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For: Yang X, Gao S, Guo L, Wang B, Jia Y, Zhou J, Che Y, Jia P, Lin J, Xu T, Sun J, Ye K. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. Nat Commun 2021;12:6030. [PMID: 34654815 PMCID: PMC8521590 DOI: 10.1038/s41467-021-26330-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 09/29/2021] [Indexed: 01/07/2023]  Open
Number Cited by Other Article(s)
1
Qin K, Liu F, Zhang C, Deng R, Fernie AR, Zhang Y. Systems and synthetic biology for plant natural product pathway elucidation. Cell Rep 2025;44:115715. [PMID: 40382775 DOI: 10.1016/j.celrep.2025.115715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 03/05/2025] [Accepted: 04/26/2025] [Indexed: 05/20/2025]  Open
2
Huang Z, Dai C, Gong L, Shi P, Bai J, Shen Q, Pan H, Zhong S, Chen L, Chu Y, Xu J, Qiu X, Liao B, Lin H. Diversified quantity, gene structure, and expression profile of OPR gene family of A. annua. Int J Biol Macromol 2025;306:141490. [PMID: 40015404 DOI: 10.1016/j.ijbiomac.2025.141490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 02/23/2025] [Accepted: 02/24/2025] [Indexed: 03/01/2025]
3
Machado RSR, Bonhomme V, Soteras R, Jeanty A, Bouby L, Evin A, Fernandes Martins MJ, Gonçalves S, Antolín F, Salavert A, Oliveira HR. The origins and spread of the opium poppy (Papaver somniferum L.) revealed by genomics and seed morphometrics. Philos Trans R Soc Lond B Biol Sci 2025;380:20240198. [PMID: 40370019 PMCID: PMC12079135 DOI: 10.1098/rstb.2024.0198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 03/14/2025] [Accepted: 03/26/2025] [Indexed: 05/16/2025]  Open
4
Liu C, Xu H, Li Z, Wang Y, Qiao S, Zhang H. Application and Progress of Genomics in Deciphering the Genetic Regulation Mechanisms of Plant Secondary Metabolites. PLANTS (BASEL, SWITZERLAND) 2025;14:1316. [PMID: 40364345 PMCID: PMC12073800 DOI: 10.3390/plants14091316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 04/23/2025] [Accepted: 04/25/2025] [Indexed: 05/15/2025]
5
Zhang RG, Shang HY, Milne R, Almeida-Silva F, Chen H, Zhou MJ, Shu H, Jia KH, Van de Peer Y, Ma YP. SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics. Nucleic Acids Res 2025;53:gkaf320. [PMID: 40248914 PMCID: PMC12006799 DOI: 10.1093/nar/gkaf320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 03/10/2025] [Accepted: 04/10/2025] [Indexed: 04/19/2025]  Open
6
Chen Z, Xun L, Lu Y, Yang X, Chen M, Yang T, Mei Z, Yang Y, Yang X, Yang Y. The chromosome-scale genomes of two Tinospora species reveal differential regulation of the MEP pathway in terpenoid biosynthesis. BMC Biol 2025;23:84. [PMID: 40114206 PMCID: PMC11927234 DOI: 10.1186/s12915-025-02185-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Accepted: 03/04/2025] [Indexed: 03/22/2025]  Open
7
Bidon B, Yaakoub H, Lanoue A, Géry A, Séguin V, Magot F, Hoffmann C, Courdavault V, Bouchara JP, Gangneux JP, Frisvad JC, Rokas A, Goldman GH, Nevez G, Le Gal S, Davolos D, Garon D, Papon N. Tracing the Origin and Evolution of the Fungal Mycophenolic Acid Biosynthesis Pathway. Genome Biol Evol 2025;17:evaf039. [PMID: 40052422 PMCID: PMC11934065 DOI: 10.1093/gbe/evaf039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2025] [Indexed: 03/26/2025]  Open
8
Priego‐Cubero S, Liu Y, Toyomasu T, Gigl M, Hasegawa Y, Nojiri H, Dawid C, Okada K, Becker C. Evolution and diversification of the momilactone biosynthetic gene cluster in the genus Oryza. THE NEW PHYTOLOGIST 2025;245:2681-2697. [PMID: 39887739 PMCID: PMC11840401 DOI: 10.1111/nph.20416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 12/31/2024] [Indexed: 02/01/2025]
9
Priego-Cubero S, Knoch E, Wang Z, Alseekh S, Braun KH, Chapman P, Fernie AR, Liu C, Becker C. Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster in Solanaceae. Proc Natl Acad Sci U S A 2025;122:e2420164122. [PMID: 39977312 PMCID: PMC11874288 DOI: 10.1073/pnas.2420164122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Accepted: 01/07/2025] [Indexed: 02/22/2025]  Open
10
Hong UVT, Tamiru-Oli M, Hurgobin B, Lewsey MG. Genomic and cell-specific regulation of benzylisoquinoline alkaloid biosynthesis in opium poppy. JOURNAL OF EXPERIMENTAL BOTANY 2025;76:35-51. [PMID: 39046316 PMCID: PMC11659185 DOI: 10.1093/jxb/erae317] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 07/22/2024] [Indexed: 07/25/2024]
11
Li Y, Chen J, Zhi J, Huang D, Zhang Y, Zhang L, Duan X, Zhang P, Qiu S, Geng J, Feng J, Zhang K, Yang X, Gao S, Xia W, Zhou Z, Qiao Y, Li B, Li Q, Li T, Chen W, Xiao Y. The ABC transporter SmABCG1 mediates tanshinones export from the peridermic cells of Salvia miltiorrhiza root. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2025;67:135-149. [PMID: 39575678 DOI: 10.1111/jipb.13806] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 10/26/2024] [Indexed: 01/16/2025]
12
Wu L, Ma T, Zang C, Xu Z, Sun W, Luo H, Yang M, Song J, Chen S, Yao H. Glycyrrhiza, a commonly used medicinal herb: Review of species classification, pharmacology, active ingredient biosynthesis, and synthetic biology. J Adv Res 2024:S2090-1232(24)00538-1. [PMID: 39551128 DOI: 10.1016/j.jare.2024.11.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 11/05/2024] [Accepted: 11/12/2024] [Indexed: 11/19/2024]  Open
13
Tian Y, Kong L, Li Q, Wang Y, Wang Y, An Z, Ma Y, Tian L, Duan B, Sun W, Gao R, Chen S, Xu Z. Structural diversity, evolutionary origin, and metabolic engineering of plant specialized benzylisoquinoline alkaloids. Nat Prod Rep 2024;41:1787-1810. [PMID: 39360417 DOI: 10.1039/d4np00029c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
14
Carr SC, Rehman F, Hagel JM, Chen X, Ng KKS, Facchini PJ. Two ubiquitous aldo-keto reductases in the genus Papaver support a patchwork model for morphine pathway evolution. Commun Biol 2024;7:1410. [PMID: 39472466 PMCID: PMC11522673 DOI: 10.1038/s42003-024-07100-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 10/18/2024] [Indexed: 11/02/2024]  Open
15
Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2024;23:579-594. [PMID: 37952099 PMCID: PMC11812042 DOI: 10.1093/bfgp/elad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023]  Open
16
Gao S, Jia Y, Guo H, Xu T, Wang B, Bush SJ, Wan S, Zhang Y, Yang X, Ye K. The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation. CELL GENOMICS 2024;4:100626. [PMID: 39084227 PMCID: PMC11406182 DOI: 10.1016/j.xgen.2024.100626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/16/2024] [Accepted: 07/09/2024] [Indexed: 08/02/2024]
17
Feng L, Teng F, Li N, Zhang JC, Zhang BJ, Tsai SN, Yue XL, Gu LF, Meng GH, Deng TQ, Tong SW, Wang CM, Li Y, Shi W, Zeng YL, Jiang YM, Yu W, Ngai SM, An LZ, Lam HM, He JX. A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms. PLANT COMMUNICATIONS 2024;5:100891. [PMID: 38561965 PMCID: PMC11287142 DOI: 10.1016/j.xplc.2024.100891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 02/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
18
Yan K, Zhu H, Cao G, Meng L, Li J, Zhang J, Liu S, Wang Y, Feng R, Soaud SA, Elhamid MAA, Heakel RMY, Wei Q, El-Sappah AH, Ru D. Chromosome genome assembly of the Camphora longepaniculata (Gamble) with PacBio and Hi-C sequencing data. FRONTIERS IN PLANT SCIENCE 2024;15:1372127. [PMID: 38993944 PMCID: PMC11238478 DOI: 10.3389/fpls.2024.1372127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/21/2024] [Indexed: 07/13/2024]
19
Pokorny L, Pellicer J, Woudstra Y, Christenhusz MJM, Garnatje T, Palazzesi L, Johnson MG, Maurin O, Françoso E, Roy S, Leitch IJ, Forest F, Baker WJ, Hidalgo O. Genomic incongruence accompanies the evolution of flower symmetry in Eudicots: a case study in the poppy family (Papaveraceae, Ranunculales). FRONTIERS IN PLANT SCIENCE 2024;15:1340056. [PMID: 38947944 PMCID: PMC11212465 DOI: 10.3389/fpls.2024.1340056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/18/2024] [Indexed: 07/02/2024]
20
Yang X, Zheng G, Jia P, Wang S, Ye K. Pindel-TD: A Tandem Duplication Detector Based on A Pattern Growth Approach. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024;22:qzae008. [PMID: 38862430 PMCID: PMC11425056 DOI: 10.1093/gpbjnl/qzae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 06/13/2024]
21
An Z, Gao R, Chen S, Tian Y, Li Q, Tian L, Zhang W, Kong L, Zheng B, Hao L, Xin T, Yao H, Wang Y, Song W, Hua X, Liu C, Song J, Fan H, Sun W, Chen S, Xu Z. Lineage-Specific CYP80 Expansion and Benzylisoquinoline Alkaloid Diversity in Early-Diverging Eudicots. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2309990. [PMID: 38477432 PMCID: PMC11109638 DOI: 10.1002/advs.202309990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/07/2024] [Indexed: 03/14/2024]
22
Hu J, Wang Z, Sun Z, Hu B, Ayoola AO, Liang F, Li J, Sandoval JR, Cooper DN, Ye K, Ruan J, Xiao CL, Wang D, Wu DD, Wang S. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biol 2024;25:107. [PMID: 38671502 PMCID: PMC11046930 DOI: 10.1186/s13059-024-03252-4] [Citation(s) in RCA: 111] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024]  Open
23
Zhang T, Zhou L, Pu Y, Tang Y, Liu J, Yang L, Zhou T, Feng L, Wang X. A chromosome-level genome reveals genome evolution and molecular basis of anthraquinone biosynthesis in Rheum palmatum. BMC PLANT BIOLOGY 2024;24:261. [PMID: 38594606 PMCID: PMC11005207 DOI: 10.1186/s12870-024-04972-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/01/2024] [Indexed: 04/11/2024]
24
Xiang KL, Wu SD, Lian L, He WC, Peng D, Peng HW, Zhang XN, Li HL, Xue JY, Shan HY, Xu GX, Liu Y, Wu ZQ, Wang W. Genomic data and ecological niche modeling reveal an unusually slow rate of molecular evolution in the Cretaceous Eupteleaceae. SCIENCE CHINA. LIFE SCIENCES 2024;67:803-816. [PMID: 38087029 DOI: 10.1007/s11427-023-2448-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/11/2023] [Indexed: 04/06/2024]
25
The RanOmics group, Becker A, Bachelier JB, Carrive L, Conde e Silva N, Damerval C, Del Rio C, Deveaux Y, Di Stilio VS, Gong Y, Jabbour F, Kramer EM, Nadot S, Pabón-Mora N, Wang W. A cornucopia of diversity-Ranunculales as a model lineage. JOURNAL OF EXPERIMENTAL BOTANY 2024;75:1800-1822. [PMID: 38109712 PMCID: PMC10967251 DOI: 10.1093/jxb/erad492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 12/20/2023]
26
Zhang D, Li YY, Zhao X, Zhang C, Liu DK, Lan S, Yin W, Liu ZJ. Molecular insights into self-incompatibility systems: From evolution to breeding. PLANT COMMUNICATIONS 2024;5:100719. [PMID: 37718509 PMCID: PMC10873884 DOI: 10.1016/j.xplc.2023.100719] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/18/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
27
Lei W, Zhu H, Cao M, Zhang F, Lai Q, Lu S, Dong W, Sun J, Ru D. From genomics to metabolomics: Deciphering sanguinarine biosynthesis in Dicranostigma leptopodum. Int J Biol Macromol 2024;257:128727. [PMID: 38092109 DOI: 10.1016/j.ijbiomac.2023.128727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/15/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023]
28
Yang Y, Li Z, Zong H, Liu S, Du Q, Wu H, Li Z, Wang X, Huang L, Lai C, Zhang M, Wang W, Chen X. Identification and Validation of Magnolol Biosynthesis Genes in Magnolia officinalis. Molecules 2024;29:587. [PMID: 38338333 PMCID: PMC10856379 DOI: 10.3390/molecules29030587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]  Open
29
Jia C, Lai Q, Zhu Y, Feng J, Dan X, Zhang Y, Long Z, Wu J, Wang Z, Qumu X, Wang R, Wang J. Intergrative metabolomic and transcriptomic analyses reveal the potential regulatory mechanism of unique dihydroxy fatty acid biosynthesis in the seeds of an industrial oilseed crop Orychophragmus violaceus. BMC Genomics 2024;25:29. [PMID: 38172664 PMCID: PMC10765717 DOI: 10.1186/s12864-023-09906-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024]  Open
30
Guo M, Lv H, Chen H, Dong S, Zhang J, Liu W, He L, Ma Y, Yu H, Chen S, Luo H. Strategies on biosynthesis and production of bioactive compounds in medicinal plants. CHINESE HERBAL MEDICINES 2024;16:13-26. [PMID: 38375043 PMCID: PMC10874775 DOI: 10.1016/j.chmed.2023.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/26/2023] [Indexed: 02/21/2024]  Open
31
Diaz-Bárcena A, Fernandez-Pacios L, Giraldo P. Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L. Biomolecules 2023;14:2. [PMID: 38275743 PMCID: PMC10813097 DOI: 10.3390/biom14010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024]  Open
32
Liu Q, Ye L, Li M, Wang Z, Xiong G, Ye Y, Tu T, Schwarzacher T, Heslop-Harrison JSP. Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena. BMC PLANT BIOLOGY 2023;23:627. [PMID: 38062402 PMCID: PMC10704644 DOI: 10.1186/s12870-023-04644-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
33
Xu Y, Bush SJ, Yang X, Xu L, Wang B, Ye K. Evolutionary analysis of conserved non-coding elements subsequent to whole-genome duplication in opium poppy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023;116:1804-1824. [PMID: 37706612 DOI: 10.1111/tpj.16466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
34
Yao L, Wu X, Jiang X, Shan M, Zhang Z, Li Y, Yang A, Li Y, Yang C. Subcellular compartmentalization in the biosynthesis and engineering of plant natural products. Biotechnol Adv 2023;69:108258. [PMID: 37722606 DOI: 10.1016/j.biotechadv.2023.108258] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
35
Zhang RG, Shang HY, Jia KH, Ma YP. Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations. Brief Bioinform 2023;25:bbad513. [PMID: 38189536 PMCID: PMC10772947 DOI: 10.1093/bib/bbad513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/27/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]  Open
36
Sun W, Yin Q, Wan H, Gao R, Xiong C, Xie C, Meng X, Mi Y, Wang X, Wang C, Chen W, Xie Z, Xue Z, Yao H, Sun P, Xie X, Hu Z, Nelson DR, Xu Z, Sun X, Chen S. Characterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis. Nat Commun 2023;14:6470. [PMID: 37833361 PMCID: PMC10576086 DOI: 10.1038/s41467-023-42253-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 10/05/2023] [Indexed: 10/15/2023]  Open
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023;203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
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Hu J, Qiu S, Wang F, Li Q, Xiang CL, Di P, Wu Z, Jiang R, Li J, Zeng Z, Wang J, Wang X, Zhang Y, Fang S, Qiao Y, Ding J, Jiang Y, Xu Z, Chen J, Chen W. Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia. Nat Commun 2023;14:4696. [PMID: 37542034 PMCID: PMC10403556 DOI: 10.1038/s41467-023-40401-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]  Open
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Zhang RG, Lu C, Li GY, Lv J, Wang L, Wang ZX, Chen Z, Liu D, Zhao Y, Shi TL, Zhang W, Tang ZH, Mao JF, Ma YP, Jia KH, Zhao W. Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes. Nat Commun 2023;14:2204. [PMID: 37076529 PMCID: PMC10115784 DOI: 10.1038/s41467-023-37939-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023]  Open
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Yang X, Gao S, Xu T, Wang B, Jia Y, Ye K. Reply to "Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes". Nat Commun 2023;14:2203. [PMID: 37076521 PMCID: PMC10115862 DOI: 10.1038/s41467-023-37940-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023]  Open
41
Zhang F, Qiu F, Zeng J, Xu Z, Tang Y, Zhao T, Gou Y, Su F, Wang S, Sun X, Xue Z, Wang W, Yang C, Zeng L, Lan X, Chen M, Zhou J, Liao Z. Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family. Nat Commun 2023;14:1446. [PMID: 36922496 PMCID: PMC10017790 DOI: 10.1038/s41467-023-37133-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 03/02/2023] [Indexed: 03/17/2023]  Open
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Jia Y, Xu Y, Wang B, Guo L, Guo M, Che X, Ye K. The tissue-specific chromatin accessibility landscape of Papaver somniferum. Front Genet 2023;14:1136736. [PMID: 37007951 PMCID: PMC10050356 DOI: 10.3389/fgene.2023.1136736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/03/2023] [Indexed: 03/17/2023]  Open
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Becker A, Yamada Y, Sato F. California poppy (Eschscholzia californica), the Papaveraceae golden girl model organism for evodevo and specialized metabolism. FRONTIERS IN PLANT SCIENCE 2023;14:1084358. [PMID: 36938015 PMCID: PMC10017456 DOI: 10.3389/fpls.2023.1084358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
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Bryson AE, Lanier ER, Lau KH, Hamilton JP, Vaillancourt B, Mathieu D, Yocca AE, Miller GP, Edger PP, Buell CR, Hamberger B. Uncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory. Nat Commun 2023;14:343. [PMID: 36670101 PMCID: PMC9860074 DOI: 10.1038/s41467-023-35845-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023]  Open
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Méteignier LV, Nützmann HW, Papon N, Osbourn A, Courdavault V. Emerging mechanistic insights into the regulation of specialized metabolism in plants. NATURE PLANTS 2023;9:22-30. [PMID: 36564633 DOI: 10.1038/s41477-022-01288-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
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Chang J, Duong TA, Schoeman C, Ma X, Roodt D, Barker N, Li Z, Van de Peer Y, Mizrachi E. The genome of the king protea, Protea cynaroides. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023;113:262-276. [PMID: 36424853 PMCID: PMC10107735 DOI: 10.1111/tpj.16044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 05/07/2023]
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Yang X, Zhao X, Qu S, Jia P, Wang B, Gao S, Xu T, Zhang W, Huang J, Ye K. Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing. FUNDAMENTAL RESEARCH 2022;2:946-953. [PMID: 38933383 PMCID: PMC11197534 DOI: 10.1016/j.fmre.2022.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/17/2022] [Accepted: 02/27/2022] [Indexed: 01/10/2023]  Open
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Cheng W, Yao Y, Wang Q, Chang X, Shi Z, Fang X, Chen F, Chen S, Zhang Y, Zhang F, Zhu D, Deng Z, Lu L. Characterization of benzylisoquinoline alkaloid methyltransferases in Liriodendron chinense provides insights into the phylogenic basis of angiosperm alkaloid diversity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022;112:535-548. [PMID: 36062348 DOI: 10.1111/tpj.15966] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
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Guo L, Yao H, Chen W, Wang X, Ye P, Xu Z, Zhang S, Wu H. Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era. HORTICULTURE RESEARCH 2022;9:uhac223. [PMID: 36479585 PMCID: PMC9720450 DOI: 10.1093/hr/uhac223] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
50
Wu D, Hu Y, Akashi S, Nojiri H, Guo L, Ye C, Zhu Q, Okada K, Fan L. Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022;111:1354-1367. [PMID: 35781905 PMCID: PMC9544640 DOI: 10.1111/tpj.15893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 05/31/2023]
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