscript can be considered fully robust. In particular, the rationale for generating a new plastome despite the existence of an earlier P. acidus assembly needs to be explicitly stated, along with any improvements your dataset contributes. My specific comments and questions are below: • What is the explicit justification for re-sequencing P. acidus given the available GenBank plastome (N C_070169)? Please indicate whether your assembly provides concrete improvements or corrections (for example, IR boundary resolution, the extent of ycf1 / rps19 pseudogenization, or annotation differences). • The manuscript reports inconsistent gene counts: the Abstract lists 113 unique genes (79 PCGs, 30 tRNAs, 4 rRNAs) whereas the Results and Table 1 suggest 130 total genes (85 PCGs, 37 tRNAs, 8 rRNAs). Please clarify which numbers refer to unique genes versus totals including IR duplicates, and ensure Table 1 reflects accurate gene names and counts. • Table 1 contains several typographical issues (for example, Cyrillic characters in rpo -genes, duplicated trnM-CAU , and the inclusion of “ rps1 ”). Please correct these using your GeSeq output, and explicitly indicate that rps12 is a trans‑spliced gene. • Please specify the seed sequence and parameters used in NOVOPlasty, and describe how you validated genome circularization and IR/SC junction accuracy (for example, via read‑mapping coverage, junction‑spanning reads, or targeted PCR). • For the phylogenetic analyses, please report the exact models used in IQ‑TREE and MrBayes, using each program’s proper nomenclature. Indicate whether you performed model selection (e.g., ModelFinder), partitioning (gene or codon level), alignment trimming or masking, or any saturation testing. • If you have compared your plastome directly to NC_070169 (e.g., pairwise divergence, structural differences, annotation discrepancies), please summarize the key findings. If not, a brief comparison would strengthen the manuscript. Overall, the work is promising and close to solid, but addressing these issues will substantially improve clarity, reproducibility, and the manuscript’s contribution to plastome resources for Phyllanthus . Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Plant genomics and evolution 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) Sahu SK. Peer Review Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r439860) 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/12-1059/v3#referee-response-439860 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Fukasawa Y. 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 Dec 2025 | for Version 3 Yoshinori Fukasawa , Center for Bioscience Research and Education Utsunomiya University, Tochigi, Japan 0 Views copyright © 2025 Fukasawa Y. 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 I agree with the other reviewers. The manuscript clearly describes the importance of P. acidus as a species and provides a technically sound chloroplast assembly with appropriate sequencing and annotation procedures. These strengths are appreciated. However, there is already an existing P. acidus chloroplast genome available in NCBI, and the Genome Note guidelines require authors to explain “ why and how the genomes were sequenced .” Simply removing the earlier incorrect statement (“has not been studied”) or adding comments on the species’ economic or medicinal value does not address the core issue raised by the reviewer. The manuscript should explicitly clarify the rationale for resequencing the chloroplast genome despite the presence of a previously published assembly—e.g., whether the new (meta)data provide validation, improved quality, structural corrections, or broader comparative relevance. Minor technical corrections Additionally, several tool names should be standardized (e.g., GeSeq, IQ-TREE), and the substitution model should match the nomenclature actually used in IQ-TREE or MrBayes, as “GTRGAMMA” is not a conventional model designation in those programs. 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? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Bioinformatics, genome assembly, and computational genomics. 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) Fukasawa Y. Peer Review Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r435864) 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/12-1059/v3#referee-response-435864 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Li Q. 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. 08 Dec 2025 | for Version 3 Qiang Li , Nanjing Forestry University, Nanjing, China; Anhui Normal University, Wuhu, Anhui, China 0 Views copyright © 2025 Li Q. 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 finished reading the revised manuscript. The article reads very well, and I have no further comments. 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) Li Q. Peer Review Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.190830.r434949) 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/12-1059/v3#referee-response-434949 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Lee S. 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. 03 Nov 2025 | for Version 2 Shiou Yih Lee , INTI International University, Nilai, Malaysia 0 Views copyright © 2025 Lee S. 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 The manuscript describes on the characterisation of the chloroplast genome sequence of Phyllanthus acidus. My comments are as follows: 1. There is one chloroplast genome sequence of P. acidus in NCBI. The problem statement and objective of this study are not very relevant. 2. How did the authors extract the protein-coding sequences from the chloroplast genome sequence for phylogenetic analysis? 3. As there is another record of P. acidus in NCBI GenBank, no discussion or comparison was conducted between that and the one from this study. The placement of P. acidus of this study in the phylogenetic tree was not described in the Results. There is no discussion on the findings from the phylogenetic analysis. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Yes Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise forestry, molecular phylogenetics and evolutionary 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 21 Nov 2025 Hoang Dang Khoa Do, NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam Dear Reviewer, Thank you very much for your comments and suggestions. We revised the manuscript based on your suggestions. Please check our responses as mentioned below. The manuscript describes on the characterisation of the chloroplast genome sequence of Phyllanthus acidus . My comments are as follows: 1. There is one chloroplast genome sequence of P. acidus in NCBI. The problem statement and objective of this study are not very relevant. Response: Thank you very much for your comment. In the original version, we did not mention as "The current study explored the characteristics of the P. acidus cp genome which has not been studied" which was added in the revised version. We are so sorry for the wrong information. We revised this information in the newest version of our manuscript. 2. How did the authors extract the protein-coding sequences from the chloroplast genome sequence for phylogenetic analysis? Response: Thank you very much for your question. We added the program for extracting protein-coding genes which is Geneious Prime v2023.0 in the revised manuscript. 3. As there is another record of P. acidus in NCBI GenBank, no discussion or comparison was conducted between that and the one from this study. The placement of P. acidus of this study in the phylogenetic tree was not described in the Results. There is no discussion on the findings from the phylogenetic analysis. Response: Thank you very much for your comment. We submitted our manuscript as a Genome Note type which requires "brief descriptions of genome sequences that include details of why and how the genomes were sequenced; they do not include any analyses or conclusions.". Therefore, we focused on description of our target genome and did not do comparative genomic analyses. In addition, in Genome Note type, the regulation does not allow a Discussion part in the manuscript ( https://f1000research.com/for-authors/article-guidelines/genome-notes ). Therefore, we did not discuss in depth about phylogenetic analysis in our manuscript. We added more details about phylogenetic relationship between Phyllanthus acidus in the main text. Thank you. View more View less Competing Interests We do not have any conflicts of interest. reply Respond Report a concern Lee SY. Peer Review Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.189635.r426288) 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/12-1059/v2#referee-response-426288 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2025 Li Q. 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. 03 Nov 2025 | for Version 2 Qiang Li , Nanjing Forestry University, Nanjing, China; Anhui Normal University, Wuhu, Anhui, China 0 Views copyright © 2025 Li Q. 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 Phyllanthus is one of the taxonomic difficulties genera of Phyllanthaceae. It contains approximately 800 species, mainly distributed in the tropical and subtropical regions of the world, and a few are in the northern temperate zone. Previous studies have demonstrated that Phyllanthus is a paraphyletic group. Several solutions have been proposed for dividing Phyllanthus species. Some researchers classified previously established classifications into Phyllanthus sensu lato, such as (Kathriarachchi et al. 2006), who placed Breynia, Glochidion and Synostemon into Phyllanthus . Others split Phyllanthus into several monophyletic genera. However, these taxonomic evidence lack support from genomics. Therefore, we need to obtain more genomic data of this genus to better resolve the taxonomic controversies within it. I believe this is also the most important significance of this manuscript reporting the chloroplast genome of Phyllanthus acidus . The primary objective of this manuscript is to assemble and provide a basic description of the Phyllanthus acidus genome. The methods and content are straightforward and easy to follow. I have two main concerns that I hope the authors will address to enhance the quality of the manuscript. [1] I agree with the previous reviewer's opinion that the introduction lacks the significance of studying the chloroplast genome of this species. I suggest that the authors could add a concise introduction. For example, there is controversy over the broad and narrow senses of the genus Phyllanthus , and this molecular phylogenetic debate lacks evidence from genomics. Therefore, the genome sequenced in this study lays the foundation for resolving the taxonomic controversy of the genus Phyllanthus in the future. [2] OrganellarGenomeDRAW requires a reference genome for annotating chloroplast genomes, and the authors should specify which species' chloroplast genome was used as the reference. 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? Yes References 1. Nguyen H, Nguyen T, Vu M, Do H: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae). F1000Research . 2025; 12 . Publisher Full Text Competing Interests No competing interests were disclosed. Reviewer Expertise My research areas primarily encompass speciation, phylogenetics, and the conservation of endangered plants. Currently, I mainly utilize chloroplast genomes, mitochondrial genomes, and nuclear genomes to address evolutionary questions. 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 21 Nov 2025 Hoang Dang Khoa Do, NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam Dear Reviewer, Thank you very much for your helpful comments. We revised the manuscript based on your comments. Please check our response as mentioned below. The primary objective of this manuscript is to assemble and provide a basic description of the Phyllanthus acidus genome. The methods and content are straightforward and easy to follow. I have two main concerns that I hope the authors will address to enhance the quality of the manuscript. [1] I agree with the previous reviewer's opinion that the introduction lacks the significance of studying the chloroplast genome of this species. I suggest that the authors could add a concise introduction. For example, there is controversy over the broad and narrow senses of the genus Phyllanthus, and this molecular phylogenetic debate lacks evidence from genomics. Therefore, the genome sequenced in this study lays the foundation for resolving the taxonomic controversy of the genus Phyllanthus in the future. Response: Thank you very much for your suggestion. We revised the second part of the Introduction with an adding of a previous comparative genomic analysis based on complete chloroplast genomes of Phyllanthus which indicated a non-monophyletic status of Phyllanthus species. In addition, we modified the aims of the current study as "Therefore, in the current study, we explored the characteristics of the P. acidus cp genome and its phylogenetic implication to gain more genomic information about the chloroplast genome evolution and to provide more data to resolve controversy of phylogenetic relationships within the Phyllanthus genus and closely related taxa in Phyllanthaceae .". [2] OrganellarGenomeDRAW requires a reference genome for annotating chloroplast genomes, and the authors should specify which species' chloroplast genome was used as the reference. Response: Thank you very much for your suggestion. We checked the paper ( https://doi.org/10.1093/nar/gkz238 ) and the website ( https://chlorobox.mpimp-golm.mpg.de/OGDraw.html ) of OGDRAW and we did not find any regulation to select a reference genome for annotation chloroplast genome before drawing the chloroplast genome map. The input of OGDRAW is an annotated file (a GenBank flat file) of chloroplast genome which included all information of genes. Then OGDRAW will converts annotations in GenBank format to graphical maps. For annotating chloroplast genome using GESEQ, there is an option for selecting the reference genome. We selected the default reference set of the Geseq which is "MPI-MP Reference Set chloroplast land plants (CDS + rRNA)". We did not use a reference genome from Phyllanthus species because we would like to compare our sequence to the land plant database. The more annotation information we compare, the more accuracy of chloroplast genome annotation we get. Thank you. View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Li Q. Peer Review Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.189635.r426285) 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/12-1059/v2#referee-response-426285 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Rey 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. 22 Jan 2024 | for Version 1 Jessica D. Rey , Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines Manila, Manila, Metro Manila, Philippines 0 Views copyright © 2024 Rey 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) 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 is a good genome note on the sequencing and assembly of the plastome of Phyllanthus acidus . However, the paper lacks enough details on the reasons behind investigating the species (i.e., limited genetic and genomic resources? problems with identification?). The protocol on sequencing and assembly is appropriate and is clearly described in the paper. To improve data transparency, I suggest including supplementary data such as depth of coverage/read mapping depth and the list of genes which are hard to annotate (i.e., cis-splicing/trans-splicing genes). In addition, I would also like to suggest the use of at least two different methods of phylogenetic analyses (e.g., Maximum likelihood and Bayesian inference) and to indicate the statistical support values [of the two methods] in the tree. Lastly, to improve readability of the paper I would like to recommend checking for grammatical errors. 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? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Molecular characterization of different plant species i.e. Philippine endemic medicinal plants, strawberry varieties planted in the Philippines, genetics of disease resistance cultivated rice, soilless culture of leafy and fruiting vegetables 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 15 Oct 2025 Hoang Dang Khoa Do, NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam Dear Reviewers, Thank you very much for your helpful comments. 1/ We added the reason for conducting genomic research about Phyllanthus acidus in the Introduction as “which has not been studied”. 2/ We added the information of depth of coverage/read mapping depth and cis-splicing/trans-splicing genes as supplementary files. 3/ We revised the phylogenetic tree with the Bayesian inference method. Best regards. View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Rey JD. Peer Review Report For: The complete chloroplast genome of Phyllanthus acidus (L.) Skeels (Phyllanthaceae) [version 3; peer review: 1 approved, 4 approved with reservations] . F1000Research 2025, 12 :1059 ( https://doi.org/10.5256/f1000research.153464.r202362) 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/12-1059/v1#referee-response-202362 Alongside their report, reviewers assign a status to the article: Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. 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