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A Method of DNA Extraction from Plants for Metagenomic Analysis Based on the Example of Grape Vitis amurensis Rupr.

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Abstract

A new method for extracting DNA from plants is proposed, using the example of wild grapes Vitis amurensis Rupr. for further preparation of libraries for metagenomic analysis. The method is based on the isolation of DNA by an inexpensive CTAB method with an additional stage of DNA purification using silica spin columns (CTAB-spin method). A comparative analysis of the results of metagenomic analysis of endophytes on DNA isolated using the proposed CTAB-spin method and using the commercial kit ZymoBIOMICS DNA Miniprep (Zymo Research) was performed. It was found that when using the CTAB-spin method, the number of sequences of the 16S rRNA site and the diversity of bacterial genera were 2.8 and 1.2 times greater, respectively, than when using the ZymoBIOMICS kit. At the same time, the number of sequences of the internal transcribed spacer 1 (ITS1) and the biodiversity of endophytic fungi did not differ significantly during DNA extraction by two methods. Thus, the proposed method of DNA isolation for metagenomic analysis is an available and effective alternative to commercial kits for the isolation of plant DNA for new-generation sequencing methods.

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REFERENCES

  1. Behjati, S. and Tarpey, P.S., ADS—Educ. Pract., 2013, vol. 98, pp. 236–238.

    Google Scholar 

  2. Slatko, B.E., Gardner, A.F., and Ausubel, F.M., Curr. Protoc. Mol. Biol., 2018, vol. 122, p. e59. https://doi.org/10.1002/cpmb.59

    Article  PubMed  PubMed Central  Google Scholar 

  3. Kulski, J.K., Next-Generation Sequencing—An Overview of the History, Tools, and “Omic” Applications, Kulski, J.K., Ed., IntechOpen, 2016, p. 60. https://doi.org/10.5772/61964

  4. Lam, H.Y.K., Clark, M.J., Chen, R., Chen, R., Natsoulis, G., O’Huallachain, M., et al., Nat. Biotechnol., 2012, vol. 30, pp. 78–82.

    Article  CAS  Google Scholar 

  5. Wang, Z., Gerstein, M., and Snyder, M., Nat. Rev. Genet., 2009, vol. 10, pp. 57–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Rabbani, B., Tekin, M., and Mahdieh, N., J. Hum. Genet., 2014, vol. 59, pp. 5–15.

    Article  CAS  PubMed  Google Scholar 

  7. Leo, V.C., Morgan, N.V., Bem, D., Jones, M.L., Lowe, G.C., Lordkipanidze, M., et al., J. Thromb. Haemostas., 2015, vol. 13, pp. 643–650.

    Article  CAS  Google Scholar 

  8. Kulski, J.K., Suzuki, S., Ozaki, Y., Mitsunaga, S., Inoko, H., and Shiina, T., Phase HLA Genotyping by NGS—A Comparison Between two Massively Parallel Sequencing Bench-top Systems, the Roche GS Junior and Ion Torrent PGM, Xi, Y., Ed., IntechOpen, 2014, pp. 141–181.

    Google Scholar 

  9. Pelizzola, M. and Ecker, J.R., FEBS Lett., 2011, vol. 585, pp. 1994–2000.

    Article  CAS  PubMed  Google Scholar 

  10. Simner, P.J., Miller, S., and Carroll, K.C., Clin. Infect. Dis., 2018, vol. 66, pp. 778–788.

    Article  CAS  PubMed  Google Scholar 

  11. Boers, S.A., Jansen, R., and Hays, J.P., Eur. J. Clin. Microbiol. Infect. Dis., 2019, vol. 38, pp. 1059–1070.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chiu, C.Y. and Miller, S.A., Nat. Rev. Genet., 2019, vol. 20, pp. 341–355.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Iquebal, M.A., Jagannadham, J., Jaiswal, S., Prabha, R., Rai, A., and Kumar, D., Front. Microbiol., 2022, vol. 13, p. 708335. https://doi.org/10.3389/fmicb.2022.708335

    Article  PubMed  PubMed Central  Google Scholar 

  14. Fan, Y., Gao, L., Chang, P., and Li, Z., Ann. Microbiol., 2020, vol. 70, p. 30. https://doi.org/10.1186/s13213-020-01574-9

    Article  Google Scholar 

  15. Cureau, N., Threlfall, R., Marasini, D., Lavefve, L., and Carbonero, F., Microbiol. Ecol., 2021, vol. 82, pp. 845–858.

    Article  CAS  Google Scholar 

  16. Marasco, R., Rolli, E., Fusi, M., Michoud, G., and Daffonchio, D., Microbiome, 2018, vol. 6, p. 3. https://doi.org/10.1186/s40168-017-0391-2

    Article  PubMed  PubMed Central  Google Scholar 

  17. Deyett, E. and Rolshausen, P.E., Front. Plant Sci., 2019, vol. 10, p. 1246. https://doi.org/10.3389/fpls.2019.01246

    Article  PubMed  PubMed Central  Google Scholar 

  18. Kiselev, K.V., Tyunin, A.P., and Karetin, Y.A., Plant Cell Rep., 2015, vol. 34, pp. 311–320.

    Article  CAS  PubMed  Google Scholar 

  19. Ogneva, Z.V., Dubrovina, A.S., and Kiselev, K.V., Biol. Plant., 2016, vol. 60, pp. 628–634.

    Article  CAS  Google Scholar 

  20. Aleynova, O.A., Nityagovsky, N.N., Dubrovina, A.S., and Kiselev, K.V., Plants, 2022, vol. 11, p. 1128. https://doi.org/10.3390/plants10071276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Deyett, E. and Rolshausen, P.E., FEMS Microbiol. Ecol., 2020, vol. 96, p. fiaa053. https://doi.org/10.1093/femsec/fiaa053

  22. Bolyen, E., Rideout, J.R., Dillon, M.R., Bokulich, N.A., and Abnet, C.C., Al-Ghalith, M., et al., Nat. Biotechnol., 2019, vol. 37, pp. 852–857.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Callahan, B.J., McMurdie, P.J., Rosen, M.J., Han, A.W., Johnson, A.J.A., and Holmes, S.P., Nat. Methods, 2016, vol. 13, pp. 581–583.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., et al., J. Machine Learn. Res., 2011, vol. 12, pp. 2825–2830.

    Google Scholar 

  25. Bokulich, N.A., Kaehler, B.D., Rideout, J.R., Dillon, M., Bolyen, E., et al., Microbiome, 2018, vol. 6, p. 90. https://doi.org/10.1186/s40168-018-0470-z

    Article  PubMed  PubMed Central  Google Scholar 

  26. Nilsson, R.H., Larsson, K.-H., Taylor, A.F.S., Bengtsson-Palme, J., Jeppesen, T.S., Schigel, D., et al., Nucleic Acids Res., 2019, vol. 47, pp. D259–D264.

    Article  CAS  PubMed  Google Scholar 

  27. McMurdie, P.J. and Holmes, S., PLoS One, 2013, vol. 8, p. e61217. https://doi.org/10.1371/journal.pone.0061217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L.D., Francois, R., et al., J. Open Source Software, 2019, vol. 4, p. 1686. https://doi.org/10.21105/joss.01686

    Article  Google Scholar 

  29. Oksanen, J., Blanchet, F.G., Friendly, M., Kindt, R., Legendre, P., McGlinn, D., et al., Vegan: Community Ecology Package, R Package Version 2.5-7. 2020. https://cran.r-project.org/web/packages/vegan/vegan.pdf. Accessed January 9, 2023.

  30. Gu, Z., Eils, R., and Schlesner, M., Bioinformatics, 2016, vol. 32, pp. 2847–2849.

    Article  CAS  PubMed  Google Scholar 

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Funding

The research was supported by the Russian Science Foundation, project no. 22-74-10001, https://rscf.ru/project/22-74-10001.

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Authors and Affiliations

  1. Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch, Russian Academy of Sciences, Laboratory of Biotechnology, 690022, Vladivostok, Russia

    K. V. Kiselev, N. N. Nityagovsky & O. A. Aleynova

Authors
  1. K. V. Kiselev
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  2. N. N. Nityagovsky
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  3. O. A. Aleynova
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Correspondence to O. A. Aleynova.

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The authors declare that they have no conflicts of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

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Translated by E. Makeeva

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Kiselev, K.V., Nityagovsky, N.N. & Aleynova, O.A. A Method of DNA Extraction from Plants for Metagenomic Analysis Based on the Example of Grape Vitis amurensis Rupr.. Appl Biochem Microbiol 59, 361–367 (2023). https://doi.org/10.1134/S0003683823030110

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  • DOI: https://doi.org/10.1134/S0003683823030110

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