Rapid and economical protocols for genomic and metagenomic DNA extraction from oak (Quercus brantii Lindl.)

  • Elahe Ahmadi
  • Mojegan Kowsari
  • Davoud Azadfar
  • Gholamreza Salehi Jouzani
Original Paper

Abstract

Key message

Two new efficient, fast and low-cost metagenomic DNA extraction methods were developed for different Persian oak tissues (leaf, stem, root, and rhizospheric) and soil samples.

Context

The new “omics” studies on the genus Quercus are of importance to help finding efficient strategies for overcoming environmental challenges, and to do this, presence of efficient DNA extraction protocols for different Quercus species are very critical.

Aims

The objective of the present study was to develop new efficient methods for extraction of metagenomic DNA (mDNA) from of Persian oak (Quercus brantii Lindl.) tissues.

Methods

The efficiency of two newly developed mDNA extraction methods, including indirect SDS-based (ISB or concentrate method) and one spin column-based method (SCB) were compared to that of two classical direct methods, including CTAB-based and SDS-based methods, and two commercial mDNA extraction kits.

Results

The maximum average yield of mDNA for all samples (leaf, stem, root, bulk, and rhizospheric soils) was obtained by SCB (258 ng/μl) and ISB (189 ng/μl) methods, respectively. Successful PCR amplification for 16SrRNA and ITS sequence was consistently observed for ISB, SCB, and kit-extracted mDNAs, which confirmed the high purity of mDNA extracted by these methods. The new methods showed more than 96% quantitative PCR efficiency, and partial restriction digestion and metagenomic library construction confirmed the high efficiency of the newly developed methods.

Conclusion

It could be concluded that two new protocols enhanced efficiency (yield, purity, and cost) of mDNA extraction from different tissues of Persian oak.

Keywords

Indirect SDS-based method (ISB) Metagenomic DNA extraction Microbiome Oak decline Quercus brantii Spin column-based method (SCB) 

Notes

Acknowledgements

The authors are very grateful to Eng. Ebrahim Karimi, Eng. Morteza Ebrahimi Rastaghi, Eng. Saadi Karami, and Eng. Amin Alidadi for their kind technical assistances in development of the protocols.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. 1.Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran (ABRII)Agricultural Research, Education and Extension Organization (AREEO)KarajIran
  2. 2.Department of Silviculture and Forest EcologyFaculty of Forest Sciences, Gorgan University of Agricultural Sciences and Natural ResourcesGorganIran

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