Genome-Wide Identification and Transcriptome Analysis of P450 Superfamily Genes in Flax (Linum usitatissimum L.)
Abstract
1. Introduction
2. Result
2.1. LuP450 Genes Identification and Chromosomal Localization
2.2. Phylogenetic and Classification Relationship of LuP450 Genes
2.3. Conserved Motif and Gene Structure Analysis of LuP450 Genes
2.4. Cis-Acting Elements Analysis of LuP450 Genes
2.5. Intragenomic Covariance Analysis of the LuP450 Gene
2.6. Analysis of P450 Gene Covariance Among Different Genomes
2.7. Expression Pattern Analysis of LuP450 Genes
2.8. RT-qPCR Validation
2.9. Protein–Protein Interaction Analysis
3. Discussion
4. Materials and Methods
4.1. Identification Physiological Features of LuP450 Genes
4.2. Phylogenetic Analysis of LuP450 Genes
4.3. Conserved Domain and Motif Analysis of LuP450 Genes
4.4. Gene Structure, Chromosomal Localization, and Cis-Acting Elements Analysis of LuP450 Genes
4.5. Subcellular Localization Prediction of LuP450 Genes
4.6. Intragenomic Covariance Analysis of LuP450 Genes
4.7. Intergenomic Covariance Analysis of the LuP450 Gene
4.8. LuP450 Gene Expression Analysis
4.9. Protein–Protein Interaction Network Analysis of LuP450 Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Fu, Y.B. Flax domesticationprocesses as inferred from genome-wide SNP data. Sci. Rep. 2025, 15, 8731. [Google Scholar] [CrossRef] [PubMed]
- Huis, R.; Hawkins, S.; Neutelings, G. Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.). BMC Plant Biol. 2010, 10, 71. [Google Scholar] [CrossRef]
- Jenab, M.; Thompson, L.U. The influence of flaxseed and lignans on colon carcinogenesis and beta-glucuronidase activity. Carcinogenesis 1996, 17, 1343–1348. [Google Scholar] [CrossRef]
- Wu, C.F.; Xu, X.M.; Huang, S.H.; Deng, M.C.; Feng, A.J.; Peng, J.; Yuan, J.P.; Wang, J.H. An efficient fermentation method for the degradation of cyanogenic glycosides in flaxseed. Food Addit. Contam. Part A Chem. Anal. Control Expo. Risk Assess. 2012, 29, 1085–1091. [Google Scholar] [CrossRef]
- Oomah, B.D.; Mazza, G.; Kenaschuk, E.O. Cyanogenic compounds in flaxseed. J. Agric. Food Chem. 1992, 40, 1346–1348. [Google Scholar] [CrossRef]
- Niedźwiedź-Siegień, I. Cyanogenic Glucosides In Linum Usitatissimum. Phytochemistry 1998, 49, 59–63. [Google Scholar] [CrossRef]
- Zuk, M.; Pelc, K.; Szperlik, J.; Sawula, A.; Szopa, J. Metabolism of the Cyanogenic Glucosides in Developing Flax: Metabolic Analysis, and Expression Pattern of Genes. Metabolites 2020, 10, 288. [Google Scholar] [CrossRef]
- Werck-Reichhart, D.; Feyereisen, R. Cytochromes P450: A success story. Genome Biol. 2000, 1, reviews3003.1. [Google Scholar] [CrossRef]
- Danielson, P.Á. The cytochrome P450 superfamily: Biochemistry, evolution and drug metabolism in humans. Curr. Drug Metab. 2002, 3, 561–597. [Google Scholar] [CrossRef]
- Frear, D.S.; Swanson, H.R.; Tanaka, F.S. N-demethylation of substituted 3-(phenyl)-1-methylureas: Isolation and characterization of a microsomal mixed function oxidase from cotton. Phytochemistry 1969, 8, 2157–2169. [Google Scholar] [CrossRef]
- Minerdi, D.; Savoi, S.; Sabbatini, P. Role of Cytochrome P450 Enzyme in Plant Microorganisms’ Communication: A Focus on Grapevine. Int. J. Mol. Sci. 2023, 24, 4695. [Google Scholar] [CrossRef] [PubMed]
- Schuler, M.A.; Werck-Reichhart, D. Functional Genomics of P450S. Annu. Rev. Plant Biol. 2003, 54, 629–667. [Google Scholar] [CrossRef] [PubMed]
- Lin, X.; Tang, B.; Li, Z.; Shi, L.; Zhu, H. Genome-wide identification and expression analyses of CYP450 genes in sweet potato (Ipomoea batatas L.). BMC Genom. 2024, 25, 58. [Google Scholar] [CrossRef] [PubMed]
- Shen, C.; Li, X. Genome-wide analysis of the P450 gene family in tea plant (Camellia sinensis) reveals functional diversity in abiotic stress. BMC Genom. 2023, 24, 535. [Google Scholar] [CrossRef]
- Kahn, R.A.; Fahrendorf, T.; Halkier, B.A.; Møller, B.L. Substrate specificity of the cytochrome P450 enzymes CYP79A1 and CYP71E1 involved in the biosynthesis of the cyanogenic glucoside dhurrin in Sorghum bicolor (L.) Moench. Arch. Biochem. Biophys. 1999, 363, 9–18. [Google Scholar] [CrossRef]
- Busk, P.K.; Møller, B.L. Dhurrin synthesis in sorghum is regulated at the transcriptional level and induced by nitrogen fertilization in older plants. Plant Physiol. 2002, 129, 1222–1231. [Google Scholar] [CrossRef]
- Davis, R. Cyanogens. In Toxic Substances in Crop Plants; DeMello, J.P., DeMello, F., Duffus, C.M., Duffus, J.M., Eds.; Royal Society of Chemistry; Cambridge University Press: Cambridge, UK, 1991; pp. 202–225. [Google Scholar]
- Pankov, K.V.; McArthur, A.G.; Gold, D.A.; Nelson, D.R.; Goldstone, J.V.; Wilson, J.Y. The cytochrome P450 (CYP) superfamily in cnidarians. Sci. Rep. 2021, 11, 9834. [Google Scholar] [CrossRef]
- Nelson, D.R. Cytochrome P450 diversity in the tree of life. Biochim. Biophys. Acta BBA—Proteins Proteom. 2018, 1866, 141–154. [Google Scholar] [CrossRef]
- Nelson, D.R. The cytochrome p450 homepage. Hum. Genom. 2009, 4, 59–65. [Google Scholar] [CrossRef]
- Nelson, D.; Werck-Reichhart, D. A P450-centric view of plant evolution. Plant J. 2011, 66, 194–211. [Google Scholar] [CrossRef]
- Ackah, M.; Boateng, N.A.S.; Dhanasekaran, S.; Zhang, H.; Yang, Q. Genome wide and comprehensive analysis of the cytochrome P450 (CYPs) gene family in Pyrus bretschneideri: Expression patterns during Sporidiobolus pararoseus Y16 enhanced with ascorbic acid (VC) treatment. Plant Physiol. Biochem. 2024, 206, 108303. [Google Scholar] [CrossRef] [PubMed]
- Vasav, A.P.; Barvkar, V.T. Phylogenomic analysis of cytochrome P450 multigene family and their differential expression analysis in Solanum lycopersicum L. suggested tissue specific promoters. BMC Genom. 2019, 20, 116. [Google Scholar] [CrossRef]
- Fang, Y.; Jiang, J.; Du, Q.; Luo, L.; Li, X.; Xie, X. Cytochrome P450 Superfamily: Evolutionary and Functional Divergence in Sorghum (Sorghum bicolor) Stress Resistance. J. Agric. Food Chem. 2021, 69, 10952–10961. [Google Scholar] [CrossRef] [PubMed]
- Zhang, X.; Xue, L.; Chen, R.; Ma, Q.; Ma, D.; Liu, X. Genome-wide identification of the cytochrome P450 family and analysis of CYP regarding salt tolerance in Medicago sativa L. Grass Res. 2023, 3, 21. [Google Scholar] [CrossRef]
- Zhang, K.; Qin, Y.; Sun, W.; Shi, H.; Zhao, S.; He, L.; Li, C.; Zhao, J.; Pan, J.; Wang, G.; et al. Phylogenomic Analysis of Cytochrome P450 Gene Superfamily and Their Association with Flavonoids Biosynthesis in Peanut (Arachis hypogaea L.). Genes 2023, 14, 1944. [Google Scholar] [CrossRef] [PubMed]
- Ji, J.; Cao, W.; Yang, L.; Fang, Z.; Zhang, Y.; Zhuang, M.; Lv, H.; Wang, Y.; Liu, Y.; Li, Z.; et al. Genome-wide analysis of cabbage cytochrome P450 genes and characterization of BoCYP704B1, a gene responsible for cabbage anther development. Sci. Hortic. 2021, 283, 110096. [Google Scholar] [CrossRef]
- Babu, P.R.; Rao, K.V.; Reddy, V.D. Structural organization and classification of cytochrome P450 genes in flax (Linum usitatissimum L.). Gene 2013, 513, 156–162. [Google Scholar] [CrossRef]
- Nelson, D.R.; Koymans, L.; Kamataki, T.; Stegeman, J.J.; Feyereisen, R.; Waxman, D.J.; Waterman, M.R.; Gotoh, O.; Coon, M.J.; Estabrook, R.W.; et al. P450 superfamily: Update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 1996, 6, 1–42. [Google Scholar] [CrossRef]
- Liu, X.-M.; Xu, X.; Li, B.-H.; Yao, X.-X.; Zhang, H.-h.; Wang, G.-Q.; Han, Y.-J. Genomic and transcriptomic insights into cytochrome P450 monooxygenase genes involved in nicosulfuron tolerance in maize (Zea mays L.). J. Integr. Agric. 2018, 17, 1790–1799. [Google Scholar] [CrossRef]
- Chen, Y.; Klinkhamer, P.G.L.; Memelink, J.; Vrieling, K. Diversity and evolution of cytochrome P450s of Jacobaea vulgaris and Jacobaea aquatica. BMC Plant Biol. 2020, 20, 342. [Google Scholar] [CrossRef]
- Dauda, W.P.; Abraham, P.; Glen, E.; Adetunji, C.O.; Ghazanfar, S.; Ali, S.; Al-Zahrani, M.; Azameti, M.K.; Alao, S.E.L.; Zarafi, A.B.; et al. Robust Profiling of Cytochrome P450s (P450ome) in Notable Aspergillus spp. Life 2022, 12, 451. [Google Scholar] [CrossRef]
- Zhang, W.; Li, H.; Li, Q.; Wang, Z.; Zeng, W.; Yin, H.; Qi, K.; Zou, Y.; Hu, J.; Huang, B.; et al. Genome-wide identification, comparative analysis and functional roles in flavonoid biosynthesis of cytochrome P450 superfamily in pear (Pyrus spp.). BMC Genom. Data 2023, 24, 58. [Google Scholar] [CrossRef]
- Xia, Y.; Yang, J.; Ma, L.; Yan, S.; Pang, Y. Genome-Wide Identification and Analyses of Drought/Salt-Responsive Cytochrome P450 Genes in Medicago truncatula. Int. J. Mol. Sci. 2021, 22, 9957. [Google Scholar] [CrossRef] [PubMed]
- Ibraheem, O.; Botha, C.E.J.; Bradley, G. In silico analysis of cis-acting regulatory elements in 5′ regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana. Comput. Biol. Chem. 2010, 34, 268–283. [Google Scholar] [CrossRef] [PubMed]
- Li, X.; Wang, L.; Li, W.; Zhang, X.; Zhang, Y.; Dong, S.; Song, X.; Zhao, J.; Chen, M.; Yuan, X. Genome-Wide Identification and Expression Profiling of Cytochrome P450 Monooxygenase Superfamily in Foxtail Millet. Int. J. Mol. Sci. 2023, 24, 11053. [Google Scholar] [CrossRef]
- Otto, S.P.; Yong, P. The evolution of gene duplicates. Adv. Genet. 2002, 46, 451–483. [Google Scholar] [PubMed]
- Hanada, K.; Zou, C.; Lehti-Shiu, M.D.; Shinozaki, K.; Shiu, S.H. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiol. 2008, 148, 993–1003. [Google Scholar] [CrossRef]
- Hao, Y.; Dong, Z.; Zhao, Y.; Tang, W.; Wang, X.; Li, J.; Wang, L.; Hu, Y.; Fang, L.; Guan, X.; et al. Phylogenomic analysis of cytochrome P450 multigene family and its differential expression analysis in pepper (Capsicum annuum L.). Front. Plant Sci. 2022, 13, 1078377. [Google Scholar] [CrossRef]
- Hurst, L.D. The Ka/Ks ratio: Diagnosing the form of sequence evolution. Trends Genet. 2002, 18, 486. [Google Scholar] [CrossRef]
- Navarro, A.; Barton, N.H. Chromosomal speciation and molecular divergence–accelerated evolution in rearranged chromosomes. Science 2003, 300, 321–324. [Google Scholar] [CrossRef]
- Kannangara, R.; Motawia, M.S.; Hansen, N.K.; Paquette, S.M.; Olsen, C.E.; Moller, B.L.; Jorgensen, K. Characterization and expression profile of two UDP-glucosyltransferases, UGT85K4 and UGT85K5, catalyzing the last step in cyanogenic glucoside biosynthesis in cassava. Plant J. 2011, 68, 287–301. [Google Scholar] [CrossRef] [PubMed]
- Zhao, X.; Yi, L.; Zuo, Y.; Gao, F.; Cheng, Y.; Zhang, H.; Zhou, Y.; Jia, X.; Su, S.; Zhang, D.; et al. High-Quality Genome Assembly and Genome-Wide Association Study of Male Sterility Provide Resources for Flax Improvement. Plants 2023, 12, 2773. [Google Scholar] [CrossRef]
- Stajich, J.E.; Block, D.; Boulez, K.; Brenner, S.E.; Chervitz, S.A.; Dagdigian, C.; Fuellen, G.; Gilbert, J.G.; Korf, I.; Lapp, H.; et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002, 12, 1611–1618. [Google Scholar] [CrossRef]
- He, Z.; Zhang, H.; Gao, S.; Lercher, M.J.; Chen, W.-H.; Hu, S. Evolview v2: An online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res. 2016, 44, W236–W241. [Google Scholar] [CrossRef] [PubMed]
- Lescot, M.; Déhais, P.; Thijs, G.; Marchal, K.; Moreau, Y.; Van de Peer, Y.; Rouzé, P.; Rombauts, S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002, 30, 325–327. [Google Scholar] [CrossRef]
- Chen, C.; Wu, Y.; Li, J.; Wang, X.; Zeng, Z.; Xu, J.; Liu, Y.; Feng, J.; Chen, H.; He, Y.; et al. TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining. Mol. Plant 2023, 16, 1733–1742. [Google Scholar] [CrossRef]
- Horton, P.; Park, K.J.; Obayashi, T.; Fujita, N.; Harada, H.; Adams-Collier, C.J.; Nakai, K. WoLF PSORT: Protein localization predictor. Nucleic Acids Res. 2007, 35, W585–W587. [Google Scholar] [CrossRef]
- Koch, M.A.; Haubold, B.; Mitchell-Olds, T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 2000, 17, 1483–1498. [Google Scholar] [CrossRef] [PubMed]
- Sun, J.; Lu, F.; Luo, Y.; Bie, L.; Xu, L.; Wang, Y. OrthoVenn3: An integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res. 2023, 51, W397–W403. [Google Scholar] [CrossRef]
- Szklarczyk, D.; Franceschini, A.; Kuhn, M.; Simonovic, M.; Roth, A.; Minguez, P.; Doerks, T.; Stark, M.; Muller, J.; Bork, P.; et al. The STRING database in 2011: Functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2011, 39, D561–D568. [Google Scholar] [CrossRef]
- Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N.S.; Wang, J.T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13, 2498–2504. [Google Scholar] [CrossRef] [PubMed]
- Bader, G.D.; Hogue, C.W. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 2003, 4, 2. [Google Scholar] [CrossRef] [PubMed]
Gene ID | Forward Primer | Reverse Primer |
---|---|---|
EF1A-F | GCTGCCAACTTCACATCTCA | GATCGCCTGTCAATCTTGGT |
LuP450-357-CYP81C | CACACACTCACCCAACGCTACG | CGACGGACGGCGAGGAGAG |
LuP450-355-CYP81Q | GACATGGAAGAGGCGGATCAGTTC | GCCAAAGCCAACCCATTTCAAGAG |
LuP450-187-CYP72A | TGATGATGCTGGCGAGTTTAACCC | TCCTCGGACCCCACCCAAATG |
LuP450-411-CYP71BE | CGTCAAGTGTGATAGCCAGGTCAG | ACCTCCAGCCAACTCCAGACTG |
LuP450-249-CYP71D | AGCGGCGAGGGAGGTGTTC | TCGGAGCGGTCGTAGGTGATG |
LuP450-383-CYP82L | CTTCTGTCCAACCACCGCATCG | AACGCCAACTCCTCCAACAACTG |
LuP450-189-CYP82J | CGTTCCACCACCAGTCATCCAC | AGAGGGTTAGGGCGAGAGGTTTC |
LuP450-389-CYP709F | ACCCAGTATCTTCCTACGCCATCG | CCATAACCACCACCACCACCTTTG |
LuP450-395-CYP71AS | GACAAAGGCAGGGTGACAGAAGAC | GAGAGGAGCGGGTGGGTGAAG |
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2025 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
Share and Cite
Wu, Y.; Sa, R.; Mu, Y.; Zhou, Y.; Li, Z.; Song, X.; Tang, L.; Liu, D.; Yi, L. Genome-Wide Identification and Transcriptome Analysis of P450 Superfamily Genes in Flax (Linum usitatissimum L.). Int. J. Mol. Sci. 2025, 26, 3637. https://doi.org/10.3390/ijms26083637
Wu Y, Sa R, Mu Y, Zhou Y, Li Z, Song X, Tang L, Liu D, Yi L. Genome-Wide Identification and Transcriptome Analysis of P450 Superfamily Genes in Flax (Linum usitatissimum L.). International Journal of Molecular Sciences. 2025; 26(8):3637. https://doi.org/10.3390/ijms26083637
Chicago/Turabian StyleWu, Yang, Rula Sa, Yingnan Mu, Yu Zhou, Zhiwei Li, Xixia Song, Lili Tang, Dandan Liu, and Liuxi Yi. 2025. "Genome-Wide Identification and Transcriptome Analysis of P450 Superfamily Genes in Flax (Linum usitatissimum L.)" International Journal of Molecular Sciences 26, no. 8: 3637. https://doi.org/10.3390/ijms26083637
APA StyleWu, Y., Sa, R., Mu, Y., Zhou, Y., Li, Z., Song, X., Tang, L., Liu, D., & Yi, L. (2025). Genome-Wide Identification and Transcriptome Analysis of P450 Superfamily Genes in Flax (Linum usitatissimum L.). International Journal of Molecular Sciences, 26(8), 3637. https://doi.org/10.3390/ijms26083637