{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T12:09:57Z","timestamp":1773662997301,"version":"3.50.1"},"reference-count":49,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2022,1,20]],"date-time":"2022-01-20T00:00:00Z","timestamp":1642636800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003336","name":"Bulgarian Science Fund","doi-asserted-by":"publisher","award":["DN 16\/3"],"award-info":[{"award-number":["DN 16\/3"]}],"id":[{"id":"10.13039\/501100003336","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>We present a study on the taxonomy of eleven Thymus species, belonging to two sections and occurring naturally in Bulgaria. Four DNA barcoding markers\u2014matK, rbcL, trnH-psbA and ITS\u2014were applied to discriminate the species and to reveal their phylogenetic relationships. The results showed that rbcL has the lowest discriminating power regarding the studied species, while the other markers yielded results fitting better to the existing taxonomic schemes based on morphological traits. However, even in the case of better performing markers, the results were not straightforward\u2014morphologically distinct species belonging to different sections were grouped together, and closely related species appeared genetically distinct. The results are typical for taxonomically complex groups, such as the genus Thymus, characterized in Bulgaria with great diversity, high percentage of endemism and still requiring a full and comprehensive taxonomic study. The results are discussed in the light of unresolved taxonomic problems and application of DNA barcoding methods.<\/jats:p>","DOI":"10.3390\/plants11030270","type":"journal-article","created":{"date-parts":[[2022,1,20]],"date-time":"2022-01-20T22:51:06Z","timestamp":1642719066000},"page":"270","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["DNA Barcoding Study of Representative Thymus Species in Bulgaria"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6476-5438","authenticated-orcid":false,"given":"Ina","family":"Aneva","sequence":"first","affiliation":[{"name":"Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petar","family":"Zhelev","sequence":"additional","affiliation":[{"name":"Department of Dendrology, University of Forestry, 1797 Sofia, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6059-8003","authenticated-orcid":false,"given":"Georgi","family":"Bonchev","sequence":"additional","affiliation":[{"name":"Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4217-3394","authenticated-orcid":false,"given":"Irina","family":"Boycheva","sequence":"additional","affiliation":[{"name":"Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stiliana","family":"Simeonova","sequence":"additional","affiliation":[{"name":"Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denitsa","family":"Kancheva","sequence":"additional","affiliation":[{"name":"Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1111\/boj.12034","article-title":"DNA barcoding to analyse taxonomically complex groups in plants: The case of Thymus (Lamiaceae)","volume":"171","author":"Federici","year":"2013","journal-title":"Bot. J. Linn. Soc."},{"key":"ref_2","first-page":"199","article-title":"Notes on Thymus L. (Labiatae) in Europe. I. Supraspecific classification and nomenclature","volume":"64","author":"Jalas","year":"1971","journal-title":"Bot. J. Linn. Soc."},{"key":"ref_3","first-page":"172","article-title":"Thymus","volume":"Volume 3","author":"Tutin","year":"1972","journal-title":"Flora Europaea"},{"key":"ref_4","unstructured":"Strid, A., and Tan, K. (1986). Thymus L.. Mountain Flora of Greece, Edinburgh University Press."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Stahl-Biskup, E., and S\u00e1ez, F. (2002). The history, botany and taxonomy of genus Thymus. Thyme. The Genus Thymus, Taylor & Francis.","DOI":"10.4324\/9780203216859"},{"key":"ref_6","first-page":"135","article-title":"Verso una revisione biosistematatica del genere Thymus L.","volume":"Volume 2010","author":"Bartolucci","year":"2009","journal-title":"Italia: Considerazioni Nomenclaturali, Sistematiche e Criticit\u00e0 Tassonomica"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1111\/j.1755-0998.2009.02640.x","article-title":"Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae)","volume":"9","author":"Starr","year":"2009","journal-title":"Mol. Ecol. Resour."},{"key":"ref_8","first-page":"288","article-title":"Thymus L.","volume":"Volume 9","author":"Velchev","year":"1989","journal-title":"Flora of PR Bulgaria"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Tsekos, I., and Moustakas, M. (1998). The serpentine flora in the Eastern Rhodopes Mountains (Bulgaria). Progress in Botanical Research: Proceedings of the 1st Balkan Botanical Congress, Kluwer Acdemic Publishers.","DOI":"10.1007\/978-94-011-5274-7"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"163","DOI":"10.5735\/085.057.0122","article-title":"Thymus jalasianus (Lamiaceae), a new species from the serpentine area of the Eastern Rhodope Mountains, Bulgaria","volume":"57","author":"Stoyanov","year":"2020","journal-title":"Ann. Bot. Fenn."},{"key":"ref_11","first-page":"352","article-title":"Thymus aznavourii (Lamiaceae): First records for Bulgarian and Greek flora","volume":"74","author":"Stoyanov","year":"2021","journal-title":"Compt. Rend. Acad. Bulg. Sci. Sci. Math. Nat."},{"key":"ref_12","first-page":"101","article-title":"Survey on the distribution, diversity and phytochemistry of genus Thymus in Bulgaria","volume":"10","author":"Aneva","year":"2018","journal-title":"Ecol. Balk."},{"key":"ref_13","first-page":"197","article-title":"Essential oil composition of the Balkan endemic Thymus longedentatus (Degen & Urum.) Ronniger","volume":"18","author":"Aneva","year":"2019","journal-title":"BLACPMA"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e2100498","DOI":"10.1002\/cbdv.202100498","article-title":"Essential oil composition of five Thymus species from Bulgaria","volume":"18","author":"Trendafilova","year":"2021","journal-title":"Chem. Biodivers."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"654","DOI":"10.1016\/j.flora.2012.06.018","article-title":"Genetic diversity and relationships among species of the genus Thymus L. (section Serpyllum)","volume":"207","author":"Liber","year":"2012","journal-title":"Flora"},{"key":"ref_16","first-page":"85","article-title":"The essential oil composition of Thymus tosevii and Thymus macedonicus from Bulgaria","volume":"139","author":"Kulevanova","year":"2000","journal-title":"Boll. Chim. Farm."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1016\/S0305-1978(03)00040-1","article-title":"External leaf flavonoids of Thymus species from Macedonia","volume":"31","author":"Marin","year":"2003","journal-title":"Biochem. Syst. Ecol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1080\/0972060X.2008.10643652","article-title":"Investigation of extracts from Thyme (Thymus vulgaris L.) for application in cosmetics","volume":"11","author":"Damianova","year":"2008","journal-title":"J. Essent. Oil Bear. Plants"},{"key":"ref_19","first-page":"1123","article-title":"Volatile constituents of two rare subspecies of Thymus praecox","volume":"5","year":"2010","journal-title":"Nat. Prod. Commun."},{"key":"ref_20","first-page":"335","article-title":"Chemical composition and bioactivity of essential oil from Thymus species in Balkan Peninsula","volume":"14","year":"2003","journal-title":"Phytochem. Rev."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.2307\/2446465","article-title":"The spatial genetic structure of cytoplasmic (cpDNA) and nuclear (allozyme) markers within and among populations of the gynodioecious Thymus vulgaris (Labiatae) in southern France","volume":"84","author":"Tarayre","year":"1997","journal-title":"Am. J. Bot."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Stahl-Biskup, E., and S\u00e1ez, F. (2002). Population structure and the spatial dynamics of genetic polymorphism in thyme. Thyme. The Genus Thymus, Taylor & Francis.","DOI":"10.4324\/9780203216859"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Soorni, A., Borna, T., Alemardan, A., Chakrabarti, M., Hunt, A.G., and Bombarely, A. (2019). Transcriptome landscape variation in the genus Thymus. Genes, 10.","DOI":"10.3390\/genes10080620"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1098\/rspb.2002.2218","article-title":"Biological identifications through DNA barcodes","volume":"270","author":"Hebert","year":"2003","journal-title":"Proc. R. Soc. Lond. B"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Hollingsworth, P.M., Graham, S.W., and Little, D.P. (2011). Choosing and using a plant DNA barcode. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0019254"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1111\/jse.12254","article-title":"Plant DNA barcodes: Applications today and in the future","volume":"55","author":"Kress","year":"2017","journal-title":"J. Syst. Evol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Kress, W.J., and Erickson, D.L. (2012). DNA Barcodes: Methods and Protocols, Humana Press, Springer Science\u00fePublishing Media, LLC.","DOI":"10.1007\/978-1-61779-591-6"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.ympev.2010.01.016","article-title":"Molecular phylogeny of Menthinae (Lamiaceae, Nepetoideae, Mentheae)\u2014Taxonomy, biogeography and conflicts","volume":"55","author":"Meimberg","year":"2010","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Zhao, F., Chen, Y.-P., Salmaki, Y., Drew, B.T., Wilson, T.C., Scheen, A.-C., Celep, F., Br\u00e4uchler, C., Bendiksby, M., and Wang, Q. (2021). An updated tribal classification of Lamiaceae based on plastome phylogenomics. BMC Biol., 19.","DOI":"10.1186\/s12915-020-00931-z"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"933","DOI":"10.3732\/ajb.1100549","article-title":"Phylogenetics, biogeography, and staminal evolution in the tribe Mentheae (Lamiaceae)","volume":"99","author":"Drew","year":"2012","journal-title":"Am. J. Bot."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1016\/j.foodres.2010.12.032","article-title":"A comparative study of different DNA barcoding markers for the identification of some members of Lamiaceae","volume":"44","author":"Bruni","year":"2011","journal-title":"Food Res. Int."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1111\/j.1755-0998.2012.03129.x","article-title":"DNA barcoding in native plants of the Labiatae (Lamiaceae) family from Chios Island (Greece) and the adjacent \u00c7esme-Karaburun Peninsula (Turkey)","volume":"12","author":"Theodoridis","year":"2012","journal-title":"Mol. Ecol. Resour."},{"key":"ref_33","first-page":"102","article-title":"A Comparative phenotypic and ITS based genotypic study in Thyme species (Thymus L. Lamiaceae)","volume":"24","author":"Abdolahinia","year":"2011","journal-title":"Int. J. Plant Res."},{"key":"ref_34","first-page":"179","article-title":"Molecular authentication of Thymus persicus based on nrDNA ITS sequence data","volume":"19","author":"Sonboli","year":"2013","journal-title":"Iran J. Bot."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"CBOL Plant Working Group (2009). A DNA barcode for land plants. Proc. Natl. Acad. Sci. USA, 206, 12794\u201312797.","DOI":"10.1073\/pnas.0905845106"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2923","DOI":"10.1073\/pnas.0709936105","article-title":"DNA barcoding the floras of biodiversity hotspots","volume":"105","author":"Lahaye","year":"2008","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1111\/j.1471-8286.2007.02002.x","article-title":"Testing candidate plant barcode regions in the Myristicaceae","volume":"8","author":"Newmaster","year":"2008","journal-title":"Mol. Ecol. Resour."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Chen, S., Yao, H., Han, J., Liu, C., Song, J., Shi, L., Zhu, Y., Ma, X., Gao, T., and Pang, X. (2010). Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0008613"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1111\/j.1755-0998.2011.02984.x","article-title":"Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae)","volume":"11","author":"Muellner","year":"2011","journal-title":"Mol. Ecol. Resour."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Kress, W.J., and Erickson, D.L. (2007). A two-locus global DNA barcode for land plants: The coding rbcL gene complements the noncoding trnH-psbA spacer region. PLoS ONE, 2.","DOI":"10.1371\/journal.pone.0000508"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1111\/j.1755-0998.2008.02439.x","article-title":"Selecting barcoding loci for plants: Evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants","volume":"9","author":"Hollingsworth","year":"2009","journal-title":"Mol. Ecol. Resour."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1469-8137.2004.00957.x","article-title":"Plant speciation\u2014Rise of the poor cousins","volume":"161","author":"Rieseberg","year":"2004","journal-title":"New Phytol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1038\/nature04402","article-title":"The nature of plant species","volume":"440","author":"Rieseberg","year":"2006","journal-title":"Nature"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1016\/j.tree.2005.01.012","article-title":"Conserving taxonomic complexity","volume":"20","author":"Ennos","year":"2005","journal-title":"Trends Ecol. Evol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Munro, H.N. (1969). Evolution of protein molecules. Mammalian Protein Metabolism, Academic Press.","DOI":"10.1016\/B978-1-4832-3211-9.50010-3"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1007\/BF02101694","article-title":"Dating of the Human-Ape Splitting by a molecular Clock of Mitochondrial DNA","volume":"22","author":"Hasegawa","year":"1985","journal-title":"J. Mol. Evol."},{"key":"ref_49","first-page":"512","article-title":"Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees","volume":"10","author":"Tamura","year":"1993","journal-title":"Mol. Biol. Evol."}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/11\/3\/270\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:04:27Z","timestamp":1760133867000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/11\/3\/270"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,20]]},"references-count":49,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2022,2]]}},"alternative-id":["plants11030270"],"URL":"https:\/\/doi.org\/10.3390\/plants11030270","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,20]]}}}