{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T06:23:52Z","timestamp":1787207032409,"version":"build-2736575974"},"reference-count":54,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T00:00:00Z","timestamp":1787184000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"\n Introduction<\/jats:title>\n \n Bupleurum L<\/jats:italic>\n . (Apiaceae), a taxonomically intricate genus of about 190 species and a source of Radix Bupleuri (Chai Hu), is difficult to discriminate because of convergent morphology, infraspecific variation, and limited genomic sampling. This study aimed to characterize plastome variation, identify and validate candidate molecular markers, reconstruct plastid phylogenetic relationships, and assess candidate plastid RNA-editing sites in\n Bupleurum<\/jats:italic>\n .\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n We assembled six plastomes from subgenus\n Bupleurum<\/jats:italic>\n , screened 51\n Bupleurum<\/jats:italic>\n plastomes for diagnostic loci, reconstructed whole-plastome and partitioned protein-coding-sequence phylogenies, and predicted plastid C-to-U RNA-editing candidates across the six newly assembled plastomes using a PREP-Cp-compatible workflow. Candidate barcode performance was evaluated against the reference plastome phylogenies, and codon-based models were used to test for positive selection.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n The plastomes were 154,496\u2013155,778 bp with the canonical quadripartite structure and GC contents of 37.67\u201337.73%. Gene content was stable (131\u2013132 genes; 86\u201387 protein-coding genes);\n B. falcatum<\/jats:italic>\n subsp.\n cernuum<\/jats:italic>\n lacked\n ycf15<\/jats:italic>\n but contained an additional inverted-repeat-associated\n ycf1<\/jats:italic>\n annotation. A\/U-ending synonymous codons were favoured. Finite pairwise Ka\/Ks estimates were below 1 for most genes, and site-specific codon models detected no positive selection. Each plastome contained 55\u201361 pure microsatellites, dominated by A\/T mononucleotide motifs. MarkerSeek ranked 265 features and identified\n atpF\u2013atpH<\/jats:italic>\n ,\n petA\u2013psbJ<\/jats:italic>\n ,\n rpl32\u2013trnL-UAG<\/jats:italic>\n , and\n ycf1<\/jats:italic>\n as leading candidate barcodes.\n ycf1<\/jats:italic>\n recovered 38 of 41 nodes strongly supported by both reference trees, whereas a partitioned four-locus analysis recovered 40 of 41 and distinguished all 51 accession sequences. However, only one of seven multi-accession operational binomial groups was monophyletic, and only one showed a positive local barcode gap. The whole-plastome phylogeny recovered\n Bupleurum<\/jats:italic>\n as monophyletic relative to\n Chamaesium<\/jats:italic>\n . The two sampled\n Penninervia<\/jats:italic>\n accessions occupied early-diverging positions without forming an exclusive clade.\n B. falcatum<\/jats:italic>\n subsp.\n cernuum<\/jats:italic>\n was sister to\n B. ranunculoides<\/jats:italic>\n , with\n B. ranunculoides<\/jats:italic>\n subsp. telonense sister to that pair. A partitioned 74-CDS analysis recovered the same key relationships and 45 of 50 internal bipartitions. Across the six newly assembled plastomes, 57\u201363 nonsynonymous C-to-U candidates were predicted per accession (367 total) in 21\u201322 genes; 269 affected the second codon position and 98 the first.\n <\/jats:p>\n <\/jats:sec>\n \n Discussion<\/jats:title>\n \n Bupleurum<\/jats:italic>\n plastomes are structurally conservative but retain localised divergence useful for marker development. Concordant whole-plastome and CDS genealogies support genus monophyly, whereas sparse\n Penninervia<\/jats:italic>\n sampling and maternal plastid inheritance preclude rejecting traditional subgeneric classification. The predicted RNA-editing sites represent candidates for future experimental validation rather than an established\n Bupleurum<\/jats:italic>\n editome. These genomic resources support authentication, conservation, and evolutionary research in\n Bupleurum<\/jats:italic>\n .\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fpls.2026.1916637","type":"journal-article","created":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T05:28:20Z","timestamp":1787203700000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative chloroplast genomics of six Bupleurum (Apiaceae) accessions: candidate barcodes, phylogeny based on available plastomes, and candidate RNA-editing sites"],"prefix":"10.3389","volume":"17","author":[{"given":"Yujie","family":"He","sequence":"first","affiliation":[{"name":"Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University","place":["Qingdao, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingxuan","family":"Wu","sequence":"additional","affiliation":[{"name":"Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University","place":["Qingdao, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aohan","family":"Wang","sequence":"additional","affiliation":[{"name":"Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University","place":["Qingdao, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengwen","family":"Gao","sequence":"additional","affiliation":[{"name":"Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao University","place":["Qingdao, Shandong, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,20]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. 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