Overview of coffee genome (Coffea canephora L.) and its function in stress response and caffeine biosynthesis

Main Article Content

Overview of coffee genome (Coffea canephora L.) and its function in stress response and caffeine biosynthesis

Tác giả

Nguyễn Đình Sỹ
Nguyễn Văn Tịnh
Trần Văn Cường
Nguyễn Ngọc Hữu

Tóm tắt

Coffea canephora, a coffee species belonging to the Rubiaceae family, is one of the most popular cultivated coffee worldwide. In this study, we overview some important aspects of the genetic genome in C. canephora and also review the candidate genes that involve biotic and abiotic stress response and caffeine biosynthesis in the Coffea genome. It is reported that the C. canephora genome consists of 25,574 protein-coding genes, 2,573 organellar-to-nuclear genome transfers, 6,812 predicted transposable elements (TEs), and 92 microRNA precursors. Coffee-caffeine is synthesized from xanthosine via three methylation steps by NMT genes in C. canephora genome: NMT2: cc02_g09350; DXMT: cc01_g00720; XMT: cc09_g06970; MXMT: cc00_g24720; NMT3: cc09_g06960; MTL: cc09_g06950. C. canephora genome sequence has recently become a new tool for investigating and analyzing coffee resistance and quality at the molecular level.

Article Details

Chuyên mục
Khoa học Tự nhiên
Tiểu sử của Tác giả

Nguyễn Đình Sỹ

Khoa Khoa học Tự nhiên và Công nghệ, Trường Đại học Tây Nguyên;
Tác giả liên hệ: Nguyễn Đình Sỹ; ĐT: 0961367958; Email: ndsy@ttn.edu.vn

Nguyễn Văn Tịnh

Bộ môn Khoa học cơ bản, Đại học Y Dược Buôn Ma Thuột

Trần Văn Cường

Khoa Nông lâm Nghiệp, Trường Đại học Tây Nguyên

Nguyễn Ngọc Hữu

Khoa Nông lâm Nghiệp, Trường Đại học Tây Nguyên

Tài liệu tham khảo

  • Shibin Mohanan (2013). "Involvement of a novel intronic microRNA in cross regulation of N-methytransferase genes involved in caffeine biosynthesis in Coffea canephora". Gene. 519, 107-112.
  • Privat, I., Bardil, A., Gomez, A.B., Severac, D., Dantec, C., Fuentes, I., Mueller, L., Joët, T., David, P., Foucrier, S., Dussert, S., Leroy, T., Journot, L., Kochko, A.D., Campa, C., Combes, M.C., Lashermes, P., Bertrand, B., (2011). The 'PUCE CAFE' Project: the First 15K coffee microarray, a new tool for discovering candidate genes correlated to agronomic and quality traits. BMC Genomics 12, 5.
  • Mishra MK, Slater A (2012), Recent advances in the genetic transformation of coffee. Biotechnol Res Internat 2012:580857.
  • A. Dereeper, R. Guyot, C. Tranchant-Dubreuil, F. Anthony, X. Argout, F. de Bellis, M. C., Combes, F. Gavory, A. de Kochko, D. Kudrna, T. Leroy, J. Poulain, M. Rondeau, X., Song, R. Wing, P. Lashermes, BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution. Plant Mol. Biol. 83, 177–189 (2013). Medline doi:10.1007/ s11103-013-0077-5.
  • A. Pallavicini, L. Del Terra, M.R. Sondahl, (2004). Transcriptomics of resistance response in Coffea arabica L, in Proceedings of the 20th International conference on coffee science (ASIC '04), Bangalore, India, 66– 67.
  • L.G.E. Vieira, A.C. Andrade, C. Colombo, (2006). Brazillian coffee genome project: an EST based genomic resource. Brazillian Journal of Plant Physiology, 18, 1, 95–108.
  • F. Denoeud, L. Carretero-Paulet, A. Dereeper, G. Droc, R. Guyot, M. Pietrella, C. Zheng, A. Alberti, F. Anthony, G. Aprea, J. Aury, P. Bento, M. Bernard, S. Bocs, C. Campa, A. Cenci, M. Combes, D. Crouzillat, C. Da Silva, L. Daddiego, F.D. Bellis, S. Dussert, O. Garsmeur, T. Gayraud, V. Guignon, K. Jahn, V. Jamilloux, T. Joët, K. Labadie, T. Lan, J. Leclercq, M. Lepelley, T. Leroy, L.T. Li, P. Librado, L. Lopez, A. Muñoz, B. Noel, A. Pallavicini, G. Perrotta, V. Poncet, D. Pot, Priyono, M. Rigoreau, M. Rouard, J. Rozas, C. Tranchant-Dubreuil, R. VanBuren, Q. Zhang, A.C. Andrade, X. Argout, B. Bertrand, A.D. Kochko, G. Graziosi, R.J. Henry, Jayarama, R. Ming, C. Nagai, S. Rounsley, D. Sankoff, G. Giuliano, V.A. Albert, P. Wincker, P. Lashermes, (2014). The coffee genome provides insight into the convergent evolution of caffeine biosynthesis, Science, 345, 1181.
  • Alves, et al. (2017). Differential fine-tuning of gene expression regulation in coffee leaves by CcDREB1D promoter haplotypes under water deficit. J. Exp. Bot. 68 (11): 3017-3031.
  • Barbosa, et al. (2010). α -Amylase inhibitor-1 gene from Phaseolus vulgaris expressed in Coffea arabica plants inhibitsα-amylases from the coffee berry borer pest. BMC Biotechnol. 10: 44.
  • Bulgarelli, R. G., P. Araujo, T. Tezotto, P. Mazzafera, and S.A.L. Andrade, (2016). Expression of metallothionein genes in coffee leaves in response to the absence or excess of Cu and Zn. Theor. Exp. Plant Physiol. 28(4): 1-13.
  • Cavallari, B., C.F. Petitot, A.S. Severino, F.E. Maia, and D. Fernandez (2013). In Microbial Pathogens and Strategies for Combating Them: Science, Technology and Education. 1- 774 (ed A. MéndezVilas) (Formatex Research Center, Badajoz).
  • Cavallari, F.B., F.B. Severino, M.P. Maluf, and I.G. Maia. (2009). Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol. Biol. 10(1): 1-11.
  • Cotta, et al. (2014). Lipid transfer proteins in coffee: isolation of Coffea orthologs, Coffea arabica homeologs, expression during coffee fruit development and promoter analysis in transgenic tobacco plants. Plant Mol. Biol. 85(1-2): 11-31.
  • Erika, et al., (2015). Seed-specific stable expression of the α-AI1 inhibitor in coffee grains and the in vivo implications for the development of the coffee berry Borer. Trop. Plant Biol. 8(3-4): 98-107.
  • Fernandes, et al., (2017). A panel of the most suitable reference genes for RT-qPCR expression studies of coffee: screening their stability under different conditions. Tree Genet. Genomes. 13(6): 1-13.
  • Joseph, J.T., N.J. Poolakkalody, and J.M. Shah., (2018). Plant reference genes for development and stress response studies. J. Biosci. 43(1): 73-187.
  • Nguyen, S. and K. Hunseung, (2017). An endoplasmic reticulumlocalized Coffea arabica BURP domaincontaining protein affects the response of transgenic, Arabidopsis plants to diverse abiotic stresses. Plant Cell Rep. 36(11)
  • Nguyen, S., T.Z.T. Sai, G. Nawaz, K. Lee, and H. Kang, (2016). Abiotic stresses affect differently the intron splicing and expression of chloroplast genes in coffee plants (Coffea arabica) and rice (Oryza sativa). J. Plant Physiol. 201(142): 85-94.
  • Silva, K.J.P., N. Mahna, Z. Mou, and K.M. Folta, (2018). NPR1 as a transgenic crop protection strategy in horticultural species. Hortic. Res. 5(1): 1-15.
  • Torres, et al., (2019). Expression of DREB-Like Genes in C. canephora and C. arabica Subjected to Various Types of Abiotic Stress. Tropical Plant Biology. doi:10.1007/s12042-019-09223-5.
  • McCarthy, A. A. et al., (2007). Cloning, expression, crystallization and preliminary X-ray analysis of the XMT and DXMT N-methyltransferases from Coffea canephora (robusta), Acta Crystallographica Section F: Structural Biology and Crystallization Communications. International Union of Crystallography, 63(4), pp. 304–307. doi: 10.1107/S1744309107009268.
  • Perrois, C. et al. (2015). Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta), Planta, 241(1), pp. 179–191. doi: 10.1007/s00425-014-2170-7.
  • Raharimalala, N. et al. (2021). The absence of the caffeine synthase gene is involved in the naturally decaffeinated status of Coffea humblotiana, a wild species from Comoro archipelago, Scientific Reports. Nature Publishing Group UK, 11(1), pp. 1–14. doi: 10.1038/s41598-021-87419-0.
  • Zhou, M. Z. et al. (2020). N-Methyltransferases of Caffeine Biosynthetic Pathway in Plants, Journal of Agricultural and Food Chemistry, 68(52), pp. 15359–15372. doi: 10.1021/acs.jafc.0c06167.
  • C. Noirot, C. Gaspin, T. Schiex, J. Gouzy (2008). LeARN: A platform for detecting, clustering and annotating non-coding RNAs. BMC Bioinformatics 9, 21. Medline doi:10.1186/1471-2105-9-21
  • J. T. Cuperus, N. Fahlgren, J. C. Carrington (2011). Evolution and functional diversification of MIRNA genes. Plant Cell 23, 431–442. Medline doi:10.1105/tpc.110.082784.