{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T12:18:14Z","timestamp":1789993094813,"version":"4.0.1"},"reference-count":68,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010857","name":"Jiangxi Provincial Natural Science Foundation","doi-asserted-by":"publisher","award":["20232BAB205050"],"award-info":[{"award-number":["20232BAB205050"]}],"id":[{"id":"10.13039\/501100010857","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Jiangxi Academy of Forestry","award":["2023512702"],"award-info":[{"award-number":["2023512702"]}],"id":[{"id":"https:\/\/ror.org\/05808qp03","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Jiangxi Academy of Forestry","award":["2026502701"],"award-info":[{"award-number":["2026502701"]}],"id":[{"id":"https:\/\/ror.org\/05808qp03","id-type":"ROR","asserted-by":"crossref"}]},{"award":["2023512702"],"award-info":[{"award-number":["2023512702"]}],"id":[{"id":"https:\/\/ror.org\/05808qp03","id-type":"ROR","asserted-by":"publisher"}]},{"award":["2026502701"],"award-info":[{"award-number":["2026502701"]}],"id":[{"id":"https:\/\/ror.org\/05808qp03","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>1-Deoxy-D-xylulose 5-phosphate synthase (DXS) catalyzes the rate-limiting step of the plastidial 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway and governs carbon flux toward terpenoid biosynthesis. The Lauraceae constitute an economically important plant lineage characterized by specialized terpenoid metabolism and divergent essential-oil chemotypes; however, the evolutionary dynamics and functional divergence of the DXS gene family across this family remain poorly understood. Here, we performed a comprehensive pan-genomic survey of the DXS family across 14 Lauraceae genomes, integrating phylogenomics, synteny analysis, selection-pressure assessment, structural-variation profiling, spatiotemporal expression profiling, and heterologous functional validation. We identified 92 DXS genes assigned to six orthogroups. DXS2 and DXS4 were conserved ohnologs likely derived from the Lauraceae-specific whole-genome duplication, whereas DXS5 and DXS6 underwent recent lineage-specific duplications. All DXS orthogroups were under purifying selection (Ka\/Ks &lt; 1), with divergent selection intensities among subclades within Clade 2. Structural variations in DXS genes were predominantly located in introns and untranslated regions rather than coding regions. Spatiotemporal expression profiling in Camphora officinarum revealed distinct tissue-specific expression patterns: CoDXS2 was specifically expressed in developing fruits, CoDXS4 exhibited flower-bud-specific expression, and CoDXS6 was highly expressed in developing leaves and fruits. Notably, CoDXS6 transcript abundance showed a strong positive correlation with monoterpenoid accumulation (r = 0.945, p &lt; 0.001), and functional assays confirmed its canonical catalytic activity. Furthermore, CoDXS6 exhibited 6.32- to 9.18-fold higher leaf expression in terpenoid-dominant chemotypes compared with phenylpropanoid-dominant chemotypes. Collectively, retention following recent whole-genome duplication, recent genome-specific duplications, and regulatory variations jointly drove the functional divergence of Lauraceae DXS genes, highlighting CoDXS6 as a key contributor to leaf monoterpenoid biosynthesis in C. officinarum.<\/jats:p>","DOI":"10.3390\/plants15182886","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T11:05:53Z","timestamp":1789988753000},"page":"2886","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Analysis of the DXS Pan-Gene Family Reveals Evolutionary Conservation and Regulatory Divergence Underpinning Terpenoid Metabolism in Lauraceae"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-3623-6795","authenticated-orcid":false,"given":"Chao","family":"Fu","sequence":"first","affiliation":[{"name":"Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species (NO. 2024SSY04091), Jiangxi Academy of Forestry, Nanchang 330032, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Siyang","family":"Tao","sequence":"additional","affiliation":[{"name":"Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species (NO. 2024SSY04091), Jiangxi Academy of Forestry, Nanchang 330032, China"},{"name":"College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"}]},{"given":"Shifang","family":"Wen","sequence":"additional","affiliation":[{"name":"Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species (NO. 2024SSY04091), Jiangxi Academy of Forestry, Nanchang 330032, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Xindong","family":"Wang","sequence":"additional","affiliation":[{"name":"Jiangxi Provincial Key Laboratory of Improved Variety Breeding and Efficient Utilization of Native Tree Species (NO. 2024SSY04091), Jiangxi Academy of Forestry, Nanchang 330032, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"ref_1","first-page":"63","article-title":"Biosynthesis and Biological Functions of Terpenoids in Plants","volume":"Volume 148","author":"Schrader","year":"2015","journal-title":"Biotechnology of Isoprenoids"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Li, C., Zha, W., Li, W., Wang, J., and You, A. (2023). Advances in the Biosynthesis of Terpenoids and Their Ecological Functions in Plant Resistance. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms241411561"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1146\/annurev-arplant-050312-120116","article-title":"Network Analysis of the MVA and MEP Pathways for Isoprenoid Synthesis","volume":"64","author":"Coman","year":"2013","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1104\/pp.007138","article-title":"Elucidation of the Methylerythritol Phosphate Pathway for Isoprenoid Biosynthesis in Bacteria and Plastids. A Metabolic Milestone Achieved through Genomics","volume":"130","author":"Boronat","year":"2002","journal-title":"Plant Physiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1042\/bst0280785","article-title":"Non-Mevalonate Isoprenoid Biosynthesis: Enzymes, Genes and Inhibitors","volume":"28","author":"Lichtenthaler","year":"2000","journal-title":"Biochem. Soc. Trans."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.plipres.2011.12.001","article-title":"A Raison d\u2019\u00eatre for Two Distinct Pathways in the Early Steps of Plant Isoprenoid Biosynthesis?","volume":"51","author":"Hemmerlin","year":"2012","journal-title":"Prog. Lipid Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2100","DOI":"10.1073\/pnas.95.5.2100","article-title":"A Family of Transketolases That Directs Isoprenoid Biosynthesis via a Mevalonate-Independent Pathway","volume":"95","author":"Lange","year":"1998","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2676","DOI":"10.1074\/jbc.M610235200","article-title":"Crystal Structure of 1-Deoxy-d-Xylulose 5-Phosphate Synthase, a Crucial Enzyme for Isoprenoids Biosynthesis","volume":"282","author":"Xiang","year":"2007","journal-title":"J. Biol. Chem."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Joshi, J., Mimura, M., Suzuki, M., Wu, S., Gregory, J.F., Hanson, A.D., and McCarty, D.R. (2021). The Thiamin-Requiring 3 Mutation of Arabidopsis 5-Deoxyxylulose-Phosphate Synthase 1 Highlights How the Thiamin Economy Impacts the Methylerythritol 4-Phosphate Pathway. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.721391"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"100512","DOI":"10.1016\/j.xplc.2022.100512","article-title":"MEP Pathway Products Allosterically Promote Monomerization of Deoxy-D-Xylulose-5-Phosphate Synthase to Feedback-Regulate Their Supply","volume":"4","author":"Di","year":"2023","journal-title":"Plant Commun."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1007\/s10529-005-7849-1","article-title":"Differential Expression of Three 1-Deoxy-D-Xylulose-5-Phosphate Synthase Genes in Rice","volume":"27","author":"Kim","year":"2005","journal-title":"Biotechnol. Lett."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.gene.2012.10.071","article-title":"Functional and Evolutionary Analysis of DXL1, a Non-Essential Gene Encoding a 1-Deoxy-D-Xylulose 5-Phosphate Synthase like Protein in Arabidopsis thaliana","volume":"524","author":"Talavera","year":"2013","journal-title":"Gene"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"110960","DOI":"10.1016\/j.plantsci.2021.110960","article-title":"Reassessing the Evolution of the 1-Deoxy-D-Xylulose 5-Phosphate Synthase Family Suggests a Possible Novel Function for the DXS Class 3 Proteins","volume":"310","author":"Cordoba","year":"2021","journal-title":"Plant Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s10725-021-00784-8","article-title":"A Systematic Review of 1-Deoxy-D-Xylulose-5-Phosphate Synthase in Terpenoid Biosynthesis in Plants","volume":"96","author":"Tian","year":"2022","journal-title":"Plant Growth Regul."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1104\/pp.114.245191","article-title":"Deoxyxylulose 5-Phosphate Synthase Controls Flux through the Methylerythritol 4-Phosphate Pathway in Arabidopsis","volume":"165","author":"Wright","year":"2014","journal-title":"Plant Physiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/jxb\/erp190","article-title":"Unravelling the Regulatory Mechanisms That Modulate the MEP Pathway in Higher Plants","volume":"60","author":"Cordoba","year":"2009","journal-title":"J. Exp. Bot."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"109961","DOI":"10.1016\/j.plaphy.2025.109961","article-title":"Functional Characterization of 1-Deoxy-D-Xylulose-5-Phosphate Synthase (DXS) Genes from Monarda citriodora Establishes the Key Role of McDXS2 in Specialized Terpenoid Biosynthesis","volume":"225","author":"Sharma","year":"2025","journal-title":"Plant Physiol. Biochem."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/s00709-018-1297-y","article-title":"Changes in the Expression of Some Genes Involved in the Biosynthesis of Secondary Metabolites in Cuminum cyminum L. under UV Stress","volume":"256","author":"Ghasemi","year":"2019","journal-title":"Protoplasma"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.jphotobiol.2017.10.002","article-title":"Effect of UV Radiation and Its Implications on Carotenoid Pathway in Bixa orellana L","volume":"176","author":"Sankari","year":"2017","journal-title":"J. Photochem. Photobiol. B Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.3390\/molecules15042302","article-title":"Effect of Sugars on Artemisinin Production in Artemisia annua L.: Transcription and Metabolite Measurements","volume":"15","author":"Arsenault","year":"2010","journal-title":"Molecules"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1111\/j.1365-3040.2009.01980.x","article-title":"Regulation of Isoprene Emission from Poplar Leaves throughout a Day","volume":"32","author":"Wiberley","year":"2009","journal-title":"Plant Cell Environ."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1007\/s10142-019-00654-7","article-title":"Implication of Salt Stress Induces Changes in Pigment Production, Antioxidant Enzyme Activity, and qRT-PCR Expression of Genes Involved in the Biosynthetic Pathway of Bixa orellana L","volume":"19","author":"Sankari","year":"2019","journal-title":"Funct. Integr. Genom."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1007\/s12010-014-0876-4","article-title":"Effects of Streptomyces Pactum Act12 on Salvia miltiorrhiza Hairy Root Growth and Tanshinone Synthesis and Its Mechanisms","volume":"173","author":"Yan","year":"2014","journal-title":"Appl. Biochem. Biotechnol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1007\/s00299-005-0109-y","article-title":"Precursor Limitations in Methyl Jasmonate-Induced Catharanthus roseus Cell Cultures","volume":"25","author":"Royce","year":"2006","journal-title":"Plant Cell Rep."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/j.1399-3054.2012.01603.x","article-title":"PEG and ABA Trigger Methyl Jasmonate Accumulation to Induce the MEP Pathway and Increase Tanshinone Production in Salvia miltiorrhiza Hairy Roots","volume":"146","author":"Yang","year":"2012","journal-title":"Physiol. Plant."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1446","DOI":"10.1093\/plphys\/kiae114","article-title":"The Ginkgo biloba microRNA160\u2013ERF4 Module Participates in Terpene Trilactone Biosynthesis","volume":"195","author":"Zheng","year":"2024","journal-title":"Plant Physiol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1093\/pcp\/pcad023","article-title":"The Heat Shock Transcription Factor PtHSF1 Mediates Triacylglycerol and Fucoxanthin Synthesis by Regulating the Expression of GPAT3 and DXS in Phaeodactylum tricornutum","volume":"64","author":"Song","year":"2023","journal-title":"Plant Cell Physiol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"140860","DOI":"10.1016\/j.ijbiomac.2025.140860","article-title":"LcMYB43 Enhances Monoterpene Biosynthesis by Activating 1-Deoxy-D-Xylulose-5-Phosphate Synthase Gene Expression in Litsea cubeba","volume":"304","author":"Ni","year":"2025","journal-title":"Int. J. Biol. Macromol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1111\/nph.17977","article-title":"SlWRKY35 Positively Regulates Carotenoid Biosynthesis by Activating the MEP Pathway in Tomato Fruit","volume":"234","author":"Yuan","year":"2022","journal-title":"New Phytol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Li, D., Lin, H.-Y., Wang, X., Bi, B., Gao, Y., Shao, L., Zhang, R., Liang, Y., Xia, Y., and Zhao, Y.-P. (2023). Genome and Whole-Genome Resequencing of Cinnamomum camphora Elucidate Its Dominance in Subtropical Urban Landscapes. BMC Biol., 21.","DOI":"10.1186\/s12915-023-01692-1"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"uhac216","DOI":"10.1093\/hr\/uhac216","article-title":"Chromosome-Level Genome Assembly and Resequencing of Camphor Tree (Cinnamomum camphora) Provides Insight into Phylogeny and Diversification of Terpenoid and Triglyceride Biosynthesis of Cinnamomum","volume":"9","author":"Wang","year":"2022","journal-title":"Hortic. Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1111\/pbi.13749","article-title":"The Chromosome-level Genome Sequence of the Camphor Tree Provides Insights into Lauraceae Evolution and Terpene Biosynthesis","volume":"20","author":"Shen","year":"2022","journal-title":"Plant Biotechnol. J."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Yan, K., Zhu, H., Cao, G., Meng, L., Li, J., Zhang, J., Liu, S., Wang, Y., Feng, R., and Soaud, S.A. (2024). Chromosome Genome Assembly of the Camphora longepaniculata (Gamble) with PacBio and Hi-C Sequencing Data. Front. Plant Sci., 15.","DOI":"10.3389\/fpls.2024.1372127"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/s41477-018-0337-0","article-title":"Stout Camphor Tree Genome Fills Gaps in Understanding of Flowering Plant Genome Evolution","volume":"5","author":"Chaw","year":"2019","journal-title":"Nat. Plants"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1038\/s41597-024-03293-1","article-title":"Chromosome-Level Genome Assembly of the Threatened Resource Plant Cinnamomum chago","volume":"11","author":"Tao","year":"2024","journal-title":"Sci. Data"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"112733","DOI":"10.1016\/j.plantsci.2025.112733","article-title":"Decoding the Chemodiversity Blueprint: Chromosome-Scale Genome Assembly Unveils Photosynthesis-Terpenoid Coordination in Cinnamomum burmanni through Genomic and miRNA Regulatory Networks","volume":"360","author":"Hou","year":"2025","journal-title":"Plant Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"100410","DOI":"10.1016\/j.xplc.2022.100410","article-title":"The Chromosome-Scale Genome of Phoebe bournei Reveals Contrasting Fates of Terpene Synthase (TPS)-a and TPS-b Subfamilies","volume":"3","author":"Han","year":"2022","journal-title":"Plant Commun."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1038\/s41467-020-15493-5","article-title":"The Litsea Genome and the Evolution of the Laurel Family","volume":"11","author":"Chen","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1038\/s41597-025-04891-3","article-title":"Chromosome-Level Genome Assembly of the Traditional Medicinal Plant Lindera aggregata","volume":"12","author":"Shi","year":"2025","journal-title":"Sci. Data"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"104761","DOI":"10.1016\/j.isci.2022.104761","article-title":"Genome of Lindera glauca Provides Insights into the Evolution of Biosynthesis Genes for Aromatic Compounds","volume":"25","author":"Xiong","year":"2022","journal-title":"iScience"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Tian, X.-C., Guo, J.-F., Yan, X.-M., Shi, T.-L., Nie, S., Zhao, S.-W., Bao, Y.-T., Li, Z.-C., Kong, L., and Su, G.-J. (2023). Unique Gene Duplications and Conserved Microsynteny Potentially Associated with Resistance to Wood Decay in the Lauraceae. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1122549"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"uhae119","DOI":"10.1093\/hr\/uhae119","article-title":"A Telomere-to-Telomere Gap-Free Reference Genome Assembly of Avocado Provides Useful Resources for Identifying Genes Related to Fatty Acid Biosynthesis and Disease Resistance","volume":"11","author":"Yang","year":"2024","journal-title":"Hortic. Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"121423","DOI":"10.1016\/j.indcrop.2025.121423","article-title":"Functional Diversification of Bornyl Diphosphate Synthase in Lauraceae: An Evolutionary Framework for Borneol-Oriented Molecular Breeding","volume":"233","author":"Ma","year":"2025","journal-title":"Ind. Crops Prod."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Cai, Y., Shi, L., Chen, F., Zhang, Q., Yao, J., Xiu, Y., Lu, C., and Lin, S. (2025). 1-Deoxy-D-Xylulose-5-Phosphate Synthase 1 as a Crucial Regulatory Enzyme for Terpenoid Biosynthesis in the Leaves of Cinnamomum burmannii. Horticulturae, 12.","DOI":"10.3390\/horticulturae12010036"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/s41438-020-00368-z","article-title":"The Phoebe Genome Sheds Light on the Evolution of Magnoliids","volume":"7","author":"Chen","year":"2020","journal-title":"Hortic. Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"uhaf116","DOI":"10.1093\/hr\/uhaf116","article-title":"High-Quality Lindera megaphylla Genome Analysis Provides Insights into Genome Evolution and Allows for the Exploration of Genes Involved in Terpenoid Biosynthesis","volume":"12","author":"Liu","year":"2025","journal-title":"Hortic. Res."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Woodhouse, M.R., Schnable, J.C., Pedersen, B.S., Lyons, E., Lisch, D., Subramaniam, S., and Freeling, M. (2010). Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs. PLoS Biol., 8.","DOI":"10.1371\/journal.pbio.1000409"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1944","DOI":"10.1101\/gr.080978.108","article-title":"Unraveling Ancient Hexaploidy through Multiply-Aligned Angiosperm Gene Maps","volume":"18","author":"Tang","year":"2008","journal-title":"Genome Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/s13059-019-1650-2","article-title":"Gene Duplication and Evolution in Recurring Polyploidization\u2013Diploidization Cycles in Plants","volume":"20","author":"Qiao","year":"2019","journal-title":"Genome Biol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1046\/j.1365-313X.1996.9050649.x","article-title":"CLA1, a Novel Gene Required for Chloroplast Development, Is Highly Conserved in Evolution","volume":"9","author":"Mandel","year":"1996","journal-title":"Plant J."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1016\/j.tree.2020.03.002","article-title":"A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation","volume":"35","author":"Oomen","year":"2020","journal-title":"Trends Ecol. Evol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/nrg2063","article-title":"The Evolutionary Significance of Cis-Regulatory Mutations","volume":"8","author":"Wray","year":"2007","journal-title":"Nat. Rev. Genet."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"22901","DOI":"10.1074\/jbc.M100854200","article-title":"1-Deoxy-d-Xylulose-5-Phosphate Synthase, a Limiting Enzyme for Plastidic Isoprenoid Biosynthesis in Plants","volume":"276","author":"Cantero","year":"2001","journal-title":"J. Biol. Chem."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Di, X., and Rodriguez-Concepcion, M. (2023). Exploring the Deoxy-D-Xylulose-5-Phosphate Synthase Gene Family in Tomato (Solanum lycopersicum). Plants, 12.","DOI":"10.3390\/plants12223886"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.plaphy.2014.05.013","article-title":"Molecular Cloning and Characterization of Three cDNAs Encoding 1-Deoxy-d-Xylulose-5-Phosphate Synthase in Aquilaria Sinensis (Lour.) Gilg","volume":"82","author":"Xu","year":"2014","journal-title":"Plant Physiol. Biochem."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"12405","DOI":"10.1074\/jbc.RA119.009321","article-title":"X-Ray Crystallography-Based Structural Elucidation of Enzyme-Bound Intermediates along the 1-Deoxy-d-Xylulose 5-Phosphate Synthase Reaction Coordinate","volume":"294","author":"Chen","year":"2019","journal-title":"J. Biol. Chem."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2820","DOI":"10.1111\/febs.12823","article-title":"Defining Critical Residues for Substrate Binding to 1-deoxy-D-xylulose 5-phosphate Synthase\u2014Active Site Substitutions Stabilize the Predecarboxylation Intermediate C2\u03b1-lactylthiamin Diphosphate","volume":"281","author":"Patel","year":"2014","journal-title":"FEBS J."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1089\/10665270050081478","article-title":"A Greedy Algorithm for Aligning DNA Sequences","volume":"7","author":"Zhang","year":"2000","journal-title":"J. Comput. Biol."},{"key":"ref_59","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_60","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_61","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_62","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e49","DOI":"10.1093\/nar\/gkr1293","article-title":"MCScanX: A Toolkit for Detection and Evolutionary Analysis of Gene Synteny and Collinearity","volume":"40","author":"Wang","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/S1672-0229(10)60008-3","article-title":"KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies","volume":"8","author":"Wang","year":"2010","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","article-title":"TBtools-II: A \u201cOne for All, All for One\u201d Bioinformatics Platform for Biological Big-Data Mining","volume":"16","author":"Chen","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2\u2212\u0394\u0394Ct Method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Qiu, F., Wang, X., Zheng, Y., Wang, H., Liu, X., and Su, X. (2019). Full-Length Transcriptome Sequencing and Different Chemotype Expression Profile Analysis of Genes Related to Monoterpenoid Biosynthesis in Cinnamomum porrectum. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20246230"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1016\/j.febslet.2005.12.092","article-title":"A Mutant Pyruvate Dehydrogenase E1 Subunit Allows Survival of Escherichia coli Strains Defective in 1-deoxy-D-xylulose 5-phosphate Synthase","volume":"580","author":"Boronat","year":"2006","journal-title":"FEBS Lett."}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2886\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T11:59:15Z","timestamp":1789991955000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2886"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,21]]},"references-count":68,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["plants15182886"],"URL":"https:\/\/doi.org\/10.3390\/plants15182886","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,21]]}}}