The Last Decade of Medicinal Plant Genomics: Advances and Challenges

Junfeng Chen; Yuchen Zhang; Yajing Li; Yiru Liu; Qing Li; Zongyou Lv; Milen I. Georgiev; Pan Liao

doi:10.1016/j.eng.2025.09.024

Engineering ›› DOI: 10.1016/j.eng.2025.09.024

review-article

The Last Decade of Medicinal Plant Genomics: Advances and Challenges

Junfeng Chen ^a^,^#
, Yuchen Zhang ^b^,^#
, Yajing Li ^a^,^#
, Yiru Liu ^a
, Qing Li ^a^,^c
, Zongyou Lv ^a
, Milen I. Georgiev ^d^,^e^,^*
, Pan Liao ^b^,^f^,^g^,^*

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Abstract

Over the past decade (2014–2025), owing to increasing genome sequencing technologies and decreasing cost, research on medicinal plant genomes (MPGs) has expanded extensively. This advancement has significantly accelerated progress in multiple areas, including elucidating specialized metabolic pathways, conserving endangered species, advancing molecular breeding strategies, and accelerating metabolic engineering innovations. Here, we attempt to provide a contemporary view of MPGs, including analyses of sequenced species and assembly data, the advantages of illustrating the metabolic pathways of active compounds, and demonstrating how MPGs facilitate the metabolic biosynthesis characterization of medicinal plants.

Keywords

Medicinal plant / Genome sequencing / Active metabolites / Biosynthesis pathway / Multiomics

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Junfeng Chen, Yuchen Zhang, Yajing Li, Yiru Liu, Qing Li, Zongyou Lv, Milen I. Georgiev, Pan Liao. The Last Decade of Medicinal Plant Genomics: Advances and Challenges. Engineering DOI:10.1016/j.eng.2025.09.024

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References

Publishing order | Descend order by publishing year | Descend order by cited within

[1]	Marks RA, Hotaling S, Frandsen PB, VanBuren R.Representation and participation across 20 years of plant genome sequencing.Nat Plants 2021; 7(12):1571-1578.

[2]	Schwacke R, Bolger M, Usadel B.PubPlant—a continuously updated online resource for sequenced and published plant genomes.Front Plant Sci 2025; 16:1603547.

[3]	Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, et al.The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).Nature 2008; 452(7190):991-996.

[4]	Xie L, Gong X, Yang K, Huang Y, Zhang S, Shen L, et al.Technology-enabled great leap in deciphering plant genomes.Nat Plants 2024; 10(4):551-566.

[5]	Zhang J, Yang Y, Si J, Chen D, Dong C, Chuan D, et al.Artificial intelligence in the discovery and modification of biological elements in medicinal plants.Med Plant Biol 2025; 4(1):e012.

[6]	Li J, Lv M, Du L, Yunga A, Hao S, Zhang Y, et al.An enormous Paris polyphylla genome sheds light on genome size evolution and polyphyllin biogenesis. bioRxiv (2020), Article 126920

[7]	Xu S, Chen R, Zhang X, Wu Y, Yang L, Sun Z, et al.The evolutionary tale of lilies: giant genomes derived from transposon insertions and polyploidization.The Innovation 2024; 5(6):100726.

[8]	Zeng P, Zong H, Han Y, Zhang W, Tian Z, Zhou B, et al.Two Melanthiaceae genomes with dramatic size difference provide insights into giant genome evolution and maintenance.Nat Plants 2025; 11(8):1500-1513.

[9]	Smit SJ, Lichman BR.Plant biosynthetic gene clusters in the context of metabolic evolution.Nat Prod Rep 2022; 39(7):1465-1482.

[10]	Shang Y, Ma Y, Zhou Y, Zhang H, Duan L, Chen H, et al.Biosynthesis, regulation, and domestication of bitterness in cucumber.Science 2014; 346(6213):1084-1088.

[11]	Zhong Y, Xun W, Wang X, Tian S, Zhang Y, Li D, et al.Root-secreted bitter triterpene modulates the rhizosphere microbiota to improve plant fitness.Nat Plants 2022; 8(8):887-896.

[12]	Li Y, Chen J, Zhi J, Huang D, Zhang Y, Zhang L, et al.The ABC transporter SmABCG1 mediates tanshinones export from the peridermic cells of Salvia miltiorrhiza root.J Integr Plant Biol 2025; 67(1):135-149.

[13]	Chakraborty P.Herbal genomics as tools for dissecting new metabolic pathways of unexplored medicinal plants and drug discovery.Biochim Open 2018; 6:9-16.

[14]	Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, et al.Review on the development and applications of medicinal plant genomes.Front Plant Sci 2021; 12:791219.

[15]	Su X, Yang L, Wang D, Shu Z, Yang Y, Chen S, et al.1 K Medicinal Plant Genome Database: an integrated database combining genomes and metabolites of medicinal plants.Hortic Res 2022; 9:uhac075.

[16]	Chen T, Yang M, Cui G, Tang J, Shen Y, Liu J, et al.IMP: bridging the gap for medicinal plant genomics.Nucleic Acids Res 2024; 52(D1):D1347-D1354.

[17]	Cheng LT, Wang ZL, Zhu QH, Ye M, Ye CY.A long road ahead to reliable and complete medicinal plant genomes.Nat Commun 2025; 16(1):2150.

[18]	Lang D, Zhang S, Ren P, Liang F, Sun Z, Meng G, et al.Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore.GigaScience 2020; 9(12):giaa123.

[19]	Zhang G, Tian Y, Zhang J, Shu L, Yang S, Wang W, et al.Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge).GigaScience 2015; 4:62.

[20]	Xu H, Song J, Luo H, Zhang Y, Li Q, Zhu Y, et al.Analysis of the genome sequence of the medicinal plant Salvia miltiorrhiza.Mol Plant 2016; 9(6):949-952.

[21]	Song Z, Lin C, Xing P, Fen Y, Jin H, Zhou C, et al.A high-quality reference genome sequence of Salvia miltiorrhiza provides insights into tanshinone synthesis in its red rhizomes.Plant Genome 2020; 13(3):e20041.

[22]	Pan X, Chang Y, Li C, Qiu X, Cui X, Meng F, et al.Chromosome-level genome assembly of Salvia miltiorrhiza with orange roots uncovers the role of Sm2OGD3 in catalyzing 15,16-dehydrogenation of tanshinones.Hortic Res 2023; 10(6):uhad069.

[23]	Tian M, Luo L, Jin B, Liu J, Chen T, Tang J, et al.Highly efficient Agrobacterium rhizogenes-mediated gene editing system in Salvia miltiorrhiza inbred line bh2-7.Plant Biotechnol J 2025; 23(6):2406-2417.

[24]	Pei T, Zhu S, Liao W, Fang Y, Liu J, Kong Y, et al.Gap-free genome assembly and CYP450 gene family analysis reveal the biosynthesis of anthocyanins in Scutellaria baicalensis.Hortic Res 2023; 10(12):uhad235.

[25]	Zhou X, Fan HY, Feng XY, Ruan Z, Yuan J, Han Q, et al.PGCP: a comprehensive database of plant genomes for comparative phylogenomics.Plant Biotechnol J 2025; 23(7):2928-2930.

[26]	Chen W, Yu Z, Leng L, Sun D, Liu H, Gong R, et al.Artificial intelligence-curated repository of gene-encoded natural diverse components from herbal medicines.

[27]	Swamidatta SH, Lichman BR.Beyond co-expression: pathway discovery for plant pharmaceuticals.Curr Opin Biotechnol 2024; 88:103147.

[28]	Guo L, Winzer T, Yang X, Li Y, Ning Z, He Z, et al.The opium poppy genome and morphinan production.Science 2018; 362(6412):343-347.

[29]	Zhang RG, Lu C, Li GY, Lv J, Wang L, Wang ZX, et al.Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes.Nat Commun 2023; 14(1):2204.

[30]	Mao L, Kawaide H, Higuchi T, Chen M, Miyamoto K, Hirata Y, et al.Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants.Proc Natl Acad Sci USA 2020; 117(22):12472-12480.

[31]	Bryson AE, Lanier ER, Lau KH, Hamilton JP, Vaillancourt B, Mathieu D, et al.Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory.Nat Commun 2023; 14(1):343.

[32]	Wang Z, Peters RJ.Dynamic evolution of terpenoid biosynthesis in the Lamiaceae.Mol Plant 2023; 16(6):963-965.

[33]	Li H, Wu S, Lin R, Xiao Y, Malaco AL Morotti, Wang Y, et al.The genomes of medicinal skullcaps reveal the polyphyletic origins of clerodane diterpene biosynthesis in the family Lamiaceae.Mol Plant 2023; 16(3):549-570.

[34]	Scheler U, Brandt W, Porzel A, Rothe K, Manzano D, Bo Džić, et al.Elucidation of the biosynthesis of carnosic acid and its reconstitution in yeast.Nat Commun 2016; 7(1):12942.

[35]	Ma Y, Cui G, Chen T, Ma X, Wang R, Jin B, et al.Expansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza.Nat Commun 2021; 12(1):685.

[36]	Hu J, Qiu S, Wang F, Li Q, Xiang CL, Di P, et al.Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia.Nat Commun 2023; 14(1):4696.

[37]	Forman V, Luo D, Geu-Flores F, Lemcke R, Nelson DR, Kampranis SC, et al.A gene cluster in Ginkgo biloba encodes unique multifunctional cytochrome P450s that initiate ginkgolide biosynthesis.Nat Commun 2022; 13(1):5143.

[38]	Sun W, Yin Q, Wan H, Gao R, Xiong C, Xie C, et al.Characterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis.Nat Commun 2023; 14(1):6470.

[39]	Mai Y, Hu H, Ji W, Xiao Y, Zhou H, Zeng Z, et al.Evolution and functional characterization of a biosynthetic gene cluster for saponin biosynthesis in Sapindaceae.Mol Plant 2025; 18(7):1089-1093.

[40]	Mochida K, Sakurai T, Seki H, Yoshida T, Takahagi K, Sawai S, et al.Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume.Plant J 2017; 89(2):181-194.

[41]	Li Y, Xia C, Luo M, Huang Y, Xia Z, Li Y, et al.Comparative genomics of three medicinal Glycyrrhiza species unveiled novel candidates for the production of important bioactive compounds.Plant J 2025; 122(4):e70223.

[42]	Zhou Y, Ma Y, Zeng J, Duan L, Xue X, Wang H, et al.Convergence and divergence of bitterness biosynthesis and regulation in Cucurbitaceae.Nat Plants 2016; 2(16183):16183.

[43]	Lichman BR, Godden GT, Hamilton JP, Palmer L, Kamileen MO, Zhao D, et al.The evolutionary origins of the cat attractant nepetalactone in catnip.Sci Adv 2020; 6(20):eaba0721.

[44]	Rodríguez-López CE, Jiang Y, Kamileen MO, Lichman BR, Hong B, Vaillancourt B, et al.Phylogeny-aware chemoinformatic analysis of chemical diversity in Lamiaceae enables iridoid pathway assembly and discovery of aucubin synthase.Mol Biol Evol 2022; 39(4):msac057.

[45]	Rai A, Hirakawa H, Nakabayashi R, Kikuchi S, Hayashi K, Rai M, et al.Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis.Nat Commun 2021; 12(1):405.

[46]	Sun W, Xu Z, Song C, Chen S.Herbgenomics: decipher molecular genetics of medicinal plants.The Innovation 2022; 3(6):100322.

[47]	Li CY, Yang L, Liu Y, Xu ZG, Gao J, Huang YB, et al.The sage genome provides insight into the evolutionary dynamics of diterpene biosynthesis gene cluster in plants.Cell Rep 2022; 40(7):111236.

[48]	Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, et al.Plant genome resequencing and population genomics: current status and future prospects.Mol Plant 2023; 16(8):1252-1268.

[49]	Liao B, Shen X, Xiang L, Guo S, Chen S, Meng Y, et al.Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield.Mol Plant 2022; 15(8):1310-1328.

[50]	Zhang Y, Shen Q, Leng L, Zhang D, Chen S, Shi Y, et al.Incipient diploidization of the medicinal plant Perilla within 10,000 years.Nat Commun 2021; 12(1):5508.

[51]	Yu H, Liao J, Jiang Y, Zhong M, Tao S, Chai S, et al.Ecotype-specific phenolic acid accumulation and root softness in Salvia miltiorrhiza are driven by environmental and genetic factors.Plant Biotechnol J 2025; 23(6):2224-2241.

[52]	Xu F, Cheng Q, Liu S, Jiang S, Zhang J, Mao X, et al.MRBIGR: a versatile toolbox for genetic regulation inference from population-scale multi-omics data.Plant Commun 2025; 6(3):101197.

[53]	Kimmel K, Dee LE, Avolio ML, Ferraro PJ.Causal assumptions and causal inference in ecological experiments.Trends Ecol Evol 2021; 36(12):1141-1152.

[54]	Yu X, Liu Z, Sun X.Single-cell and spatial multi-omics in the plant sciences: technical advances, applications, and perspectives.Plant Commun 2023; 4(3):100508.

[55]	Chen C, Zhang X, Yue M.Spatial multi-omics in medicinal plants: from biosynthesis pathways to industrial applications.Trends Plant Sci 2024; 29(5):510-513.

[56]	Li C, Wood JC, Vu AH, Hamilton JP, Rodriguez CE Lopez, Payne RME, et al.Single-cell multi-omics in the medicinal plant Catharanthus roseus.Nat Chem Biol 2023; 19(8):1031-1041.

[57]	Sun S, Shen X, Li Y, Li Y, Wang S, Li R, et al.Single-cell RNA sequencing provides a high-resolution roadmap for understanding the multicellular compartmentation of specialized metabolism.Nat Plants 2023; 9(1):179-190.

[58]	Wu S, Morotti ALM, Yang J, Wang E, Tatsis EC.Single-cell RNA sequencing facilitates the elucidation of the complete biosynthesis of the antidepressant hyperforin in St. John’s wort.Mol Plant 2024; 17(9):1439-1457.

[59]	McClune CJ, Liu JC, Wick C, De R La Peña, Lange BM, Fordyce PM, et al.Discovery of FoTO1 and Taxol genes enables biosynthesis of baccatin III.Nature 2025; 643(8071):582-592.

[60]	Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, et al.TBtools-II: a “one for all, all for one” bioinformatics platform for biological big-data mining.Mol Plant 2023; 16(11):1733-1742.

[61]	Choi SR, Lee M.Transformer architecture and attention mechanisms in genome data analysis: a comprehensive review.Biology 2023; 12(7):1033.

[62]	Consens ME, Dufault C, Wainberg M, Forster D, Karimzadeh M, Goodarzi H, et al.Transformers and genome language models.Nat Mach Intell 2025; 7(3):346-362.

[63]	Farooq MA, Gao S, Hassan MA, Huang Z, Rasheed A, Hearne S, et al.Artificial intelligence in plant breeding.Trends Genet 2024; 40(10):891-908.

[64]	Jiang Z, Peng Z, Wei Z, Sun J, Luo Y, Bie L, et al.A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes.Nucleic Acids Res 2024; 52(19):e92.

[65]	Wen H, Yang J, Zhao X, Wang X, Lei J, Li Y, et al.TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.Genome Biol 2025; 26(1):227.

[66]	Latysheva N, Cheng J, Novati G, Taylor KR, Ward T.AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model.bioRxiv 2025.

[67]	Gosai SJ, Castro RI, Fuentes N, Butts JC, Mouri K, Alasoadura M, et al.Machine-guided design of cell-type-targeting cis-regulatory elements.Nature 2024; 634(8036):1211-1220.

[68]	Wang D, Tan Z, Gao J, Zhang S, Shen J, Lu Y.AI4Protein: transforming the future of protein design. Sci China Life Sci. In press.

[69]	Fei H, Li Y, Liu Y, Wei J, Chen A, Gao C.Advancing protein evolution with inverse folding models integrating structural and evolutionary constraints.Cell 2025; 188(17):4674-4692.e19.