Genome assembly of Stephania longa provides insight into cepharanthine biosynthesis

被引:0
作者
Shang, Huiying [1 ]
Lu, Yuan [1 ]
Xun, Lulu [1 ]
Wang, Kun [2 ]
Li, Bin [1 ]
Liu, Yuxuan [2 ]
Ma, Tao [3 ]
机构
[1] Inst Bot Shaanxi Prov, Xian Bot Garden Shaanxi Prov, Xian, Shaanxi, Peoples R China
[2] Northwestern Polytech Univ, Sch Ecol & Environm, Xian, Peoples R China
[3] Sichuan Univ, Coll Life Sci, Key Lab Bioresource & Ecoenvironm, Minist Educ, Chengdu, Peoples R China
来源
FRONTIERS IN PLANT SCIENCE | 2024年 / 15卷
基金
中国国家自然科学基金;
关键词
Stephania longa; genome; evolution; metabolome; gene expression; cepharanthine; ACID O-METHYLTRANSFERASE; PHYLOGENETIC ANALYSIS; GENE; IDENTIFICATION; ALIGNMENTS; TOOL; FAMILIES; DATABASE;
D O I
10.3389/fpls.2024.1414636
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
Introduction Stephania longa, a medicinal plant renowned for producing cepharanthine, has gained significance due to the compound's notable antiviral properties against SARS-CoV-2. However, a comprehensive genetic understanding of S. longa has been lacking. This study aimed to develop a high-quality, chromosome-level genome assembly to uncover the genetic intricacies and evolutionary narrative of this species. By integrating genomic data with metabolomic and transcriptomic analyses, we sought to identify key genes involved in cepharanthine biosynthesis. Methods: We employed a multi-faceted approach comprising genome assembly, phylogenetic analysis, gene family dynamics investigation, metabolomic profiling, and gene expression analysis across various tissues of S. longa. This integrated strategy enabled the identification of key genes involved in cepharanthine biosynthesis and elucidated the species' evolutionary history. Results: Our phylogenetic analysis clarified the placement of the genus Stephania within the Ranunculales order and revealed its notably high mutation rate. We identified gene family expansions and signs of positive selection likely contributing to Stephania's unique metabolic capabilities. Metabolomic profiling uncovered complex regulatory mechanisms orchestrating the biosynthesis and distribution of cepharanthine and related metabolites. Through the integration of genomic, transcriptomic, and metabolomic data, we identified genes with expression patterns and evolutionary trajectories suggesting pivotal roles in cepharanthine biosynthesis, including those involved in crucial biosynthetic steps. Discussion: This comprehensive study, integrating genomic, metabolomic, and transcriptomic approaches, provides valuable insights into S. longa's biosynthetic potential. It not only enhances our understanding of the species but also establishes a foundation for future investigations into the biosynthesis and therapeutic exploitation of cepharanthine and related alkaloids.
引用
收藏
页数:15
相关论文
共 75 条
  • [1] Gene Ontology: tool for the unification of biology
    Ashburner, M
    Ball, CA
    Blake, JA
    Botstein, D
    Butler, H
    Cherry, JM
    Davis, AP
    Dolinski, K
    Dwight, SS
    Eppig, JT
    Harris, MA
    Hill, DP
    Issel-Tarver, L
    Kasarskis, A
    Lewis, S
    Matese, JC
    Richardson, JE
    Ringwald, M
    Rubin, GM
    Sherlock, G
    [J]. NATURE GENETICS, 2000, 25 (01) : 25 - 29
  • [2] PRINTS-S: the database formerly known as PRINTS
    Attwood, TK
    Croning, MDR
    Flower, DR
    Lewis, AP
    Mabey, JE
    Scordis, P
    Selley, JN
    Wright, W
    [J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 225 - 227
  • [3] Cepharanthine: An update of its mode of action, pharmacological properties and medical applications
    Bailly, Christian
    [J]. PHYTOMEDICINE, 2019, 62
  • [4] Repbase Update, a database of repetitive elements in eukaryotic genomes
    Bao, Weidong
    Kojima, Kenji K.
    Kohany, Oleksiy
    [J]. MOBILE DNA, 2015, 6
  • [5] Bateman A, 2002, NUCLEIC ACIDS RES, V30, P276, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]
  • [6] GeneWise and genomewise
    Birney, E
    Clamp, M
    Durbin, R
    [J]. GENOME RESEARCH, 2004, 14 (05) : 988 - 995
  • [7] The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    Boeckmann, B
    Bairoch, A
    Apweiler, R
    Blatter, MC
    Estreicher, A
    Gasteiger, E
    Martin, MJ
    Michoud, K
    O'Donovan, C
    Phan, I
    Pilbout, S
    Schneider, M
    [J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (01) : 365 - 370
  • [8] Sensitive protein alignments at tree-of-life scale using DIAMOND
    Buchfink, Benjamin
    Reuter, Klaus
    Drost, Hajk-Georg
    [J]. NATURE METHODS, 2021, 18 (04) : 366 - +
  • [9] Caffeic acid O-methyltransferase is involved in the synthesis of melatonin by methylating N-acetylserotonin in Arabidopsis
    Byeon, Yeong
    Lee, Hyoung Yool
    Lee, Kyungjin
    Back, Kyoungwhan
    [J]. JOURNAL OF PINEAL RESEARCH, 2014, 57 (02) : 219 - 227
  • [10] Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    Castresana, J
    [J]. MOLECULAR BIOLOGY AND EVOLUTION, 2000, 17 (04) : 540 - 552