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High polymorphism (98.3%) was observed in the studied species. The cluster analysis classified <jats:italic>Thymus<\/jats:italic> species into five main groups. According to molecular variance (AMOVA) analysis, 63.14% of total genetic variation was obtained within the species, while 36.86% of variation was observed among species. STRUCTURE analysis was also performed to estimate the admixture of species. For instance, <jats:italic>T. carmanicus<\/jats:italic> and <jats:italic>T. transcaspicus<\/jats:italic> revealed high admixtures. HPLC analysis also demonstrated the presence of rosmarinic acid (32.3\u2013150.7\u00a0mg\/100\u00a0g DW), salvianolic acid (8\u201390\u00a0mg\/100\u00a0g DW), and cinnamic acid (1.7\u201332.3\u00a0mg\/100\u00a0g DW) as major phenolic acids, as well as apigenin, epicatechin, and naringenin as the major flavonoids. The highest phenolic and flavonoid contents were detected in <jats:italic>T. transcaspicus<\/jats:italic> (37.62\u00a0mg gallic acid equivalents (GAE) g<jats:sup>\u22121<\/jats:sup> DW) and <jats:italic>T. vulgaris<\/jats:italic> (8.72\u00a0mg quercetin equivalents (QE) g<jats:sup>\u22121<\/jats:sup> DW), respectively. The antioxidant properties and total phenolic of <jats:italic>Thymus<\/jats:italic> species were examined using DPPH and \u03b2-carotene-linoleic acid model systems and consequently <jats:italic>T. vulgaris<\/jats:italic> and <jats:italic>T. pubescens<\/jats:italic> were detected with the highest and the lowest antioxidant activities respectively. Cluster and principal Components Analysis (PCA) of the components classified the species in to three groups. Finally, similarity within some species was observed comparing molecular and phytochemical markers. For instance, <jats:italic>T. vulgaris<\/jats:italic> separated from other species according to major polyphenolic profiles and molecular analyses, as well as <jats:italic>T. transcaspicus<\/jats:italic>, <jats:italic>T. carmanicus<\/jats:italic>, and <jats:italic>T. fedtschenkoi<\/jats:italic> that were clustered in the same groups.<\/jats:p>","DOI":"10.1038\/s41598-021-84449-6","type":"journal-article","created":{"date-parts":[[2021,3,3]],"date-time":"2021-03-03T11:02:36Z","timestamp":1614769356000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":50,"title":["Polyphenolic and molecular variation in Thymus species using HPLC and SRAP analyses"],"prefix":"10.1038","volume":"11","author":[{"given":"Danial","family":"Sarfaraz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mehdi","family":"Rahimmalek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ghodratollah","family":"Saeidi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,3,3]]},"reference":[{"key":"84449_CR1","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1016\/j.phytochem.2019.03.004","volume":"162","author":"S Gharibi","year":"2019","unstructured":"Gharibi, S., Tabatabaei, B. 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