Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan

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In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of two endemic species from Uzbekistan, Astragalus nuratensis and Oxytropis pseudorosea. Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively. The chloroplast genomes were 122,316 bp in A. nuratensis and 122,708 bp in O. pseudorosea. Both genomes encoded 110 unique genes, including 76 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Consistent with members of the inverted repeat–lacking clade of Fabaceae, both species lacked the typical inverted repeat regions, resulting in a single-copy genome structure. Phylogenetic analysis based on 119 complete chloroplast genomes resolved major lineages within Astragalus and related genera with strong support. Astragalus nuratensis was placed within the Phaca clade, while Oxytropis pseudorosea formed part of a distinct Oxytropis lineage. These results provide new genomic resources for understanding evolutionary relationships and plastome evolution in Central Asian legumes." } { "@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/15-445/v1", "name": "Complete chloroplast genomes of endemic Astragalus and Oxytropis species..." } } ] } Home Browse Complete chloroplast genomes of endemic Astragalus and Oxytropis species... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Hamrayev D, Karimov B, Esanov H et al. Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.12688/f1000research.178398.1 ) 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 Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] Diyorjon Hamrayev 1 , Bobur Karimov https://orcid.org/0009-0005-5874-1033 1 , Husniddin Esanov 2 , [...] Sodik Khuzhzhiev 3 , Maxzuna Nasretdinova 4 , Oysha Jabborova 5 , Oybek Omonov 6,7 , Mohistara Sharipova 8 , Ziyoviddin Yusupov 1 , Alijon Esankulov 9 Diyorjon Hamrayev 1 , Bobur Karimov https://orcid.org/0009-0005-5874-1033 1 , [...] Husniddin Esanov 2 , Sodik Khuzhzhiev 3 , Maxzuna Nasretdinova 4 , Oysha Jabborova 5 , Oybek Omonov 6,7 , Mohistara Sharipova 8 , Ziyoviddin Yusupov 1 , Alijon Esankulov 9 PUBLISHED 27 Mar 2026 Author details Author details 1 Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan 2 Bukhara State University, Bukhara, Uzbekistan 3 Navoi State University, Navoi, Uzbekistan 4 Samarkand State Medical University, Samarkand, Uzbekistan 5 Bukhara state medical institute named after Abu Ali ibn Sino, Bukhara, Uzbekistan 6 Karshi State University, Qarshi, Kashkadarya Province, Uzbekistan 7 Turan University, Karshi, Uzbekistan 8 Jizzakh State Pedagogical University, Jizzakh, Uzbekistan 9 Tashkent Botanical Garden under the Institute of Botany, Academy of Sciences, Tashkent, Uzbekistan Diyorjon Hamrayev Roles: Writing – Original Draft Preparation Bobur Karimov Roles: Writing – Original Draft Preparation, Writing – Review & Editing Husniddin Esanov Roles: Writing – Original Draft Preparation Sodik Khuzhzhiev Roles: Writing – Original Draft Preparation Maxzuna Nasretdinova Roles: Writing – Original Draft Preparation Oysha Jabborova Roles: Writing – Original Draft Preparation Oybek Omonov Roles: Writing – Original Draft Preparation Mohistara Sharipova Roles: Writing – Original Draft Preparation Ziyoviddin Yusupov Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing Alijon Esankulov Roles: Writing – Original Draft Preparation 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 Chloroplast genomes provide important insights into plant phylogeny, genome evolution, and molecular marker development. In this study, we sequenced, assembled, and analyzed the complete chloroplast genomes of two endemic species from Uzbekistan, Astragalus nuratensis and Oxytropis pseudorosea. Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively. The chloroplast genomes were 122,316 bp in A. nuratensis and 122,708 bp in O. pseudorosea. Both genomes encoded 110 unique genes, including 76 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Consistent with members of the inverted repeat–lacking clade of Fabaceae, both species lacked the typical inverted repeat regions, resulting in a single-copy genome structure. Phylogenetic analysis based on 119 complete chloroplast genomes resolved major lineages within Astragalus and related genera with strong support. Astragalus nuratensis was placed within the Phaca clade, while Oxytropis pseudorosea formed part of a distinct Oxytropis lineage. These results provide new genomic resources for understanding evolutionary relationships and plastome evolution in Central Asian legumes. READ ALL READ LESS Keywords plastome; Fabaceae; IRLC; phylogeny; genome evolution; Central Asia Corresponding Author(s) Ziyoviddin Yusupov ( [email protected] ) Close Corresponding author: Ziyoviddin Yusupov Competing interests: No competing interests were disclosed. Grant information: This work was supported by the project “Digital Nature: Development of a digital platform for the flora of Central Uzbekistan” (2025–2029), implemented by the Institute of Botany, Academy of Sciences of the Republic of Uzbekistan. Additional support was provided by the project “Assessing climate change adaptation in endangered plants of Uzbekistan: A DNA barcoding approach” (AL-9224104464). The funders had no role in study design, data collection, analysis, decision to publish, or preparation of the manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2026 Hamrayev D 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: Hamrayev D, Karimov B, Esanov H et al. Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.12688/f1000research.178398.1 ) First published: 27 Mar 2026, 15 :445 ( https://doi.org/10.12688/f1000research.178398.1 ) Latest published: 14 May 2026, 15 :445 ( https://doi.org/10.12688/f1000research.178398.2 )  There is a newer version of this article available. Suppress this message for one day. Introduction Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers. In most angiosperms, the cp genome exhibits a conserved quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions ( Karimov et al., 2025 ). Nevertheless, structural modifications, including gene rearrangements, inversions, expansion or loss of IR regions, gene loss, and pseudogene formation, have been documented in several lineages, particularly in Fabaceae ( Cai et al., 2008 ; Son & Choi, 2022 ). Fabaceae is one of the largest families of flowering plants and includes many species of considerable ecological and agricultural importance. According to recent classifications, the family is divided into six subfamilies: Caesalpinioideae, Cercidoideae, Detarioideae, Dialioideae, Duparquetioideae, and Faboideae (Papilionoideae) ( Azani et al., 2017 ). Within Faboideae, the inverted repeat–lacking clade (IRLC) is characterized by the loss of one copy of the IR region (approximately 25 kb) in the chloroplast genome. This clade comprises about 52 genera and more than 4,000 species, and plastomes of IRLC taxa frequently show gene loss or pseudogenization (e.g., rps16, rpl22, infA, accD, and ycf4), intron loss (clpP, atpF, and rpoC1), inversions, and occasional transfer of genes to the nuclear genome ( Son & Choi, 2022 ). Within the IRLC, the genera Astragalus L. (3,095 species) and Oxytropis DC. (608 species) represent highly diverse and taxonomically complex groups ( POWO, 2026 ). In the present study, we sequenced, assembled, and analyzed the cp genomes of Oxytropis pseudorosea Filim. and Astragalus nuratensis Popov, two narrowly distributed endemic species from the Nuratau Mountains of Uzbekistan, Central Asia. Methods Leaf samples of Oxytropis pseudorosea and Astragalus nuratensis were collected in 2024 from the Nuratau Mountains, Uzbekistan, by Diyorjon Hamrayev. Species identification was carried out by Beshko Natalya ( Astragalus nuratensis ) and Doston Turdiyev ( Oxytropis pseudorosea ). Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002. Genomic DNA was isolated from leaf tissue using the Tiangen DP305 Plant Genomic DNA Kit (Beijing, China). Libraries were prepared with the NEBNext ® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA; Cat. E7370L) following the manufacturer’s protocol, with index codes added during preparation. DNA was sonicated to ~350 bp and fragments were end-repaired, A-tailed, and ligated to Illumina adapters, followed by PCR amplification. PCR products were purified using AMPure XP beads (Beverly, USA). Library quality was assessed on an Agilent 5400 system, and concentrations were quantified by qPCR (1.5 nM). Qualified libraries were pooled and sequenced on Illumina platforms using the PE150 strategy at Novogene (Beijing, China). High-quality reads were assembled de novo using NOVOPlasty v4.3.5 ( Dierckxsens et al., 2017 ), with the plastomes of Astragalus agrestis Douglas ex G. Don and Oxytropis neimonggolica C.W. Chang & Y.Z. Zhao serving as seed references. The assembly generated a single circular chloroplast genome for each species without structural ambiguities. To assess assembly accuracy and sequencing depth, clean paired-end reads were aligned to the assembled plastomes using BWA-MEM v0.7.17 ( Li, 2013 ). Alignments were subsequently sorted and indexed with SAMtools v1.19.2 ( Li et al., 2009 ). Genome annotation was conducted in Geneious v9.0.2 ( Kearse et al., 2012 ) using closely related reference plastomes. Protein-coding genes, transfer RNAs, and ribosomal RNAs were annotated, and gene boundaries were manually curated to ensure accurate start/stop codons and intron–exon junctions. Furthermore, the cp map was generated using Chloroplot ( https://irscope.shinyapps.io/chloroplot/ ) ( Zheng et al., 2020 ). For several taxa included in the phylogenetic analysis, complete chloroplast genome sequences were not available in GenBank. Only raw sequencing data (SRA accessions; SRR numbers listed in Table 1 ) were available. Therefore, the chloroplast genomes of these taxa were assembled. A total of 119 complete chloroplast genome sequences were included in the phylogenetic analysis. Of these, two plastomes were newly sequenced in this study, while the remaining 117 sequences were downloaded from the NCBI GenBank database ( Table 1 ) . Complete chloroplast genome sequences were aligned using MAFFT ( Katoh & Standley, 2013 ). The alignment was manually inspected and used to reconstruct phylogenetic relationships under the maximum likelihood criterion in IQ-TREE 2 ( Minh et al., 2020 ). The best-fit substitution model was selected using ModelFinder ( Kalyaanamoorthy et al., 2017 ), and branch support was assessed with 1,000 ultrafast bootstrap replicates ( Hoang et al., 2018 ). Table 1. List of taxa included in the phylogenetic analysis, accession numbers. For taxa lacking published chloroplast genome accessions, plastomes were assembled in this study from raw reads downloaded from the NCBI Sequence Read Archive (SRR accessions provided). Species Accession Species Accession Astragalus camptodontus SRR12136586 A. aksuensis SRR12136588 A. confertus SRR12136589 A. massanderanus SRR12136591 A. handelii SRR12136594 A. zacharensis SRR12136595 A. uliginosus SRR12136597 A. koburensis SRR12136600 A. beketowii SRR12136611 A. jessenii SRR12136613 A. tibetanus SRR12136615 A. dendroides SRR12136619 A. candissimus SRR12136622 A. platyphyllus SRR12136623 A. himalayanus SRR12136624 A. roseus SRR12136625 A. stalinskii SRR12136626 A. orbicularifolius SRR12136627 A. hamosus SRR12136635 A. heinsensis SRR12136637 A. hoantchy SRR12136647 A. saccolacys SRR12136648 A. neomondelphus SRR12136653 A. schmalhausenii SRR12136654 A. zingeri SRR12136656 A. eximius SRR12136657 A. xanthomeloides SRR12136658 A. piletocladus SRR12136659 A. parrowianus SRR12136660 A. coluteocarpus SRR12136661 A. thurberi SRR12136664 A. americanus SRR12136665 A. peduncularis SRR12136666 A. dipelta SRR12136669 A. acaulis PV802397 A. austrotristis NC_063479 A. adsurgens NC_085710 A. angustidens ON550413 A. agrestis PP328800 A. alpinus NC_063482 A. ampullarius PV870668 A. arbuscula ON550410 A. arpilobus NC_063483 A. arrectus NC_047381 A. bhotanensis NC_063484 A. biristatus MZ923743 A. calycosus var. calycosus MZ725323 A. canadensis var. brevidens PV870770 A. chinensis NC_063486 A. clevelandii ON550409 A. cognatus MZ127832 A. chinense ON550407 A. dilutus PV870843 A. effusus MZ901207 A. flexuosus var. flexuosus ON550403 A. flexus NC_083391 A. floridus NC_058825 A. galactites OY754317 A. glycyphyllos MY746310 A. gummifer NC_063487 A. gypsodes LC764834 A. iranicus NC_077545 A. juanquensis PV798172 A. khasianus ON550401 A. laksamanni NC_085734 A. leucocephalus ON550399 A. lithophilus PV870772 A. lonchocarpus LC764835 A. macropelmatus OP723863 A. melilotoides var. tenuis OP723862 A. membranaceus PV761671 A. membranaceus var. membranaceus KX255662 A. moseleios LC764836 A. mongholicus OR712437 A. mongholicus var. dahuricus MW719856 A. mongholicus var. nakaianus KR296789 A. muliensis NC_083909 A. neglectus NC_063488 A. nuratensis PX928918 A. obscurus NC_063489 A. odoratus LC764837 A. oxylottis NC_077543 A. pallasi NC_077542 A. polysladus PV910879 A. psilosepalus NC_083910 A. purpurinus OR652287 A. rumpens PX711949 A. scaberrimus MW654102 A. sereno var. sereno MZ923754 A. sieversianus NC_077540 A. sinicus OM287552 A. stipulatus OR491698 A. strictus MT120746 A. toanus var. toanus MZ923756 A. tongolensis PX754582 A. tumabtsica NC_083912 A. vulpinus ON550388 A. wootonii var. wootonii MZ923757 A. yunnanensis subsp. incanus PV156653 A. zerabulaki PX711948 Oxytropis chiliophylla PV694277 O. filiformis PV684033 O. latibracteata PV694278 Oplonia microphylla PV684029 O. neimongolica PV684030 O. proboscidea PX512474 O. pseudorosea PV684035 O. sp. TT4869–1 PX652196 Tibetia liangshanensis MF193597 Alhagi sparsifolia MW349013 Caragana korshinskii KX289923 Hedysarum taipeicum MK426698 Caragana microphylla KX289922 Corethrodendron multijugum OP748243 Carmichaelia australis PV870797 Phyllolobium chinense MZ221114 Phyllolobium camptodontum SRR12136586 Lessertia frutescens MF286764 Sphaerophysa salsula PV870675 Results Genome skimming generated a total of 39,668,027 paired-end reads for A. nuratensis and 16,998,801 paired-end reads for O. pseudorosea. After quality filtering, 39,666,696 and 16,994,332 reads were retained as high-quality reads for A. nuratensis and O. pseudorosea , respectively. Mapping of the filtered reads to the assembled chloroplast reference genomes showed that 540,829 reads (1.36%) in A. nuratensis and 1,421,542 reads (8.36%) in O. pseudorosea were successfully aligned. Properly paired reads accounted for 1.33% and 8.27% of the total reads, respectively. The chloroplast genome of Astragalus nuratensis was recovered with a mean sequencing depth of 638.13×. In contrast, the chloroplast genome of O. pseudorosea exhibited a substantially higher mean sequencing depth of 1,725.34×. The complete chloroplast genome of O. pseudorosea was 122,708 bp in length, whereas that of A. nuratensis was 122,316 bp. Both genomes encoded a total of 110 unique genes, including 76 protein-coding genes (CDS), 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes ( Figure 1 ). Consistent with other members of the inverted repeat–lacking clade (IRLC) of legumes, the typical inverted repeat regions were absent in both species, resulting in a single-copy chloroplast genome structure, a feature commonly reported in plastome studies of Astragalus and related taxa ( Moghaddam et al., 2023 ; Ma et al., 2025 ; Li et al., 2025 ). Figure 1. The circular map of the chloroplast genomes of Astragalus nuratensis was drawn using the Chloroplot to show the genes present in each region (LSC, SSC, and IRs). The transcription directions for the inner and outer genes are clockwise and anticlockwise, respectively, and each functional group of genes is distinctively color-marked. In the inner circle, the darker gray shades represent the GC content, and the lighter gray shades signify the AT content. Maximum likelihood analysis based on complete chloroplast genome sequences resolved the sampled taxa into several well-supported clades corresponding to recognized infrageneric groups within Astragalus and related genera ( Figure 2 ). Most backbone nodes received strong bootstrap support (BS ≥ 95), indicating a stable phylogenetic structure. The overall topology was consistent with previous phylogenomic studies of Astragalus , which also recovered major lineages with strong support using plastome and target-enrichment data ( Su et al., 2021 ; Buono et al., 2025 ). Figure 2. Maximum likelihood phylogenetic tree inferred from complete chloroplast genome sequences showing the relationships of Astragalus nuratensis , Oxytropis pseudorosea , and other members of the inverted repeat–lacking clade (IRLC). Species of Astragalus were distributed among the major lineages corresponding to the Hypoglottis, Neo-Astragalus, Diholcos, Astracantha, Contortuplicata, Hamosa, Trimeniaeus, and Phaca clades. Among these, the Phaca clade represented one of the largest lineages and included A. nuratensis , which grouped with other members of this clade with strong bootstrap support. Species of Oxytropis , including O. pseudorosea , formed a distinct and well-supported lineage corresponding to the Oxytropis + Coluteoid clade, clearly separated from the main Astragalus lineages, in agreement with previous plastome-based phylogenies ( Buono et al., 2025 ). In the phylogenetic tree, A. zerabulaki , another endemic species, was resolved within the Hypoglottis clade and formed a well-supported sister relationship with A. rumpens , indicating close evolutionary relationships among members of this lineage. Data availability NCBI BioProject: Raw sequencing data for Astragalus nuratensis and Oxytropis pseudorosea. Accession number PRJNA1425239. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1425239 ( Karimov, 2026a ). NCBI Sequence Read Archive (SRA): Raw sequencing data of Astragalus nuratensis and Oxytropis pseudorosea. Accession numbers SRR37271903 and SRR37271902; https://www.ncbi.nlm.nih.gov/sra/?term=SRR37271903 ; https://www.ncbi.nlm.nih.gov/sra/?term=SRR37271902 ( Karimov, 2026b ). NCBI GenBank: Chloroplast genomes of Astragalus nuratensis and Oxytropis pseudorosea. Accession numbers PX928918 and PX512474; https://www.ncbi.nlm.nih.gov/nuccore/PX928918.1 ; https://www.ncbi.nlm.nih.gov/nuccore/PX512474.1 ( Karimov, 2026c ). Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0). References Azani N, Babineau M, Bailey CD, et al. : A New Subfamily Classification of the Leguminosae Based on a Taxonomically Comprehensive Phylogeny: The Legume Phylogeny Working Group (LPWG). Taxon. 2017; 66 : 44–77. Publisher Full Text Buono D, Kadereit G, Liston A, et al. : Building a robust backbone for Astragalus using a clade-specific target enrichment bait set. Am. J. Bot. 2025; 112 (8): e70084. Publisher Full Text Cai Z, Guisinger M, Kim H-G, et al. : Extensive Reorganization of the Plastid Genome of Trifolium Subterraneum (Fabaceae) Is Associated with Numerous Repeated Sequences and Novel DNA Insertions. J. Mol. Evol. 2008; 67 : 696–704. Publisher 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): e18. Hoang DT, Chernomor O, von Haeseler A , et al. : UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 2018; 35 (2): 518–522. Publisher Full Text Kalyaanamoorthy S, Minh BQ, Wong TKF, et al. : ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods. 2017; 14 : 587–589. Publisher Full Text Karimov B: Raw sequencing data of Astragalus nuratensis and Oxytropis pseudorosea. [Dataset]. NCBI BioProject. PRJNA1425239. 2026a. Reference Source Karimov B: Raw sequencing reads of Astragalus nuratensis and Oxytropis pseudorosea. [Dataset]. NCBI Sequence Read Archive (SRA). SRR37271903, SRR37271902. 2026b. Reference Source Karimov B: Chloroplast genomes of Astragalus nuratensis and Oxytropis pseudorosea. [Dataset]. GenBank. PX928918, PX512474. 2026c. Reference Source Karimov B, Tojibaev SK, Azimova D, et al. : Comparative analysis of complete chloroplast genomes of Cousinia (Asteraceae) species. Front. Plant Sci. 2025; 16 : 1522950. Publisher Full Text Katoh K, Standley DM: MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013; 30 (4): 772–780. Publisher Full Text Kearse M, Moir R, Wilson A, et al. : Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28 (12): 1647–1649. Publisher Full Text Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arxiv:1303.3997. 2013. 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Publisher Full Text Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 27 Mar 2026 ADD YOUR COMMENT Comment Author details Author details 1 Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan 2 Bukhara State University, Bukhara, Uzbekistan 3 Navoi State University, Navoi, Uzbekistan 4 Samarkand State Medical University, Samarkand, Uzbekistan 5 Bukhara state medical institute named after Abu Ali ibn Sino, Bukhara, Uzbekistan 6 Karshi State University, Qarshi, Kashkadarya Province, Uzbekistan 7 Turan University, Karshi, Uzbekistan 8 Jizzakh State Pedagogical University, Jizzakh, Uzbekistan 9 Tashkent Botanical Garden under the Institute of Botany, Academy of Sciences, Tashkent, Uzbekistan Diyorjon Hamrayev Roles: Writing – Original Draft Preparation Bobur Karimov Roles: Writing – Original Draft Preparation, Writing – Review & Editing Husniddin Esanov Roles: Writing – Original Draft Preparation Sodik Khuzhzhiev Roles: Writing – Original Draft Preparation Maxzuna Nasretdinova Roles: Writing – Original Draft Preparation Oysha Jabborova Roles: Writing – Original Draft Preparation Oybek Omonov Roles: Writing – Original Draft Preparation Mohistara Sharipova Roles: Writing – Original Draft Preparation Ziyoviddin Yusupov Roles: Conceptualization, Writing – Original Draft Preparation, Writing – Review & Editing Alijon Esankulov Roles: Writing – Original Draft Preparation Competing interests No competing interests were disclosed. Grant information This work was supported by the project “Digital Nature: Development of a digital platform for the flora of Central Uzbekistan” (2025–2029), implemented by the Institute of Botany, Academy of Sciences of the Republic of Uzbekistan. Additional support was provided by the project “Assessing climate change adaptation in endangered plants of Uzbekistan: A DNA barcoding approach” (AL-9224104464). The funders had no role in study design, data collection, analysis, decision to publish, or preparation of the manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Article Versions (2) version 2 Revised Published: 14 May 2026, 15:445 https://doi.org/10.12688/f1000research.178398.2 version 1 Published: 27 Mar 2026, 15:445 https://doi.org/10.12688/f1000research.178398.1 Copyright © 2026 Hamrayev D 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 Hamrayev D, Karimov B, Esanov H et al. Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.12688/f1000research.178398.1 ) 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 1 VERSION 1 PUBLISHED 27 Mar 2026 Views 0 Cite How to cite this report: Fukasawa Y. Reviewer Report For: Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.5256/f1000research.196779.r473037 ) The direct URL for this report is: https://f1000research.com/articles/15-445/v1#referee-response-473037 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 27 Apr 2026 Yoshinori Fukasawa , Center for Bioscience Research and Education Utsunomiya University, Tochigi, Japan Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.196779.r473037 Dear Authors, Thank you for reporting the complete chloroplast genomes of Astragalus nuratensis and Oxytropis pseudorosea . The addition of new plastome resources for Astragalus and Oxytropis—two of the largest and most taxonomically challenging genera in the inverted ... Continue reading READ ALL Dear Authors, Thank you for reporting the complete chloroplast genomes of Astragalus nuratensis and Oxytropis pseudorosea . The addition of new plastome resources for Astragalus and Oxytropis—two of the largest and most taxonomically challenging genera in the inverted repeat–lacking clade (IRLC)—is a welcome contribution, particularly given the ongoing interest in plastome evolution within this clade. Below I offer several suggestions that I believe would strengthen the manuscript. 1. Citation for the conserved quadripartite structure of chloroplast genomes In the Introduction, the conserved quadripartite structure of angiosperm chloroplast genomes is cited as (Karimov et al. 2025). However, this is a well-established and broadly recognized feature of plastome architecture that has been described in numerous foundational works. The cited reference reports chloroplast genomes of Cousinia (Asteraceae) species and, while a valuable study in its own right, does not serve as a primary or representative source for this general statement. I would suggest replacing it with one or more widely cited references that originally established this structural model. 2. Chloroplast genome map of Oxytropis pseudorosea Figure 1 presents the chloroplast genome map of A. nuratensis only. Since the manuscript reports two newly sequenced plastomes, I would recommend including a corresponding genome map of O. pseudorosea as well, either as an additional panel in Figure 1 or as a separate figure. This would provide a more balanced presentation of the two genomes. 3. Discrepancy in gene counts between Figure 1 and the text The main text states that both genomes encode 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes (110 unique genes total). However, the annotation within Figure 1 indicates "77 genes; 4 rRNAs; 30 tRNAs" for A. nuratensis . Please verify and reconcile these numbers to ensure consistency between the figure and the text. 4. Assembly validation metrics The authors report mapping clean reads back to the assembled plastomes using BWA-MEM, which is an appropriate approach. However, the current manuscript reports only the mean sequencing depth. To further support the completeness and accuracy of the assemblies, I would suggest briefly reporting additional validation metrics, such as: (i) whether any gaps or regions of zero coverage were observed, (ii) the minimum and maximum coverage across the genome, and/or (iii) a coverage depth plot provided as supplementary material. These additions would allow readers to better assess the quality of the assembled sequences. 5. Reporting gene loss, pseudogenization, and intron loss in the IRLC context The Introduction appropriately highlights that IRLC plastomes frequently exhibit gene loss or pseudogenization (e.g., rps16, rpl22, infA, accD, ycf4 ) and intron loss (e.g., in clpP, atpF, rpoC1 ). However, the Results section does not describe which of these events, if any, were observed in the two newly sequenced plastomes. Even a brief statement confirming or contrasting the gene/intron content of A. nuratensis and O. pseudorosea with that of other IRLC members would add informative context to the genome descriptions and enhance the value of this report as a genomic resource. Summary This manuscript provides new plastome data for two IRLC species from Central Asia and meets the essential criteria for a Genome Note. The assembly and analytical approaches are technically appropriate. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Plant genomics and bioinformatics 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: Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.5256/f1000research.196779.r473037 ) The direct URL for this report is: https://f1000research.com/articles/15-445/v1#referee-response-473037 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 14 May 2026 Bobur Karimov , Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan 14 May 2026 Author Response Reviewer 2 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the constructive comments, which have helped improve the clarity and quality of the study. ... Continue reading Reviewer 2 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the constructive comments, which have helped improve the clarity and quality of the study. Below we provide point-by-point responses. 1. Citation for the conserved quadripartite structure of chloroplast genomes In the Introduction, the conserved quadripartite structure of angiosperm chloroplast genomes is cited as (Karimov et al. 2025). However, this is a well-established and broadly recognized feature of plastome architecture that has been described in numerous foundational works. The cited reference reports chloroplast genomes of Cousinia (Asteraceae) species and, while a valuable study in its own right, does not serve as a primary or representative source for this general statement. I would suggest replacing it with one or more widely cited references that originally established this structural model. Response: A more appropriate and widely accepted reference has been added to support the conserved quadripartite structure of angiosperm chloroplast genomes. 2. Chloroplast genome map of Oxytropis pseudorosea Figure 1 presents the chloroplast genome map of A. nuratensis only. Since the manuscript reports two newly sequenced plastomes, I would recommend including a corresponding genome map of O. pseudorosea as well, either as an additional panel in Figure 1 or as a separate figure. This would provide a more balanced presentation of the two genomes. Response: The chloroplast genome map of Oxytropis pseudorosea has been added accordingly to provide balanced visualization of both plastomes. 3. Discrepancy in gene counts between Figure 1 and the text The main text states that both genomes encode 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes (110 unique genes total). However, the annotation within Figure 1 indicates "77 genes; 4 rRNAs; 30 tRNAs" for A. nuratensis. Please verify and reconcile these numbers to ensure consistency between the figure and the text. Response: The gene annotation has been carefully checked, and inconsistencies between the figure and the text have been corrected to ensure full consistency. 4. Assembly validation metrics The authors report mapping clean reads back to the assembled plastomes using BWA-MEM, which is an appropriate approach. However, the current manuscript reports only the mean sequencing depth. To further support the completeness and accuracy of the assemblies, I would suggest briefly reporting additional validation metrics, such as: (i) whether any gaps or regions of zero coverage were observed, (ii) the minimum and maximum coverage across the genome, and/or (iii) a coverage depth plot provided as supplementary material. These additions would allow readers to better assess the quality of the assembled sequences. Response: Additional assembly validation metrics have been included, including minimum and maximum coverage values, assessment of zero-coverage regions, and a coverage depth plot provided as Figure 1. 5. Reporting gene loss, pseudogenization, and intron loss in the IRLC context The Introduction appropriately highlights that IRLC plastomes frequently exhibit gene loss or pseudogenization (e.g., rps16, rpl22, infA, accD, ycf4) and intron loss (e.g., in clpP, atpF, rpoC1). However, the Results section does not describe which of these events, if any, were observed in the two newly sequenced plastomes. Even a brief statement confirming or contrasting the gene/intron content of A. nuratensis and O. pseudorosea with that of other IRLC members would add informative context to the genome descriptions and enhance the value of this report as a genomic resource. Response: A brief description of gene content and intron structure has been added to the Results comparison with typical IRLC characteristics. Reviewer 2 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the constructive comments, which have helped improve the clarity and quality of the study. Below we provide point-by-point responses. 1. Citation for the conserved quadripartite structure of chloroplast genomes In the Introduction, the conserved quadripartite structure of angiosperm chloroplast genomes is cited as (Karimov et al. 2025). However, this is a well-established and broadly recognized feature of plastome architecture that has been described in numerous foundational works. The cited reference reports chloroplast genomes of Cousinia (Asteraceae) species and, while a valuable study in its own right, does not serve as a primary or representative source for this general statement. I would suggest replacing it with one or more widely cited references that originally established this structural model. Response: A more appropriate and widely accepted reference has been added to support the conserved quadripartite structure of angiosperm chloroplast genomes. 2. Chloroplast genome map of Oxytropis pseudorosea Figure 1 presents the chloroplast genome map of A. nuratensis only. Since the manuscript reports two newly sequenced plastomes, I would recommend including a corresponding genome map of O. pseudorosea as well, either as an additional panel in Figure 1 or as a separate figure. This would provide a more balanced presentation of the two genomes. Response: The chloroplast genome map of Oxytropis pseudorosea has been added accordingly to provide balanced visualization of both plastomes. 3. Discrepancy in gene counts between Figure 1 and the text The main text states that both genomes encode 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes (110 unique genes total). However, the annotation within Figure 1 indicates "77 genes; 4 rRNAs; 30 tRNAs" for A. nuratensis. Please verify and reconcile these numbers to ensure consistency between the figure and the text. Response: The gene annotation has been carefully checked, and inconsistencies between the figure and the text have been corrected to ensure full consistency. 4. Assembly validation metrics The authors report mapping clean reads back to the assembled plastomes using BWA-MEM, which is an appropriate approach. However, the current manuscript reports only the mean sequencing depth. To further support the completeness and accuracy of the assemblies, I would suggest briefly reporting additional validation metrics, such as: (i) whether any gaps or regions of zero coverage were observed, (ii) the minimum and maximum coverage across the genome, and/or (iii) a coverage depth plot provided as supplementary material. These additions would allow readers to better assess the quality of the assembled sequences. Response: Additional assembly validation metrics have been included, including minimum and maximum coverage values, assessment of zero-coverage regions, and a coverage depth plot provided as Figure 1. 5. Reporting gene loss, pseudogenization, and intron loss in the IRLC context The Introduction appropriately highlights that IRLC plastomes frequently exhibit gene loss or pseudogenization (e.g., rps16, rpl22, infA, accD, ycf4) and intron loss (e.g., in clpP, atpF, rpoC1). However, the Results section does not describe which of these events, if any, were observed in the two newly sequenced plastomes. Even a brief statement confirming or contrasting the gene/intron content of A. nuratensis and O. pseudorosea with that of other IRLC members would add informative context to the genome descriptions and enhance the value of this report as a genomic resource. Response: A brief description of gene content and intron structure has been added to the Results comparison with typical IRLC characteristics. Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 14 May 2026 Bobur Karimov , Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan 14 May 2026 Author Response Reviewer 2 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the constructive comments, which have helped improve the clarity and quality of the study. ... Continue reading Reviewer 2 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the constructive comments, which have helped improve the clarity and quality of the study. Below we provide point-by-point responses. 1. Citation for the conserved quadripartite structure of chloroplast genomes In the Introduction, the conserved quadripartite structure of angiosperm chloroplast genomes is cited as (Karimov et al. 2025). However, this is a well-established and broadly recognized feature of plastome architecture that has been described in numerous foundational works. The cited reference reports chloroplast genomes of Cousinia (Asteraceae) species and, while a valuable study in its own right, does not serve as a primary or representative source for this general statement. I would suggest replacing it with one or more widely cited references that originally established this structural model. Response: A more appropriate and widely accepted reference has been added to support the conserved quadripartite structure of angiosperm chloroplast genomes. 2. Chloroplast genome map of Oxytropis pseudorosea Figure 1 presents the chloroplast genome map of A. nuratensis only. Since the manuscript reports two newly sequenced plastomes, I would recommend including a corresponding genome map of O. pseudorosea as well, either as an additional panel in Figure 1 or as a separate figure. This would provide a more balanced presentation of the two genomes. Response: The chloroplast genome map of Oxytropis pseudorosea has been added accordingly to provide balanced visualization of both plastomes. 3. Discrepancy in gene counts between Figure 1 and the text The main text states that both genomes encode 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes (110 unique genes total). However, the annotation within Figure 1 indicates "77 genes; 4 rRNAs; 30 tRNAs" for A. nuratensis. Please verify and reconcile these numbers to ensure consistency between the figure and the text. Response: The gene annotation has been carefully checked, and inconsistencies between the figure and the text have been corrected to ensure full consistency. 4. Assembly validation metrics The authors report mapping clean reads back to the assembled plastomes using BWA-MEM, which is an appropriate approach. However, the current manuscript reports only the mean sequencing depth. To further support the completeness and accuracy of the assemblies, I would suggest briefly reporting additional validation metrics, such as: (i) whether any gaps or regions of zero coverage were observed, (ii) the minimum and maximum coverage across the genome, and/or (iii) a coverage depth plot provided as supplementary material. These additions would allow readers to better assess the quality of the assembled sequences. Response: Additional assembly validation metrics have been included, including minimum and maximum coverage values, assessment of zero-coverage regions, and a coverage depth plot provided as Figure 1. 5. Reporting gene loss, pseudogenization, and intron loss in the IRLC context The Introduction appropriately highlights that IRLC plastomes frequently exhibit gene loss or pseudogenization (e.g., rps16, rpl22, infA, accD, ycf4) and intron loss (e.g., in clpP, atpF, rpoC1). However, the Results section does not describe which of these events, if any, were observed in the two newly sequenced plastomes. Even a brief statement confirming or contrasting the gene/intron content of A. nuratensis and O. pseudorosea with that of other IRLC members would add informative context to the genome descriptions and enhance the value of this report as a genomic resource. Response: A brief description of gene content and intron structure has been added to the Results comparison with typical IRLC characteristics. Reviewer 2 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the constructive comments, which have helped improve the clarity and quality of the study. Below we provide point-by-point responses. 1. Citation for the conserved quadripartite structure of chloroplast genomes In the Introduction, the conserved quadripartite structure of angiosperm chloroplast genomes is cited as (Karimov et al. 2025). However, this is a well-established and broadly recognized feature of plastome architecture that has been described in numerous foundational works. The cited reference reports chloroplast genomes of Cousinia (Asteraceae) species and, while a valuable study in its own right, does not serve as a primary or representative source for this general statement. I would suggest replacing it with one or more widely cited references that originally established this structural model. Response: A more appropriate and widely accepted reference has been added to support the conserved quadripartite structure of angiosperm chloroplast genomes. 2. Chloroplast genome map of Oxytropis pseudorosea Figure 1 presents the chloroplast genome map of A. nuratensis only. Since the manuscript reports two newly sequenced plastomes, I would recommend including a corresponding genome map of O. pseudorosea as well, either as an additional panel in Figure 1 or as a separate figure. This would provide a more balanced presentation of the two genomes. Response: The chloroplast genome map of Oxytropis pseudorosea has been added accordingly to provide balanced visualization of both plastomes. 3. Discrepancy in gene counts between Figure 1 and the text The main text states that both genomes encode 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes (110 unique genes total). However, the annotation within Figure 1 indicates "77 genes; 4 rRNAs; 30 tRNAs" for A. nuratensis. Please verify and reconcile these numbers to ensure consistency between the figure and the text. Response: The gene annotation has been carefully checked, and inconsistencies between the figure and the text have been corrected to ensure full consistency. 4. Assembly validation metrics The authors report mapping clean reads back to the assembled plastomes using BWA-MEM, which is an appropriate approach. However, the current manuscript reports only the mean sequencing depth. To further support the completeness and accuracy of the assemblies, I would suggest briefly reporting additional validation metrics, such as: (i) whether any gaps or regions of zero coverage were observed, (ii) the minimum and maximum coverage across the genome, and/or (iii) a coverage depth plot provided as supplementary material. These additions would allow readers to better assess the quality of the assembled sequences. Response: Additional assembly validation metrics have been included, including minimum and maximum coverage values, assessment of zero-coverage regions, and a coverage depth plot provided as Figure 1. 5. Reporting gene loss, pseudogenization, and intron loss in the IRLC context The Introduction appropriately highlights that IRLC plastomes frequently exhibit gene loss or pseudogenization (e.g., rps16, rpl22, infA, accD, ycf4) and intron loss (e.g., in clpP, atpF, rpoC1). However, the Results section does not describe which of these events, if any, were observed in the two newly sequenced plastomes. Even a brief statement confirming or contrasting the gene/intron content of A. nuratensis and O. pseudorosea with that of other IRLC members would add informative context to the genome descriptions and enhance the value of this report as a genomic resource. Response: A brief description of gene content and intron structure has been added to the Results comparison with typical IRLC characteristics. Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Do HDK. Reviewer Report For: Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.5256/f1000research.196779.r471852 ) The direct URL for this report is: https://f1000research.com/articles/15-445/v1#referee-response-471852 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 Apr 2026 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.196779.r471852 Dear Authors, Thank you very much for adding new genomic data about Astragalus and Oxytropis species. The content of the manuscript is suitable for Genome Note of F1000 Research. Please check my comment below. 1/ Please ... Continue reading READ ALL Dear Authors, Thank you very much for adding new genomic data about Astragalus and Oxytropis species. The content of the manuscript is suitable for Genome Note of F1000 Research. Please check my comment below. 1/ Please update the role of authors because most authors are for writing the manuscript. Who did the sampling, experiment, and analyzing the data? 2/ "Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers." Please add references for this statement. 3/ "In most angiosperms, the cp genome exhibits a conserved quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Karimov et al., 2025)." the current reference is not suitable for the statement because Karimov et al 2025 only reported complete chloroplast genomes of six Cousinia (Asteraceae) species which are not representative for most angiosperms. 4/ Please use italic font for gene names in the Introduction part. 5/ It would be better if the authors add introduction about the published chloroplast genomes of Astragalus and Oxytropis, especially Astragalus zerabulaki which was mentioned at the end of the manuscript. 6/ "Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002."; "Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively." please revise these sentences to clarify which feature is of Astragalus nuratensis and which information belongs to Oxytropis pseudorosea. 7/ "High-quality reads were assembled de novo using NOVOPlasty v4.3.5" how to get high-quality reads? Please add. 8/ "For several taxa included in the phylogenetic analysis, complete chloroplast genome sequences were not available in GenBank. Only raw sequencing data (SRA accessions; SRR numbers listed in Table 1) were available. Therefore, the chloroplast genomes of these taxa were assembled." How to complete chloroplast genomes from SRA data? Please add. 9/ Because the manuscript reports two chloroplast genome, it would be better if the authors add the chloroplast genome map of O. pseudorosea in Figure 1. 10/ "Table 1. List of taxa included in the phylogenetic analysis, accession numbers." Please revise Table 1 caption. 11/ Please correct accession number of O. pseudorosea which is not PV684035 from GenBank database in Table 1. Thank you. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Plant Chloroplast genomes I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Do HDK. Reviewer Report For: Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.5256/f1000research.196779.r471852 ) The direct URL for this report is: https://f1000research.com/articles/15-445/v1#referee-response-471852 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 14 May 2026 Bobur Karimov , Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan 14 May 2026 Author Response Reviewer 1 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the valuable comments, which helped improve the quality of the work. Below we provide ... Continue reading Reviewer 1 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the valuable comments, which helped improve the quality of the work. Below we provide point-by-point responses. Comment 1/ Please update the role of authors because most authors are for writing the manuscript. Who did the sampling, experiment, and analyzing the data? Response: The system did not provide an option to edit and resubmit the updated version with revised author contributions. Comment 2/ "Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers." Please add references for this statement. Response: Appropriate references have been added to support this statement in the revised manuscript. Comment 3/ "In most angiosperms, the cp genome exhibits a conserved quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Karimov et al., 2025)." the current reference is not suitable for the statement because Karimov et al 2025 only reported complete chloroplast genomes of six Cousinia (Asteraceae) species which are not representative for most angiosperms. Response: A more appropriate and widely accepted reference has been added to support this statement. Comment 4/ Please use italic font for gene names in the Introduction part. Response: Gene names in the Introduction have been corrected and formatted in italics. Comment 5/ It would be better if the authors add introduction about the published chloroplast genomes of Astragalus and Oxytropis, especially Astragalus zerabulaki which was mentioned at the end of the manuscript. Response: A new introductory paragraph has been added covering published chloroplast genomes of Astragalus and Oxytropis Comment 6/ "Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002."; "Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively." please revise these sentences to clarify which feature is of Astragalus nuratensis and which information belongs to Oxytropis pseudorosea. Response: The sentences have been revised to clearly distinguish species-specific voucher information and sequencing depth values. Comment 7/ "High-quality reads were assembled de novo using NOVOPlasty v4.3.5" how to get high-quality reads? Please add. Response: Raw sequencing reads were directly used, and NOVOPlasty performs internal quality filtering during the assembly process. Comment 8/ "For several taxa included in the phylogenetic analysis, complete chloroplast genome sequences were not available in GenBank. Only raw sequencing data (SRA accessions; SRR numbers listed in Table 1) were available. Therefore, the chloroplast genomes of these taxa were assembled." How to complete chloroplast genomes from SRA data? Please add.from SRA to novoplasty Response: Raw sequencing data were downloaded from SRA and assembled into chloroplast genomes using NOVOPlasty following the same assembly workflow. Comment 9/ Because the manuscript reports two chloroplast genome, it would be better if the authors add the chloroplast genome map of O. pseudorosea in Figure 1. Response: The chloroplast genome map of Oxytropis pseudorosea has been added to Figure 1. Comment 10/ "Table 1. List of taxa included in the phylogenetic analysis, accession numbers." Please revise Table 1 caption. Response: The caption of Table 1 has been revised for clarity and consistency. Comment 11/ Please correct accession number of O. pseudorosea which is not PV684035 from GenBank database in Table 1. Response: The accession number has been corrected according to the GenBank database. Reviewer 1 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the valuable comments, which helped improve the quality of the work. Below we provide point-by-point responses. Comment 1/ Please update the role of authors because most authors are for writing the manuscript. Who did the sampling, experiment, and analyzing the data? Response: The system did not provide an option to edit and resubmit the updated version with revised author contributions. Comment 2/ "Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers." Please add references for this statement. Response: Appropriate references have been added to support this statement in the revised manuscript. Comment 3/ "In most angiosperms, the cp genome exhibits a conserved quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Karimov et al., 2025)." the current reference is not suitable for the statement because Karimov et al 2025 only reported complete chloroplast genomes of six Cousinia (Asteraceae) species which are not representative for most angiosperms. Response: A more appropriate and widely accepted reference has been added to support this statement. Comment 4/ Please use italic font for gene names in the Introduction part. Response: Gene names in the Introduction have been corrected and formatted in italics. Comment 5/ It would be better if the authors add introduction about the published chloroplast genomes of Astragalus and Oxytropis, especially Astragalus zerabulaki which was mentioned at the end of the manuscript. Response: A new introductory paragraph has been added covering published chloroplast genomes of Astragalus and Oxytropis Comment 6/ "Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002."; "Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively." please revise these sentences to clarify which feature is of Astragalus nuratensis and which information belongs to Oxytropis pseudorosea. Response: The sentences have been revised to clearly distinguish species-specific voucher information and sequencing depth values. Comment 7/ "High-quality reads were assembled de novo using NOVOPlasty v4.3.5" how to get high-quality reads? Please add. Response: Raw sequencing reads were directly used, and NOVOPlasty performs internal quality filtering during the assembly process. Comment 8/ "For several taxa included in the phylogenetic analysis, complete chloroplast genome sequences were not available in GenBank. Only raw sequencing data (SRA accessions; SRR numbers listed in Table 1) were available. Therefore, the chloroplast genomes of these taxa were assembled." How to complete chloroplast genomes from SRA data? Please add.from SRA to novoplasty Response: Raw sequencing data were downloaded from SRA and assembled into chloroplast genomes using NOVOPlasty following the same assembly workflow. Comment 9/ Because the manuscript reports two chloroplast genome, it would be better if the authors add the chloroplast genome map of O. pseudorosea in Figure 1. Response: The chloroplast genome map of Oxytropis pseudorosea has been added to Figure 1. Comment 10/ "Table 1. List of taxa included in the phylogenetic analysis, accession numbers." Please revise Table 1 caption. Response: The caption of Table 1 has been revised for clarity and consistency. Comment 11/ Please correct accession number of O. pseudorosea which is not PV684035 from GenBank database in Table 1. Response: The accession number has been corrected according to the GenBank database. Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 14 May 2026 Bobur Karimov , Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan 14 May 2026 Author Response Reviewer 1 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the valuable comments, which helped improve the quality of the work. Below we provide ... Continue reading Reviewer 1 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the valuable comments, which helped improve the quality of the work. Below we provide point-by-point responses. Comment 1/ Please update the role of authors because most authors are for writing the manuscript. Who did the sampling, experiment, and analyzing the data? Response: The system did not provide an option to edit and resubmit the updated version with revised author contributions. Comment 2/ "Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers." Please add references for this statement. Response: Appropriate references have been added to support this statement in the revised manuscript. Comment 3/ "In most angiosperms, the cp genome exhibits a conserved quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Karimov et al., 2025)." the current reference is not suitable for the statement because Karimov et al 2025 only reported complete chloroplast genomes of six Cousinia (Asteraceae) species which are not representative for most angiosperms. Response: A more appropriate and widely accepted reference has been added to support this statement. Comment 4/ Please use italic font for gene names in the Introduction part. Response: Gene names in the Introduction have been corrected and formatted in italics. Comment 5/ It would be better if the authors add introduction about the published chloroplast genomes of Astragalus and Oxytropis, especially Astragalus zerabulaki which was mentioned at the end of the manuscript. Response: A new introductory paragraph has been added covering published chloroplast genomes of Astragalus and Oxytropis Comment 6/ "Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002."; "Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively." please revise these sentences to clarify which feature is of Astragalus nuratensis and which information belongs to Oxytropis pseudorosea. Response: The sentences have been revised to clearly distinguish species-specific voucher information and sequencing depth values. Comment 7/ "High-quality reads were assembled de novo using NOVOPlasty v4.3.5" how to get high-quality reads? Please add. Response: Raw sequencing reads were directly used, and NOVOPlasty performs internal quality filtering during the assembly process. Comment 8/ "For several taxa included in the phylogenetic analysis, complete chloroplast genome sequences were not available in GenBank. Only raw sequencing data (SRA accessions; SRR numbers listed in Table 1) were available. Therefore, the chloroplast genomes of these taxa were assembled." How to complete chloroplast genomes from SRA data? Please add.from SRA to novoplasty Response: Raw sequencing data were downloaded from SRA and assembled into chloroplast genomes using NOVOPlasty following the same assembly workflow. Comment 9/ Because the manuscript reports two chloroplast genome, it would be better if the authors add the chloroplast genome map of O. pseudorosea in Figure 1. Response: The chloroplast genome map of Oxytropis pseudorosea has been added to Figure 1. Comment 10/ "Table 1. List of taxa included in the phylogenetic analysis, accession numbers." Please revise Table 1 caption. Response: The caption of Table 1 has been revised for clarity and consistency. Comment 11/ Please correct accession number of O. pseudorosea which is not PV684035 from GenBank database in Table 1. Response: The accession number has been corrected according to the GenBank database. Reviewer 1 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the valuable comments, which helped improve the quality of the work. Below we provide point-by-point responses. Comment 1/ Please update the role of authors because most authors are for writing the manuscript. Who did the sampling, experiment, and analyzing the data? Response: The system did not provide an option to edit and resubmit the updated version with revised author contributions. Comment 2/ "Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers." Please add references for this statement. Response: Appropriate references have been added to support this statement in the revised manuscript. Comment 3/ "In most angiosperms, the cp genome exhibits a conserved quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Karimov et al., 2025)." the current reference is not suitable for the statement because Karimov et al 2025 only reported complete chloroplast genomes of six Cousinia (Asteraceae) species which are not representative for most angiosperms. Response: A more appropriate and widely accepted reference has been added to support this statement. Comment 4/ Please use italic font for gene names in the Introduction part. Response: Gene names in the Introduction have been corrected and formatted in italics. Comment 5/ It would be better if the authors add introduction about the published chloroplast genomes of Astragalus and Oxytropis, especially Astragalus zerabulaki which was mentioned at the end of the manuscript. Response: A new introductory paragraph has been added covering published chloroplast genomes of Astragalus and Oxytropis Comment 6/ "Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002."; "Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively." please revise these sentences to clarify which feature is of Astragalus nuratensis and which information belongs to Oxytropis pseudorosea. Response: The sentences have been revised to clearly distinguish species-specific voucher information and sequencing depth values. Comment 7/ "High-quality reads were assembled de novo using NOVOPlasty v4.3.5" how to get high-quality reads? Please add. Response: Raw sequencing reads were directly used, and NOVOPlasty performs internal quality filtering during the assembly process. Comment 8/ "For several taxa included in the phylogenetic analysis, complete chloroplast genome sequences were not available in GenBank. Only raw sequencing data (SRA accessions; SRR numbers listed in Table 1) were available. Therefore, the chloroplast genomes of these taxa were assembled." How to complete chloroplast genomes from SRA data? Please add.from SRA to novoplasty Response: Raw sequencing data were downloaded from SRA and assembled into chloroplast genomes using NOVOPlasty following the same assembly workflow. Comment 9/ Because the manuscript reports two chloroplast genome, it would be better if the authors add the chloroplast genome map of O. pseudorosea in Figure 1. Response: The chloroplast genome map of Oxytropis pseudorosea has been added to Figure 1. Comment 10/ "Table 1. List of taxa included in the phylogenetic analysis, accession numbers." Please revise Table 1 caption. Response: The caption of Table 1 has been revised for clarity and consistency. Comment 11/ Please correct accession number of O. pseudorosea which is not PV684035 from GenBank database in Table 1. Response: The accession number has been corrected according to the GenBank database. Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 27 Mar 2026 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 2 Version 2 (revision) 14 May 26 Version 1 27 Mar 26 read read Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam Yoshinori Fukasawa , Center for Bioscience Research and Education Utsunomiya University, Tochigi, Japan 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 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. 27 Apr 2026 | for Version 1 Yoshinori Fukasawa , Center for Bioscience Research and Education Utsunomiya University, Tochigi, Japan 0 Views copyright © 2026 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 (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 Dear Authors, Thank you for reporting the complete chloroplast genomes of Astragalus nuratensis and Oxytropis pseudorosea . The addition of new plastome resources for Astragalus and Oxytropis—two of the largest and most taxonomically challenging genera in the inverted repeat–lacking clade (IRLC)—is a welcome contribution, particularly given the ongoing interest in plastome evolution within this clade. Below I offer several suggestions that I believe would strengthen the manuscript. 1. Citation for the conserved quadripartite structure of chloroplast genomes In the Introduction, the conserved quadripartite structure of angiosperm chloroplast genomes is cited as (Karimov et al. 2025). However, this is a well-established and broadly recognized feature of plastome architecture that has been described in numerous foundational works. The cited reference reports chloroplast genomes of Cousinia (Asteraceae) species and, while a valuable study in its own right, does not serve as a primary or representative source for this general statement. I would suggest replacing it with one or more widely cited references that originally established this structural model. 2. Chloroplast genome map of Oxytropis pseudorosea Figure 1 presents the chloroplast genome map of A. nuratensis only. Since the manuscript reports two newly sequenced plastomes, I would recommend including a corresponding genome map of O. pseudorosea as well, either as an additional panel in Figure 1 or as a separate figure. This would provide a more balanced presentation of the two genomes. 3. Discrepancy in gene counts between Figure 1 and the text The main text states that both genomes encode 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes (110 unique genes total). However, the annotation within Figure 1 indicates "77 genes; 4 rRNAs; 30 tRNAs" for A. nuratensis . Please verify and reconcile these numbers to ensure consistency between the figure and the text. 4. Assembly validation metrics The authors report mapping clean reads back to the assembled plastomes using BWA-MEM, which is an appropriate approach. However, the current manuscript reports only the mean sequencing depth. To further support the completeness and accuracy of the assemblies, I would suggest briefly reporting additional validation metrics, such as: (i) whether any gaps or regions of zero coverage were observed, (ii) the minimum and maximum coverage across the genome, and/or (iii) a coverage depth plot provided as supplementary material. These additions would allow readers to better assess the quality of the assembled sequences. 5. Reporting gene loss, pseudogenization, and intron loss in the IRLC context The Introduction appropriately highlights that IRLC plastomes frequently exhibit gene loss or pseudogenization (e.g., rps16, rpl22, infA, accD, ycf4 ) and intron loss (e.g., in clpP, atpF, rpoC1 ). However, the Results section does not describe which of these events, if any, were observed in the two newly sequenced plastomes. Even a brief statement confirming or contrasting the gene/intron content of A. nuratensis and O. pseudorosea with that of other IRLC members would add informative context to the genome descriptions and enhance the value of this report as a genomic resource. Summary This manuscript provides new plastome data for two IRLC species from Central Asia and meets the essential criteria for a Genome Note. The assembly and analytical approaches are technically appropriate. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Plant genomics and bioinformatics 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 14 May 2026 Bobur Karimov, Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan Reviewer 2 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the constructive comments, which have helped improve the clarity and quality of the study. Below we provide point-by-point responses. 1. Citation for the conserved quadripartite structure of chloroplast genomes In the Introduction, the conserved quadripartite structure of angiosperm chloroplast genomes is cited as (Karimov et al. 2025). However, this is a well-established and broadly recognized feature of plastome architecture that has been described in numerous foundational works. The cited reference reports chloroplast genomes of Cousinia (Asteraceae) species and, while a valuable study in its own right, does not serve as a primary or representative source for this general statement. I would suggest replacing it with one or more widely cited references that originally established this structural model. Response: A more appropriate and widely accepted reference has been added to support the conserved quadripartite structure of angiosperm chloroplast genomes. 2. Chloroplast genome map of Oxytropis pseudorosea Figure 1 presents the chloroplast genome map of A. nuratensis only. Since the manuscript reports two newly sequenced plastomes, I would recommend including a corresponding genome map of O. pseudorosea as well, either as an additional panel in Figure 1 or as a separate figure. This would provide a more balanced presentation of the two genomes. Response: The chloroplast genome map of Oxytropis pseudorosea has been added accordingly to provide balanced visualization of both plastomes. 3. Discrepancy in gene counts between Figure 1 and the text The main text states that both genomes encode 76 protein-coding genes, 30 tRNA genes, and 4 rRNA genes (110 unique genes total). However, the annotation within Figure 1 indicates "77 genes; 4 rRNAs; 30 tRNAs" for A. nuratensis. Please verify and reconcile these numbers to ensure consistency between the figure and the text. Response: The gene annotation has been carefully checked, and inconsistencies between the figure and the text have been corrected to ensure full consistency. 4. Assembly validation metrics The authors report mapping clean reads back to the assembled plastomes using BWA-MEM, which is an appropriate approach. However, the current manuscript reports only the mean sequencing depth. To further support the completeness and accuracy of the assemblies, I would suggest briefly reporting additional validation metrics, such as: (i) whether any gaps or regions of zero coverage were observed, (ii) the minimum and maximum coverage across the genome, and/or (iii) a coverage depth plot provided as supplementary material. These additions would allow readers to better assess the quality of the assembled sequences. Response: Additional assembly validation metrics have been included, including minimum and maximum coverage values, assessment of zero-coverage regions, and a coverage depth plot provided as Figure 1. 5. Reporting gene loss, pseudogenization, and intron loss in the IRLC context The Introduction appropriately highlights that IRLC plastomes frequently exhibit gene loss or pseudogenization (e.g., rps16, rpl22, infA, accD, ycf4) and intron loss (e.g., in clpP, atpF, rpoC1). However, the Results section does not describe which of these events, if any, were observed in the two newly sequenced plastomes. Even a brief statement confirming or contrasting the gene/intron content of A. nuratensis and O. pseudorosea with that of other IRLC members would add informative context to the genome descriptions and enhance the value of this report as a genomic resource. Response: A brief description of gene content and intron structure has been added to the Results comparison with typical IRLC characteristics. View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Fukasawa Y. Peer Review Report For: Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.5256/f1000research.196779.r473037) 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/15-445/v1#referee-response-473037 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2026 Do H. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 03 Apr 2026 | for Version 1 Hoang Dang Khoa Do , Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, Vietnam 0 Views copyright © 2026 Do H. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Approved With Reservations info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Dear Authors, Thank you very much for adding new genomic data about Astragalus and Oxytropis species. The content of the manuscript is suitable for Genome Note of F1000 Research. Please check my comment below. 1/ Please update the role of authors because most authors are for writing the manuscript. Who did the sampling, experiment, and analyzing the data? 2/ "Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers." Please add references for this statement. 3/ "In most angiosperms, the cp genome exhibits a conserved quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Karimov et al., 2025)." the current reference is not suitable for the statement because Karimov et al 2025 only reported complete chloroplast genomes of six Cousinia (Asteraceae) species which are not representative for most angiosperms. 4/ Please use italic font for gene names in the Introduction part. 5/ It would be better if the authors add introduction about the published chloroplast genomes of Astragalus and Oxytropis, especially Astragalus zerabulaki which was mentioned at the end of the manuscript. 6/ "Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002."; "Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively." please revise these sentences to clarify which feature is of Astragalus nuratensis and which information belongs to Oxytropis pseudorosea. 7/ "High-quality reads were assembled de novo using NOVOPlasty v4.3.5" how to get high-quality reads? Please add. 8/ "For several taxa included in the phylogenetic analysis, complete chloroplast genome sequences were not available in GenBank. Only raw sequencing data (SRA accessions; SRR numbers listed in Table 1) were available. Therefore, the chloroplast genomes of these taxa were assembled." How to complete chloroplast genomes from SRA data? Please add. 9/ Because the manuscript reports two chloroplast genome, it would be better if the authors add the chloroplast genome map of O. pseudorosea in Figure 1. 10/ "Table 1. List of taxa included in the phylogenetic analysis, accession numbers." Please revise Table 1 caption. 11/ Please correct accession number of O. pseudorosea which is not PV684035 from GenBank database in Table 1. Thank you. Are the rationale for sequencing the genome and the species significance clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of the sequencing and extraction, software used, and materials provided to allow replication by others? Partly Are the datasets clearly presented in a usable and accessible format, and the assembly and annotation available in an appropriate subject-specific repository? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Plant Chloroplast genomes 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 14 May 2026 Bobur Karimov, Institute of Botany, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan Reviewer 1 We sincerely thank the reviewer for the careful evaluation of our manuscript and for the valuable comments, which helped improve the quality of the work. Below we provide point-by-point responses. Comment 1/ Please update the role of authors because most authors are for writing the manuscript. Who did the sampling, experiment, and analyzing the data? Response: The system did not provide an option to edit and resubmit the updated version with revised author contributions. Comment 2/ "Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers." Please add references for this statement. Response: Appropriate references have been added to support this statement in the revised manuscript. Comment 3/ "In most angiosperms, the cp genome exhibits a conserved quadripartite structure consisting of a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverted repeat (IR) regions (Karimov et al., 2025)." the current reference is not suitable for the statement because Karimov et al 2025 only reported complete chloroplast genomes of six Cousinia (Asteraceae) species which are not representative for most angiosperms. Response: A more appropriate and widely accepted reference has been added to support this statement. Comment 4/ Please use italic font for gene names in the Introduction part. Response: Gene names in the Introduction have been corrected and formatted in italics. Comment 5/ It would be better if the authors add introduction about the published chloroplast genomes of Astragalus and Oxytropis, especially Astragalus zerabulaki which was mentioned at the end of the manuscript. Response: A new introductory paragraph has been added covering published chloroplast genomes of Astragalus and Oxytropis Comment 6/ "Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002."; "Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638× and 1,725×, respectively." please revise these sentences to clarify which feature is of Astragalus nuratensis and which information belongs to Oxytropis pseudorosea. Response: The sentences have been revised to clearly distinguish species-specific voucher information and sequencing depth values. Comment 7/ "High-quality reads were assembled de novo using NOVOPlasty v4.3.5" how to get high-quality reads? Please add. Response: Raw sequencing reads were directly used, and NOVOPlasty performs internal quality filtering during the assembly process. Comment 8/ "For several taxa included in the phylogenetic analysis, complete chloroplast genome sequences were not available in GenBank. Only raw sequencing data (SRA accessions; SRR numbers listed in Table 1) were available. Therefore, the chloroplast genomes of these taxa were assembled." How to complete chloroplast genomes from SRA data? Please add.from SRA to novoplasty Response: Raw sequencing data were downloaded from SRA and assembled into chloroplast genomes using NOVOPlasty following the same assembly workflow. Comment 9/ Because the manuscript reports two chloroplast genome, it would be better if the authors add the chloroplast genome map of O. pseudorosea in Figure 1. Response: The chloroplast genome map of Oxytropis pseudorosea has been added to Figure 1. Comment 10/ "Table 1. List of taxa included in the phylogenetic analysis, accession numbers." Please revise Table 1 caption. Response: The caption of Table 1 has been revised for clarity and consistency. Comment 11/ Please correct accession number of O. pseudorosea which is not PV684035 from GenBank database in Table 1. Response: The accession number has been corrected according to the GenBank database. View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Do HDK. Peer Review Report For: Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan [version 1; peer review: 2 approved with reservations] . F1000Research 2026, 15 :445 ( https://doi.org/10.5256/f1000research.196779.r471852) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. 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