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Limited genomic information limits the use of this plant.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Chromosome-level 605.2 Mb genome of <jats:italic>T. mongolicus<\/jats:italic> was generated, with 96.28% anchored to 12 pseudochromosomes. The repetitive sequences were dominant, accounting for 70.98%, and 32,593 protein-coding genes were predicted. Synteny analysis revealed that Lamiaceae species generally underwent two rounds of whole genome duplication; moreover, species-specific genome duplication was identified. A recent LTR retrotransposon burst and tandem duplication might play important roles in the formation of the <jats:italic>Thymus<\/jats:italic> genome. Using comparative genomic analysis, phylogenetic tree of seven Lamiaceae species was constructed, which revealed that <jats:italic>Thyme<\/jats:italic> plants evolved recently in the family. Under the phylogenetic framework, we performed functional enrichment analysis of the genes on nodes that contained the most gene duplication events (&gt;\u200950% support) and of relevant significant expanded gene families. These genes were highly associated with environmental adaptation and biosynthesis of secondary metabolites. Combined transcriptome and metabolome analyses revealed that <jats:italic>Peroxidases<\/jats:italic>, <jats:italic>Hydroxycinnamoyl-CoA shikimate\/quinate hydroxycinnamoyl transferases<\/jats:italic>, and <jats:italic>4-coumarate-CoA ligases<\/jats:italic> genes were the essential regulators of the phenylpropanoid\u2013flavonoid pathway. Their catalytic products (e.g., apigenin, naringenin chalcone, and several apigenin-related compounds) might be responsible for the environmental tolerance and aromatic properties of <jats:italic>T. mongolicus<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>This study enhanced the understanding of the genomic evolution of <jats:italic>T. mongolicus<\/jats:italic>, enabling further exploration of its unique traits and applications, and contributed to the understanding of Lamiaceae genomics and evolutionary biology.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-024-10202-8","type":"journal-article","created":{"date-parts":[[2024,3,19]],"date-time":"2024-03-19T07:02:43Z","timestamp":1710831763000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Chromosome-level genome assembly provides insights into the genome evolution and functional importance of the phenylpropanoid\u2013flavonoid pathway in Thymus mongolicus"],"prefix":"10.1186","volume":"25","author":[{"given":"Zhenhua","family":"Dang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wentao","family":"Mi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Chi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunyun","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaling","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weibo","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,19]]},"reference":[{"issue":"06","key":"10202_CR1","first-page":"681","volume":"39","author":"LJ Xie","year":"2021","unstructured":"Xie LJ, Ye CY, Shen EH. 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