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It displays a variety of growth habits and morphologies, and is widely utilized as both ornamental and medicinal plants globally. The objective of this research is to uncover chloroplast genomes of species from Eastern Asia and Southern Africa, thereby advancing our understanding of the diversity within this genus. This study sequenced Bauhinia purpurea, Bauhinia brachycarpa var. microphylla, Bauhinia variegata var. candida, Bauhinia galpinii, and Bauhinia monandra using the Illumina platform and conducted the construction of phylogenetic trees as well as the estimation of divergence times. Compared to Asian species, the IR regions of African species underwent a contraction of approximately 100\u2013400 bp. The phylogenetic analysis indicated that Asian and African species clustered into two distinct clades, with high support. The divergence of Bauhinia s.s. species occurred in the late Paleocene, and the rps18 and cemA genes were under positive selection. Six hypervariable regions were screened for evolutionary studies and the super-barcode data were used for species delimitation. The results revealed certain differences between African and Asian species in their chloroplast genomes of Bauhinia species.<\/jats:p>","DOI":"10.3390\/ijms26010397","type":"journal-article","created":{"date-parts":[[2025,1,6]],"date-time":"2025-01-06T08:08:52Z","timestamp":1736150932000},"page":"397","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Comparative Analysis of Complete Chloroplast Genomes and Phylogenetic Relationships in Medicinally Important Pantropical Genus Bauhinia s.s. (Leguminosae) from Southern Africa and Eastern Asia"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-6971-792X","authenticated-orcid":false,"given":"Yanxiang","family":"Lin","sequence":"first","affiliation":[{"name":"College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-4450-5517","authenticated-orcid":false,"given":"Yuan","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanlin","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengzi","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4731-4499","authenticated-orcid":false,"given":"Yanfang","family":"Zheng","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2853-1087","authenticated-orcid":false,"given":"Mingqing","family":"Huang","sequence":"additional","affiliation":[{"name":"College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,1,5]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1002\/tax.12207","article-title":"Testing generic limits in Cercidoideae (Leguminosae): Insights from plastid and duplicated nuclear gene sequences","volume":"69","author":"Sinou","year":"2020","journal-title":"Taxon"},{"key":"ref_2","unstructured":"Lewis, G., Schrire, B., Mackinder, B., and Lock, M. (2005). Cercideae. Legumes of the World, Royal Botanic Gardens, Kew."},{"key":"ref_3","first-page":"374","article-title":"Bauhinia","volume":"Volume 1","year":"1753","journal-title":"Species Plantarum"},{"key":"ref_4","first-page":"6","article-title":"Bauhinia","volume":"Volume 10","author":"Wu","year":"2010","journal-title":"Flora of China"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"525","DOI":"10.3732\/ajb.92.3.525","article-title":"Hybrid origin of \u201cBauhinia blakeana\u201d (Leguminosae: Caesalpinioideae), inferred using morphological reproductive, and molecular data","volume":"92","author":"Lau","year":"2005","journal-title":"Am. J. Bot."},{"key":"ref_6","first-page":"754","article-title":"Chemical Constituents of Bauhinia brachycarpa","volume":"24","author":"Zhang","year":"2012","journal-title":"Nat. Prod. Res. Dev."},{"key":"ref_7","unstructured":"Shan, H. (2017). Anti-Nociceptive Activity Screening of the Plants from West Yunnan and Analgesic Activity of Bauhinia brachycarpa Benth. [Master\u2019s Thesis, Dali University]."},{"key":"ref_8","unstructured":"Chinese Herbalism Editorial Board, State Administration of Traditional Chinese Medicine of the People\u2019s Republic of China (1999). Chinese Materia Medica (Zhonghua Bencao), Shanghai Science & Technology Press."},{"key":"ref_9","unstructured":"Long, Y.G. (2020). Sedative and Antispasmodic Drugs. Fundamentals of Chinese Dong Medicine, Guizhou Science and Technology Press."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e02668","DOI":"10.1016\/j.heliyon.2019.e02668","article-title":"Antifungal and anti-mycotoxigenic activity of selected South African medicinal plants species","volume":"5","author":"Dikhoba","year":"2019","journal-title":"Heliyon"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1307801","DOI":"10.1155\/2022\/1307801","article-title":"Anti-Biofilm, Antibacterial, and Anti-Quorum Sensing Activities of Selected South African Plants Traditionally Used to Treat Diarrhoea","volume":"2022","author":"Adeyemo","year":"2022","journal-title":"Evid.-Based Complement. Altern. Med. eCAM"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"780","DOI":"10.3109\/13880200903280018","article-title":"Evaluation of Bauhinia monandra aqueous and ethanol extracts in pregnant rats","volume":"48","author":"Mendes","year":"2010","journal-title":"Pharm. Biol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.biopen.2016.03.001","article-title":"Anti-inflammatory and antinociceptive activities of Bauhinia monandra leaf lectin","volume":"2","author":"Campos","year":"2016","journal-title":"Biochim. Open"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"44","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":"Azani","year":"2017","journal-title":"Taxon"},{"key":"ref_15","first-page":"750","article-title":"Enumeration and typification of genera in tribe Cercideae","volume":"78","author":"Wunderlin","year":"1976","journal-title":"Rhodora"},{"key":"ref_16","unstructured":"Wunderlin, R., Larsen, K., and Larsen, S.S. (1987). Reorganization of the Cercideae (Fabaceae: Caesalpinioideae), Det Kongelige Danske Videnskabernes Selskab."},{"key":"ref_17","unstructured":"Polhill, R.M., and Raven, P.H. (1981). Cercideae. Advances in Legume Systematics, Part 1, Royal Botanic Gardens."},{"key":"ref_18","first-page":"37","article-title":"Notes on the Genus Bauhinia in Thailand","volume":"13","author":"Larsen","year":"1980","journal-title":"Thai For. Bull."},{"key":"ref_19","first-page":"381","article-title":"A revision of Malaysian Bauhinieae","volume":"3","year":"1956","journal-title":"Reinwardtia"},{"key":"ref_20","first-page":"55","article-title":"A cladistic analysis of Bauhinia, L. (Leguminosae: Cercideae)","volume":"7","author":"Zhang","year":"1995","journal-title":"Chin. J. Bot."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2310","DOI":"10.1126\/science.1065889","article-title":"Bayesian inference of phylogeny and its impact on evolutionary biology","volume":"294","author":"Huelsenbeck","year":"2001","journal-title":"Science"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1111\/j.1095-8339.2005.00373.x","article-title":"Bauhinia larsenii, a fossil legume from Guangxi, China","volume":"147","author":"Chen","year":"2005","journal-title":"Bot. J. Linn. Soc."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1139\/B09-065","article-title":"The genus Bauhinia s.l. (Leguminosae): A phylogeny based on the plastid trnL-trnF region","volume":"87","author":"Sinou","year":"2009","journal-title":"Botany"},{"key":"ref_24","first-page":"1","article-title":"New combinations in Schnella (Fabaceae: Caesalpinioideae: Cercideae)","volume":"49","author":"Wunderlin","year":"2010","journal-title":"Phytoneuron"},{"key":"ref_25","first-page":"1","article-title":"Reorganization of the Cercideae (Fabaceae: Caesalpinioideae)","volume":"48","author":"Wunderlin","year":"2010","journal-title":"Phytoneuron"},{"key":"ref_26","first-page":"487","article-title":"Phylogenetic Relationships in the Caesalpinioideae (Leguminosae) as Inferred from Chloroplast trnL Intron Sequences","volume":"26","author":"Bruneau","year":"2001","journal-title":"Syst. Bot."},{"key":"ref_27","first-page":"223","article-title":"Phylogenetics of Bauhinia subgenus Phanera (Leguminosae: Caesalpinioideae) based on ITS sequences of nuclear ribosomal DNA","volume":"44","author":"Hao","year":"2003","journal-title":"Bot. Bull. Acad. Sin."},{"key":"ref_28","first-page":"1","article-title":"New combination in Phanera (Fabaceae)","volume":"19","author":"Wunderlin","year":"2011","journal-title":"Phytoneuron"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"55","DOI":"10.3329\/bjpt.v19i1.10942","article-title":"Fifty new combinations in Phanera Lour. (Leguminosae: Caesalpinioideae) from Paleotropical region","volume":"19","author":"Bandyopadhyay","year":"2012","journal-title":"Bangladesh J. Plant Taxon."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1002\/tax.13177","article-title":"Phylogeny and re-circumscription of Cheniella (Leguminosae: Cercidoideae) based on plastome data and morphology, with description of three new species","volume":"73","author":"Gu","year":"2024","journal-title":"Taxon"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Wang, Q., Song, Z., Chen, Y., Shen, S., and Li, Z. (2014). Leaves and fruits of Bauhinia (Leguminosae, Caesalpinioideae, Cercideae) from the Oligocene Ningming Formation of Guangxi, South China and their biogeographic implications. BMC Evol. Biol., 14.","DOI":"10.1186\/1471-2148-14-88"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2244495","DOI":"10.1080\/14772019.2023.2244495","article-title":"The oldest fossil record of Bauhinia s.s. (Fabaceae) from the Tibetan Plateau sheds light on its evolutionary and biogeographic implications","volume":"21","author":"Gao","year":"2023","journal-title":"J. Syst. Paleontol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Jia, L.B., Hu, J.J., Zhang, S.T., Su, T., Spicer, R.A., Liu, J., Yang, J.C., Zou, P., Huang, Y.J., and Zhou, Z.K. (2022). Bauhinia (Leguminosae) Fossils from the Paleogene of Southwestern China and Its Species Accumulation in Asia. Diversity, 14.","DOI":"10.3390\/d14030173"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Meng, H.H., Jacques, F.M.B., Su, T., Huang, Y.J., Zhang, S.T., Ma, H.J., and Zhou, Z.K. (2014). New Biogeographic insight into Bauhinia s.l. (Leguminosae): Integration from fossil records and molecular analyses. BMC Evol. Biol., 14.","DOI":"10.1186\/s12862-014-0181-4"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Lin, Y., Wong, W.O., Shi, G., Shen, S., and Li, Z. (2015). Bilobate leaves of Bauhinia (Leguminosae, Caesalpinioideae, Cercideae) from the middle Miocene of Fujian Province, southeastern China and their biogeographic implications. BMC Evol. Biol., 15.","DOI":"10.1186\/s12862-015-0540-9"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.revpalbo.2015.02.001","article-title":"A tropical forest of the middle Miocene of Fujian (SE China) reveals Sino-Indian biogeographic affinities","volume":"216","author":"Jacques","year":"2015","journal-title":"Rev. Palaeobot. Palynol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"105131","DOI":"10.1016\/j.revpalbo.2024.105131","article-title":"Late Pliocene Bauhinia s.l. (Cercidoideae, Fabaceae) fossils from Tengchong, Yunnan, southwestern China","volume":"327","author":"Cao","year":"2024","journal-title":"Rev. Palaeobot. Palynol."},{"key":"ref_38","first-page":"298","article-title":"Siwalik plant fossils from Surai Khola area, western Nepal","volume":"38","author":"Awasthi","year":"1990","journal-title":"Palaeobotanist"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1007\/s12040-011-0103-4","article-title":"Study of fossil wood from the Middle\u2013Late Miocene sediments of Dhemaji and Lakhimpur districts of Assam, India and its palaeoecological and palaeophytogeographical implications","volume":"120","author":"Mehrotra","year":"2011","journal-title":"J. Earth Syst. Sci."},{"key":"ref_40","first-page":"43","article-title":"Some fossil leaves from the Kasauli Formation of Himachal Pradesh, North-west India","volume":"20","author":"Guleria","year":"2000","journal-title":"Himal. Geol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1080\/08912963.2014.917088","article-title":"Two new fossil woods from the early Miocene of Kutch, Gujarat, India and their significance","volume":"27","author":"Shukla","year":"2015","journal-title":"Hist. Biol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"331","DOI":"10.54991\/jop.1988.1632","article-title":"Late Cenozoic plant impressions from Mahuadanr valley, Palamu District, Bihar","volume":"37","author":"Bande","year":"1988","journal-title":"J. Palaeosciences"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1007\/s12549-018-0351-2","article-title":"Floral diversity and environment during the middle Siwalik sedimentation (Pliocene) in the Arunachal sub-Himalaya","volume":"99","author":"Khan","year":"2019","journal-title":"Palaeobiodivers. Palaeoenviron."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1086\/624089","article-title":"A Tertiary flora from Uganda","volume":"41","author":"Chaney","year":"1993","journal-title":"J. Geol."},{"key":"ref_45","first-page":"93","article-title":"Fossil floras from southern Ecuador","volume":"14","author":"Berry","year":"1945","journal-title":"Johns Hopkins Univ. Stud. Geol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"2287","DOI":"10.1093\/plphys\/kiad487","article-title":"Molecular evidence for enhancer\u2013promoter interactions in light responses of soybean seedlings","volume":"193","author":"Huang","year":"2023","journal-title":"Plant Physiol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Niu, Y.C., Yung, W.S., Sze, C.C., Wong, F.L., Li, M.W., Chung, G., and Lam, H.M. (2024). Developing an SNP dataset for efficiently evaluating soybean germplasm resources using the genome sequencing data of 3,661 soybean accessions. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10382-3"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"dsae025","DOI":"10.1093\/dnares\/dsae025","article-title":"Propagation path of a flowering cherry (Cerasus x yedoensis) cultivar \u2018Somei-Yoshino\u2019 traced by somatic mutations","volume":"31","author":"Shirasawa","year":"2024","journal-title":"DNA Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1111\/nph.19544","article-title":"The global distribution of angiosperm genome size is shaped by climate","volume":"242","author":"Bures","year":"2024","journal-title":"New Phytol."},{"key":"ref_50","doi-asserted-by":"crossref","unstructured":"Daniell, H., Lin, C.S., Yu, M., and Chang, W.J. (2016). Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biol., 17.","DOI":"10.1186\/s13059-016-1004-2"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"73","DOI":"10.3897\/phytokeys.239.112563","article-title":"An updated infrageneric classification of the pantropical species-rich genus Garcinia, L. (Clusiaceae) and some insights into the systematics of New Caledonian species, based on molecular and morphological evidence","volume":"239","author":"Gaudeul","year":"2024","journal-title":"Phytokeys"},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Ran, Z.H., Li, Z., Xiao, X., An, M.T., and Yan, C. (2024). Complete chloroplast genomes of 13 species of sect. Tuberculata Chang (Camellia, L.): Genomic features, comparative analysis, and phylogenetic relationships. BMC Genom., 25.","DOI":"10.1186\/s12864-024-09982-w"},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Zhao, S.Q., Gao, X.M., Yu, X.L., Yuan, T., Zhang, G.Y., Liu, C.L., Li, X.Z., Wei, P., Li, X.Y., and Liu, X. (2024). Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25042193"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1093\/sysbio\/syaa013","article-title":"Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae","volume":"69","author":"Zhang","year":"2020","journal-title":"Syst. Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1111\/nph.17956","article-title":"Species divergence with gene flow and hybrid speciation on the Qinghai-Tibet Plateau","volume":"234","author":"Wu","year":"2022","journal-title":"New Phytol."},{"key":"ref_56","doi-asserted-by":"crossref","unstructured":"Wang, Y.H., Wicke, S., Wang, H., Jin, J.J., Chen, S.Y., Zhang, S.D., Li, D.Z., and Yi, T.S. (2018). Plastid Genome Evolution in the Early-Diverging Legume Subfamily Cercidoideae (Fabaceae). Front. Plant Sci., 9.","DOI":"10.3389\/fpls.2018.00138"},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Chen, Y., Zhao, Y., Wu, W., Li, P., Li, J., An, C., Zheng, Y., Huang, M., Lin, Y., and Yan, Q. (2024). Complete Chloroplast Genomes and Phylogenetic Analysis of Woody Climbing Genus Phanera (Leguminosae). Genes, 15.","DOI":"10.3390\/genes15111456"},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Gastineau, R., Davidovich, N.A., Davidovich, O.I., Lemieux, C., Turmel, M., Wr\u00f3bel, R.J., and Witkowski, A. (2021). Extreme Enlargement of the Inverted Repeat Region in the Plastid Genomes of Diatoms from the Genus Climaconeis. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22137155"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1007\/BF02173220","article-title":"Ebb and flow of the chloroplast inverted repeat","volume":"252","author":"Goulding","year":"1996","journal-title":"Mol. Gen. Genet. MGG"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1600\/036364415X686620","article-title":"A Comparative Analysis of Whole Plastid Genomes from the Apiales: Expansion and Contraction of the Inverted Repeat, Mitochondrial to Plastid Transfer of DNA, and Identification of Highly Divergent Noncoding Regions","volume":"40","author":"Downie","year":"2015","journal-title":"Syst. Bot."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1093\/aob\/mcw065","article-title":"Variable presence of the inverted repeat and plastome stability in Erodium","volume":"117","author":"Blazier","year":"2016","journal-title":"Ann. Bot."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"E7109","DOI":"10.1073\/pnas.1807334115","article-title":"GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae","volume":"115","author":"Kiktev","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1006\/mpev.1996.0038","article-title":"The Distribution and Phylogenetic Significance of a 50-kb Chloroplast DNA Inversion in the Flowering Plant Family Leguminosae","volume":"5","author":"Doyle","year":"1996","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"519","DOI":"10.2307\/2419825","article-title":"Polymorphism for the presence of the rpL2 intron in chloroplast genomes of Bauhinia (Leguminosae)","volume":"22","author":"Lai","year":"1997","journal-title":"Syst. Bot."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1007\/s12042-016-9165-4","article-title":"Comparative Analysis of GC Content Variations in Plant Genomes","volume":"9","author":"Singh","year":"2016","journal-title":"Trop. Plant Biol."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Wang, Y., Xu, J., Hu, B., Dong, C.X., Sun, J., Li, Z.X., Ye, K.Z., Deng, F., Wang, L.L., and Aslam, M. (2023). Assembly, annotation, and comparative analysis of Ipomoea chloroplast genomes provide insights into the parasitic characteristics of Cuscuta species. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.1074697"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"120","DOI":"10.2478\/sg-2024-0012","article-title":"A Novel Set of Chloroplast SSR Markers for the Genus Juglans Reveals Within Species Differentiation","volume":"73","author":"Beck","year":"2024","journal-title":"Silvae Genet."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Chen, Y., Zhao, Y.L., Yan, Q., Wu, W., Lin, Q.Q., Chen, G., Zheng, Y., Huang, M., Fan, S., and Lin, Y. (2024). Characterization and Phylogenetic Analysis of the First Complete Chloroplast Genome of Shizhenia pinguicula (Orchidaceae: Orchideae). Genes, 15.","DOI":"10.3390\/genes15111488"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1139\/B08-058","article-title":"Phylogenetic patterns and diversification in the caesalpinioid legumes","volume":"86","author":"Bruneau","year":"2008","journal-title":"Botany"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1134\/S1062359022602968","article-title":"Morphological and DNA Barcoding Based Identification of Calotropis procera (Aiton) Dryand. and Calotropis gigantea (L.) Dryand","volume":"50","author":"Sidhu","year":"2023","journal-title":"Biol. Bull."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.3732\/ajb.0800246","article-title":"DNA barcoding will frequently fail in complicated groups: An example in wild potatoes","volume":"96","author":"Spooner","year":"2009","journal-title":"Am. J. Bot."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"3161","DOI":"10.1111\/1755-0998.13683","article-title":"Species discrimination in Schima (Theaceae): Next-generation super-barcodes meet evolutionary complexity","volume":"22","author":"Yu","year":"2022","journal-title":"Mol. Ecol. Resour."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/S0169-5347(02)00041-1","article-title":"A plea for DNA taxonomy","volume":"18","author":"Tautz","year":"2003","journal-title":"Trends Ecol. Evol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1111\/brv.12104","article-title":"Plant DNA barcoding: From gene to genome","volume":"90","author":"Li","year":"2015","journal-title":"Biol. Rev."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.pld.2023.03.012","article-title":"Plastid phylogenomics and species discrimination in the \u201cChinese\u201d clade of Roscoea (Zingiberaceae)","volume":"45","author":"Hu","year":"2023","journal-title":"Plant Divers."},{"key":"ref_76","first-page":"100530","article-title":"Applying DNA barcoding to identify the cultivated provenance of Fritillaria taipaiensis P. Y. Li and its related species","volume":"39","author":"Liang","year":"2024","journal-title":"J. Appl. Res. Med. Aromat. Plants"},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Slipiko, M., Myszczynski, K., Buczkowska, K., Baczkiewicz, A., Szczecinska, M., and Sawicki, J. (2020). Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes. BMC Plant Biol., 20.","DOI":"10.1186\/s12870-020-02435-y"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1007\/s11033-021-06749-4","article-title":"Codon usage bias","volume":"49","author":"Parvathy","year":"2022","journal-title":"Mol. Biol. Rep."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1007\/BF00309919","article-title":"Expression of the wheat chloroplast gene for CF0 subunit IV of ATP synthase","volume":"18","author":"Hoglund","year":"1990","journal-title":"Curr. Genet."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1016\/j.bbabio.2011.09.018","article-title":"Chemiosmotic coupling in oxidative and photosynthetic phosphorylation","volume":"1807","author":"Mitchell","year":"2011","journal-title":"Biochim. Biophys. Acta (BBA)\u2013Bioenerg."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1016\/j.bbabio.2010.10.015","article-title":"Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex","volume":"1807","author":"Peng","year":"2011","journal-title":"Biochim. Biophys. Acta-Bioenerg."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1104\/pp.112.196642","article-title":"The plastid genome-encoded Ycf4 protein functions as a nonessential assembly factor for photosystem I in higher plants","volume":"159","author":"Krech","year":"2012","journal-title":"Plant Physiol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"3378","DOI":"10.1002\/j.1460-2075.1994.tb06640.x","article-title":"An S18 ribosomal protein gene copy at the Arabidopsis PFL locus affects plant development by its specific expression in meristems","volume":"13","author":"Vanderhaeghen","year":"1994","journal-title":"EMBO J."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"4537","DOI":"10.1093\/nar\/gkl634","article-title":"Tobacco plastid ribosomal protein S18 is essential for cell survival","volume":"34","author":"Rogalski","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"6713","DOI":"10.1093\/emboj\/16.22.6713","article-title":"Disruption of the plastid ycf10 open reading frame affects uptake of inorganic carbon in the chloroplast of Chlamydomonas","volume":"16","author":"Rolland","year":"1997","journal-title":"EMBO J."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Jin, J.J., Yu, W.B., Yang, J.B., Song, Y., dePamphilis, C.W., Yi, T.S., and Li, D.Z. (2020). GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol., 21.","DOI":"10.1186\/s13059-020-02154-5"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"3350","DOI":"10.1093\/bioinformatics\/btv383","article-title":"Bandage: Interactive visualization of de novo genome assemblies","volume":"31","author":"Wick","year":"2015","journal-title":"Bioinformatics."},{"key":"ref_89","unstructured":"Peden, J.F. (1999). Analysis of Codon Usage. [Ph.D. Thesis, University of Nottingham]."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","article-title":"EMBOSS: The European Molecular Biology Open Software Suite","volume":"16","author":"Rice","year":"2000","journal-title":"Trends Genet. TIG"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"e15326","DOI":"10.7717\/peerj.15326","article-title":"CPJSdraw: Analysis and visualization of junction sites of chloroplast genomes","volume":"11","author":"Li","year":"2023","journal-title":"PeerJ"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"2583","DOI":"10.1093\/bioinformatics\/btx198","article-title":"MISA-web: A web server for microsatellite prediction","volume":"33","author":"Beier","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","article-title":"DnaSP v5: A software for comprehensive analysis of DNA polymorphism data","volume":"25","author":"Librado","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/j.gpb.2021.12.002","article-title":"KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences","volume":"20","author":"Zhang","year":"2022","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"1586","DOI":"10.1093\/molbev\/msm088","article-title":"PAML 4: Phylogenetic analysis by maximum likelihood","volume":"24","author":"Yang","year":"2007","journal-title":"Mol. Biol. Evol."},{"key":"ref_96","doi-asserted-by":"crossref","unstructured":"Fang, J., Zheng, L., Liu, G., and Zhu, H. (2024). Comparative Analysis of Chloroplast Genomes in Cephaleuros and Its Related Genus (Trentepohlia): Insights into Adaptive Evolution. Genes, 15.","DOI":"10.3390\/genes15070839"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1080\/23802359.2019.1698359","article-title":"Characterization and phylogenetic analysis of the complete chloroplast genome of Cercis canadensis \u2018Forest Pansy\u2019","volume":"5","author":"Feng","year":"2020","journal-title":"Mitochondrial DNA Part B"},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"3404","DOI":"10.1080\/23802359.2021.1999189","article-title":"The complete chloroplast genome sequence of the medicinal plant Cercis chinensis and phylogenetic analysis","volume":"6","author":"Hu","year":"2021","journal-title":"Mitochondrial DNA Part B"},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","article-title":"MrBayes 3: Bayesian phylogenetic inference under mixed models","volume":"19","author":"Ronquist","year":"2003","journal-title":"Bioinformatics"},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"1761","DOI":"10.1111\/1755-0998.13222","article-title":"Make every species count: Fastachar software for rapid determination of molecular diagnostic characters to describe species","volume":"20","author":"Merckelbach","year":"2020","journal-title":"Mol. Ecol. Resour."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/1\/397\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T10:23:04Z","timestamp":1759918984000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/1\/397"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,5]]},"references-count":103,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,1]]}},"alternative-id":["ijms26010397"],"URL":"https:\/\/doi.org\/10.3390\/ijms26010397","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,5]]}}}