{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T09:17:46Z","timestamp":1788167866781,"version":"build-2803163510"},"update-to":[{"DOI":"10.12688\/f1000research.180038.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:00:00Z","timestamp":1787270400000}},{"DOI":"10.12688\/f1000research.180038.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:00:00Z","timestamp":1787270400000}},{"DOI":"10.12688\/f1000research.180038.3","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:00:00Z","timestamp":1787270400000}}],"reference-count":23,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:00:00Z","timestamp":1787270400000},"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                    <ns3:italic>Dianthus helenae<\/ns3:italic>\n                    Vved. is an endemic medicinal species of the Nuratau Mountains, Uzbekistan, and its genomic resources have remained largely unavailable. In this study, we sequenced, assembled, and characterized the complete chloroplast genome of\n                    <ns3:italic>D. helenae<\/ns3:italic>\n                    and evaluated its phylogenetic position within\n                    <ns3:italic>Dianthus.<\/ns3:italic>\n                    The plastome exhibited a typical circular quadripartite structure with a total length of 149,567\u00a0bp, comprising a large single-copy (LSC) region of 82,856\u00a0bp, a small single-copy (SSC) region of 17,105\u00a0bp, and a pair of inverted repeats (IRs) of 24,803\u00a0bp each. The genome contained the typical set of chloroplast genes, including protein-coding genes, transfer RNAs, and ribosomal RNAs, with duplicated genes located in the IR regions. Phylogenetic analysis based on complete chloroplast genome sequences strongly supported the placement of\n                    <ns3:italic>D. helenae<\/ns3:italic>\n                    within\n                    <ns3:italic>Dianthus<\/ns3:italic>\n                    and recovered it as a distinct lineage relative to other sampled species. Sliding window analysis of nucleotide diversity revealed uneven sequence variation across the plastome, with higher variability in the SSC and LSC regions than in the IRs. Several highly variable loci, including\n                    <ns3:italic>trnK-UUU<\/ns3:italic>\n                    ,\n                    <ns3:italic>rps16\u2013trnQ-UUG<\/ns3:italic>\n                    ,\n                    <ns3:italic>rpl32<\/ns3:italic>\n                    ,\n                    <ns3:italic>ycf1<\/ns3:italic>\n                    , and ndh-associated regions, were identified as potential molecular markers. These results provide an important genomic resource for\n                    <ns3:italic>Dianthus<\/ns3:italic>\n                    and establish a foundation for future phylogenetic, taxonomic, conservation, and molecular identification studies of this endemic Central Asian species.\n                  <\/ns3:p>","DOI":"10.12688\/f1000research.180038.4","type":"journal-article","created":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T09:59:06Z","timestamp":1787306346000},"page":"727","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["The complete Chloroplast Genome of Dianthus Helenae, an Endemic Species with Medicinal Potential\u00a0from the Nuratau Mountains, Uzbekistan"],"prefix":"10.12688","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0991-1076","authenticated-orcid":false,"given":"Ibrokhimjon","family":"Ergashov","sequence":"first","affiliation":[{"name":"Tashkent Institute 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University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Risolat","family":"Achilova","sequence":"additional","affiliation":[{"name":"Bukhara Department of Foreign Language Teaching Methodology, Bukhara State Pedagogical Institute"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saidkamol","family":"Xaydarov","sequence":"additional","affiliation":[{"name":"Fergana Department of Botany and Biotechnology, Fergana State University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bakhrom","family":"Khujamkulov","sequence":"additional","affiliation":[{"name":"Kashkadarya Karshi State University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feruza","family":"Utayeva","sequence":"additional","affiliation":[{"name":"Bukhara Bukhara State 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":"Ziyoviddin","family":"Yusupov","sequence":"additional","affiliation":[{"name":"Tashkent Institute of Botany, Academy of Sciences of Uzbekistan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2026,8,21]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"9-50","DOI":"10.3897\/phytokeys.257.142950","article-title":"Synopsis of the genus Elymus (Poaceae) in Uzbekistan (Middle Asia) with a description of Elymus uzbekistanicus a new species from Turkestan Mts.","volume":"257","author":"K Alieva","year":"2025","journal-title":"PhytoKeys."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1186\/s13059-016-1004-2","article-title":"Chloroplast genomes: diversity, evolution, and applications in genetic engineering.","volume":"17","author":"H Daniell","year":"2016","journal-title":"Genome 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status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.208238.r513354, Hoang Dang Khoa Do, Nguyen Tat Thanh University, Ho Chi Minh City, Ho Chi Minh, 31 Aug 2026, version 4, indexed","URL":"https:\/\/f1000research.com\/articles\/15-727\/v4#referee-response-513354","order":0,"name":"referee-response-513354","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.202331.r491239, Ruslan Kalendar, University of Helsinki, Helsinki, 19 Jun 2026, version 2, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/15-727\/v2#referee-response-491239","order":1,"name":"referee-response-491239","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Ibrokhimjon Ergashov<\/b>; \n<i>Posted: 28 Jul 2026<\/i>; We sincerely thank the reviewers&nbsp;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.  Comment:&nbsp;1\/ The genome size and lengths of regions in the abstract and the results are different. Please check and revise. \n<b><b>Response:<\/b><\/b>&nbsp;Thank you for pointing out this inconsistency. We carefully rechecked the genome size and the lengths of the genomic regions reported in the Abstract and Results sections. The incorrect values have been corrected, and the data are now consistent throughout the manuscript. Comment:2\/ Please add the meaning of numbers after the gene names in Figure 2. Thank you. \n<b><b>Response:<\/b><\/b>&nbsp;Thank you for your comment. The numbers in parentheses following each gene name indicate the corresponding codon usage bias values. We have added this explanation to the legend of Figure 2.","URL":"https:\/\/f1000research.com\/articles\/15-727\/v4#referee-comment-16785","order":2,"name":"referee-comment-16785","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"The author(s) declared that no grants were involved in supporting this work","order":3,"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"}]}}