{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:44:34Z","timestamp":1791895474375,"version":"4.3.4"},"reference-count":19,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T00:00:00Z","timestamp":1774569600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>\n                    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,\n                    <ns3:italic>Astragalus nuratensis<\/ns3:italic>\n                    and\n                    <ns3:italic>Oxytropis pseudorosea.<\/ns3:italic>\n                    Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638\u00d7 and 1,725\u00d7, respectively. The chloroplast genomes were 122,316\u00a0bp in\n                    <ns3:italic>A. nuratensis<\/ns3:italic>\n                    and 122,708\u00a0bp in\n                    <ns3:italic>O. pseudorosea.<\/ns3:italic>\n                    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\u2013lacking 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\n                    <ns3:italic>Astragalus<\/ns3:italic>\n                    and related genera with strong support.\n                    <ns3:italic>Astragalus nuratensis<\/ns3:italic>\n                    was placed within the Phaca clade, while\n                    <ns3:italic>Oxytropis pseudorosea<\/ns3:italic>\n                    formed part of a distinct Oxytropis lineage. These results provide new genomic resources for understanding evolutionary relationships and plastome evolution in Central Asian legumes.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.178398.1","type":"journal-article","created":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T10:49:07Z","timestamp":1774608547000},"page":"445","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Complete chloroplast genomes of endemic Astragalus and Oxytropis species from Uzbekistan"],"prefix":"10.12688","volume":"15","author":[{"given":"Diyorjon","family":"Hamrayev","sequence":"first","affiliation":[{"name":"Tashkent Institute of Botany, Academy of Sciences of Uzbekistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-5874-1033","authenticated-orcid":false,"given":"Bobur","family":"Karimov","sequence":"additional","affiliation":[{"name":"Tashkent Institute of Botany, Academy of Sciences of Uzbekistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Husniddin","family":"Esanov","sequence":"additional","affiliation":[{"name":"Bukhara Bukhara State University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sodik","family":"Khuzhzhiev","sequence":"additional","affiliation":[{"name":"Navoi Navoi State University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maxzuna","family":"Nasretdinova","sequence":"additional","affiliation":[{"name":"Samarkand Samarkand State Medical University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oysha","family":"Jabborova","sequence":"additional","affiliation":[{"name":"Bukhara Bukhara state medical institute named after Abu Ali ibn Sino"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oybek","family":"Omonov","sequence":"additional","affiliation":[{"name":"Qarshi Kashkadarya Province Karshi State University"},{"name":"Karshi Turan University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohistara","family":"Sharipova","sequence":"additional","affiliation":[{"name":"Jizzakh Jizzakh State Pedagogical University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyoviddin","family":"Yusupov","sequence":"additional","affiliation":[{"name":"Tashkent Institute of Botany, Academy of Sciences of Uzbekistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alijon","family":"Esankulov","sequence":"additional","affiliation":[{"name":"Tashkent Tashkent Botanical Garden under the Institute of Botany, Academy of Sciences"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2026,3,27]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"44-77","DOI":"10.12705\/661.3","article-title":"A New Subfamily Classification of the Leguminosae Based on a Taxonomically Comprehensive Phylogeny: The Legume Phylogeny Working Group (LPWG).","volume":"66","author":"N Azani","year":"2017","journal-title":"Taxon."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"e70084","DOI":"10.1002\/ajb2.70084","article-title":"Building a robust backbone for Astragalus using a clade-specific target enrichment bait set.","volume":"112","author":"D Buono","year":"2025","journal-title":"Am. 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Facilitated by the Royal Botanic Gardens, Kew.","year":"2026"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1942","DOI":"10.3390\/f13111942","article-title":"Characterization of the chloroplast genome structure of Gueldenstaedtia verna (Papilionoideae) and comparative analyses among IRLC species.","volume":"13","author":"O Son","year":"2022","journal-title":"Forests."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"107025","DOI":"10.1016\/j.ympev.2020.107025","article-title":"Chloroplast phylogenomics and character evolution of eastern Asian Astragalus (Leguminosae): Tackling the phylogenetic structure of the largest genus of flowering plants in Asia.","volume":"156","author":"C Su","year":"2021","journal-title":"Mol. Phylogenet. 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Genet."}],"updated-by":[{"DOI":"10.12688\/f1000research.178398.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T00:00:00Z","timestamp":1778716800000}},{"DOI":"10.12688\/f1000research.178398.3","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000}},{"DOI":"10.12688\/f1000research.178398.4","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,7,14]],"date-time":"2026-07-14T00:00:00Z","timestamp":1783987200000}}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/15-445\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/15-445\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/15-445\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T08:29:28Z","timestamp":1779870568000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/15-445\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,27]]},"references-count":19,"URL":"https:\/\/doi.org\/10.12688\/f1000research.178398.1","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.196779.r473037","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.196779.r471852","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.196779.r471852","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.196779.r473037","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,27]]},"assertion":[{"value":"Approved with reservations, Approved with reservations","URL":"https:\/\/f1000research.com\/articles\/15-445\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.196779.r471852, Hoang Dang Khoa Do, Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, 03 Apr 2026, version 1, 2 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/15-445\/v1#referee-response-471852","order":0,"name":"referee-response-471852","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Bobur Karimov<\/b>; \n<i>Posted: 29 Apr 2026<\/i>; \n<b>Reviewer 1<\/b> 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.  \n<b>Comment 1\/<\/b> Please update the role of authors because most authors are for writing the manuscript. Who did the sampling, experiment, and analyzing the data? \n<b>Response:<\/b> The system did not provide an option to edit and resubmit the updated version with revised author contributions.  \n<b>Comment 2\/<\/b> &quot;Chloroplast (cp) genomes of angiosperms have been widely used in studies of phylogeny, sequence variation, genome evolution, and the development of molecular markers.&quot; Please add references for this statement. \n<b>Response:<\/b> Appropriate references have been added to support this statement in the revised manuscript.  \n<b>Comment 3\/<\/b> &quot;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).&quot; 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. \n<b>Response:<\/b> A more appropriate and widely accepted reference has been added to support this statement.  \n<b>Comment 4\/<\/b> Please use italic font for gene names in the Introduction part. \n<b>Response:<\/b> Gene names in the Introduction have been corrected and formatted in italics.  \n<b>Comment 5\/<\/b> 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. \n<b>Response:<\/b> A new introductory paragraph has been added covering published chloroplast genomes of \n<i>Astragalus<\/i> and \n<i>Oxytropis<\/i>  \n<b>Comment 6\/<\/b> &quot;Voucher specimens were deposited in the National Herbarium of Uzbekistan (TASH) under the accession numbers TASH-2024-AN-001 and TASH-2024-OP-002.&quot;; &quot;Genome skimming generated high-quality paired-end reads, enabling the recovery of complete plastomes with mean sequencing depths of 638&times; and 1,725&times;, respectively.&quot; please revise these sentences to clarify which feature is of Astragalus nuratensis and which information belongs to Oxytropis pseudorosea. \n<b>Response:<\/b> The sentences have been revised to clearly distinguish species-specific voucher information and sequencing depth values.  \n<b>Comment 7\/<\/b> &quot;High-quality reads were assembled de novo using NOVOPlasty v4.3.5&quot; how to get high-quality reads? Please add. \n<b>Response:<\/b> Raw sequencing reads were directly used, and NOVOPlasty performs internal quality filtering during the assembly process.  \n<b>Comment 8\/<\/b> &quot;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.&quot; How to complete chloroplast genomes from SRA data? Please add.from SRA to novoplasty \n<b>Response:<\/b> Raw sequencing data were downloaded from SRA and assembled into chloroplast genomes using NOVOPlasty following the same assembly workflow.  \n<b>Comment 9\/<\/b> 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. \n<b>Response:<\/b> The chloroplast genome map of \n<i>Oxytropis pseudorosea<\/i> has been added to Figure 1.  \n<b>Comment 10\/<\/b> &quot;Table 1. List of taxa included in the phylogenetic analysis, accession numbers.&quot; Please revise Table 1 caption. \n<b>Response:<\/b> The caption of Table 1 has been revised for clarity and consistency.  \n<b>Comment 11\/<\/b> Please correct accession number of O. pseudorosea which is not PV684035 from GenBank database in Table 1. \n<b>Response:<\/b> The accession number has been corrected according to the GenBank database.","URL":"https:\/\/f1000research.com\/articles\/15-445\/v1#referee-comment-16091","order":1,"name":"referee-comment-16091","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.196779.r473037, Yoshinori Fukasawa, Center for Bioscience Research and Education Utsunomiya University, Tochigi, 27 Apr 2026, version 1, 2 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/15-445\/v1#referee-response-473037","order":2,"name":"referee-response-473037","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Bobur Karimov<\/b>; \n<i>Posted: 29 Apr 2026<\/i>; \n<b>Reviewer 2<\/b> 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.  \n<b>1. Citation for the conserved quadripartite structure of chloroplast genomes<\/b> 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. \n<b>Response:<\/b> A more appropriate and widely accepted reference has been added to support the conserved quadripartite structure of angiosperm chloroplast genomes.  \n<b>2. Chloroplast genome map of Oxytropis pseudorosea<\/b> 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. \n<b>Response:<\/b> The chloroplast genome map of \n<i>Oxytropis pseudorosea<\/i> has been added accordingly to provide balanced visualization of both plastomes.  \n<b>3. Discrepancy in gene counts between Figure 1 and the text<\/b> 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 &quot;77 genes; 4 rRNAs; 30 tRNAs&quot; for A. nuratensis. Please verify and reconcile these numbers to ensure consistency between the figure and the text. \n<b>Response:<\/b> The gene annotation has been carefully checked, and inconsistencies between the figure and the text have been corrected to ensure full consistency.  \n<b>4. Assembly validation metrics<\/b> 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. \n<b>Response:<\/b> 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.  \n<b>5. Reporting gene loss, pseudogenization, and intron loss in the IRLC context<\/b> 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. \n<b>Response:<\/b> A brief description of gene content and intron structure has been added to the Results comparison with typical IRLC characteristics.","URL":"https:\/\/f1000research.com\/articles\/15-445\/v1#referee-comment-16092","order":3,"name":"referee-comment-16092","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by the project \u201cDigital Nature: Development of a digital platform for the flora of Central Uzbekistan\u201d (2025\u20132029), implemented by the Institute of Botany, Academy of Sciences of the Republic of Uzbekistan. Additional support was provided by the project \u201cAssessing climate change adaptation in endangered plants of Uzbekistan: A DNA barcoding approach\u201d (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.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}