| [1] |
Huang X Q， Dudareva N. Plant specialized metabolism［J］. Current Biology，2023，33（11）：R473-R478.
|
| [2] |
Fernie A R， de Vries S， de Vries J. Evolution of plant metabolism：the state-of-the-art［J］. Philosophical Transactions of the Royal Society of London Series B，Biological Sciences，2024，379（1914）：20230347.
|
| [3] |
Moghe G D， Last R L. Something old，something new：conserved enzymes and the evolution of novelty in plant specialized metabolism［J］. Plant Physiology，2015，169（3）：1512-1523.
|
| [4] |
Chae L， Kim T， Nilo-Poyanco R，et al. Genomic signatures of specialized metabolism in plants［J］. Science，2014，344（6183）：510-513.
|
| [5] |
Jiao Y N， Wickett N J， Ayyampalayam S，et al. Ancestral polyploidy in seed plants and angiosperms［J］. Nature，2011，473（7345）：97-100.
|
| [6] |
Freeling M. Bias in plant gene content following different sorts of duplication：tandem，whole-genome，segmental，or by transposition［J］. Annual Review of Plant Biology，2009，60（5）：433-453.
|
| [7] |
Wang Y P， Wang X Y， Tang H B，et al. Modes of gene duplication contribute differently to genetic novelty and redundancy，but show parallels across divergent angiosperms［J］. PLoS One，2011，6（12）：e28150.
|
| [8] |
Panchy N， Lehti-Shiu M， Shiu S H. Evolution of gene duplication in plants［J］. Plant Physiology，2016，171（4）：2294-2316.
|
| [9] |
Birchler J A， Yang H. The multiple fates of gene duplications：deletion，hypofunctionalization，subfunctionalization，neofunctionalization，dosage balance constraints，and neutral variation［J］. The Plant Cell，2022，34（7）：2466-2474.
|
| [10] |
Su W B， Jing Y， Lin S K，et al. Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe［J］. Proceedings of the National Academy of Sciences of the United States of America，2021，118（20）：e2101767118.
|
| [11] |
Hofberger J A， Lyons E， Edger P P，et al. Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family［J］. Genome Biology and Evolution，2013，5（11）：2155-2173.
|
| [12] |
Schläpfer P， Zhang P F， Wang C，et al. Genome-wide prediction of metabolic enzymes，pathways，and gene clusters in plants［J］. Plant Physiology，2017，173（4）：2041-2059.
|
| [13] |
Ma Y， Cui G H， Chen T，et al. Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza ［J］. Nature Communications，2021，12（4）：685.
|
| [14] |
Wang Y P， Ficklin S P， Wang X Y，et al. Large-scale gene relocations following an ancient genome triplication associated with the diversification of core eudicots［J］. PLoS One，2016，11（5）：e0155637.
|
| [15] |
Wang Y P， Tan X， Paterson A H. Different patterns of gene structure divergence following gene duplication in Arabidopsis ［J］. BMC Genomics，2013，14（1）：652.
|
| [16] |
Force A， Lynch M， Pickett F B，et al. Preservation of duplicate genes by complementary，degenerative mutations［J］. Genetics，1999，151（4）：1531-1545.
|
| [17] |
Kenchanmane Raju S K， Ledford M， Niederhuth C E. DNA methylation signatures of duplicate gene evolution in angiosperms［J］. Plant Physiology，2023，192（4）：2883-2901.
|
| [18] |
Wang Y， Zhang H， Ri H C，et al. Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata ［J］. Nature Communications，2022，13（4）：2224.
|
| [19] |
Ma R R， Huang W X， Hu Q，et al. Tandemly duplicated MYB genes are functionally diverged in the regulation of anthocyanin biosynthesis in soybean［J］. Plant Physiology，2024，194（4）：2549-2563.
|
| [20] |
Wu T， Bafort Q， Mortier F，et al. The immediate metabolomic effects of whole-genome duplication in the greater duckweed，Spirodela polyrhiza ［J］. American Journal of Botany，2024，111（8）：e16383.
|
| [21] |
Kliebenstein D J. A role for gene duplication and natural variation of gene expression in the evolution of metabolism［J］. PLoS One，2008，3（3）：e1838.
|
| [22] |
Tohge T， Wendenburg R， Ishihara H，et al. Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae［J］. Nature Communications，2016，7（4）：12399.
|
| [23] |
Denoeud F， Carretero-Paulet L， Dereeper A，et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis［J］. Science，2014，345（6201）：1181-1184.
|
| [24] |
Li Q S， Ramasamy S， Singh P，et al. Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy［J］. Nature Communications，2020，11（4）：1190.
|
| [25] |
Wang X， Zhang H， Kang M Y，et al. The Oplopanax elatus genome reveals dammaradienol synthase evolution enabling reconstruction of RK type ginsenosides biosynthesis［J］. Nature Communications，2026，17（4）：7907.
|
| [26] |
Xiang Y T， Liang T T， Yang R X，et al. Functional divergence of tandem duplicate SCPL acyltransferase genes reveals convergent evolution of chicoric acid biosynthesis［J］. Science Advances，2025，11（45）：eady8282.
|
| [27] |
Kerwin R E， Hart J E， Fiesel P D，et al. Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster［J］. Science Advances，2024，10（17）：eadn3991.
|
| [28] |
Grzech D， Smit S J， Alam R M，et al. Incorporation of nitrogen in antinutritional Solanum alkaloid biosynthesis［J］. Nature Chemical Biology，2025，21（1）：131-142.
|
| [29] |
Dong F， Verdenaud M， Adam G，et al. Neofunctionalization underlies the evolutionary origin of sclareol biosynthesis in the mint family［J］. Nature Communications，2026，17（4）：6745.
|
| [30] |
Shan C H， Zhou X， Zhu J J，et al. Gene duplication and clustering underlie the conservation and diversification of benzylisoquinoline alkaloid biosynthesis in plants［J］. Nature Communications，2025，16（4）：7669.
|
| [31] |
Ji W J， Osbourn A， Liu Z H. Understanding metabolic diversification in plants：branchpoints in the evolution of specialized metabolism［J］. Philosophical Transactions of the Royal Society of London Series B，Biological Sciences，2024，379（1914）：20230359.
|
| [32] |
Nützmann H W， Huang A C， Osbourn A. Plant metabolic clusters-from genetics to genomics［J］. The New Phytologist，2016，211（3）：771-789.
|
| [33] |
Maeda H A， Fernie A R. Evolutionary history of plant metabolism［J］. Annual Review of Plant Biology，2021，72（4）：185-216.
|
), WANG Yazhe, WU Qi, LIU Chuanhao, LI Xiaoyan, WANG Yu(
