DNA extraction

DNA extraction from wood can be challenging due to the highly degraded nature of wood and the presence of secondary metabolites such as phenolic and lignin compounds [1].

Methods for extracting DNA from wood:

  1. Modified CTAB protocol: This protocol involves the use of cetyltrimethylammonium bromide (CTAB) to extract DNA from wood samples. The protocol has been modified to optimize the total genomic DNA extraction protocol and increase DNA yield and purity [1].

  2. SDS-based method: This method involves the use of sodium dodecyl sulfate (SDS) to extract DNA from wood samples. The quality of extracted DNA varies across authentic wood samples [2].

  3. CCDB method: This method involves the use of a commercial kit to extract DNA from wood samples. It has been shown to be effective for extracting good quality DNA from authentic wood samples and processed wood products [2].

  4. Decontamination and sampling: This method involves decontaminating, sampling, and processing wood at various stages of decay for high-throughput extraction and purification of DNA [3].

DNA extraction from wood can be influenced by various factors such as the radial position of wood in the stem, the drying treatment, and the presence of chemical compounds that could compromise the quality of the DNA extracted [5][6].

 

Common challenges in DNA extraction from wood:

  • Presence of secondary metabolites: Wood contains high quantities of secondary metabolites such as polyphenols, tannins, and terpenoids, which can interfere with DNA extraction.
  • Degradation of DNA: The degeneration of DNA starts after the death of a cell, which results in the splitting of intact DNA into small fragments. With the influence of storage time and drying treatment, wood DNA becomes more seriously degraded.
  • Low quantity of DNA: Only small amounts of DNA are present in wood tissues, even in living trees.
  • Radial position of wood in the stem: The radial position of wood in the stem can influence the efficiency of DNA extraction.
  • Drying treatment: The drying treatment can also influence the efficiency of DNA extraction from wood.
  • Processed wood: Processed wood is mechanically treated and may contain chemical compounds that could compromise the quality of the DNA extracted

The modified CTAB protocol has been shown to be effective for extracting good quality DNA from authentic wood samples and processed wood products.

 

DNA extraction from wood has several limitations due to the highly degraded nature of wood and the presence of secondary metabolites such as phenolic and lignin compounds.

Limitations of DNA extraction from wood:

  1. Low DNA yield: Only small amounts of DNA are present in wood tissues, even in living trees, which can limit the amount of DNA that can be extracted
  2. Degradation of DNA: The degradation of DNA starts after the death of a cell, which results in the splitting of intact DNA into small fragments. With the influence of storage time and drying treatment, wood DNA becomes more seriously degraded
  3. Presence of secondary metabolites: Wood contains high quantities of secondary metabolites such as polyphenols, tannins, and terpenoids, which can interfere with DNA extraction
  4. Radial position of wood in the stem: The radial position of wood in the stem can influence the efficiency of DNA extraction
  5. Drying treatment: The drying treatment can also influence the efficiency of DNA extraction from wood
  6. Processed wood: Processed wood is mechanically treated and may contain chemical compounds that could compromise the quality of the DNA extracted
  7. Limited availability of fresh wood: DNA extraction from fresh wood is routine in studies of tropical forest species, but DNA extraction from wood is difficult due to its highly degraded nature

 

The differences in DNA extraction between fresh and dried wood can be significant due to the highly degraded nature of wood and the presence of secondary metabolites such as phenolic and lignin compounds [1].

Differences in DNA extraction between fresh and dried wood:

Fresh Wood

 Dried Wood

  • Extraction results from fresh wood samples showed thick smeared bands on both extraction methods [1][3].

  • Fresh wood samples generally contain more intact DNA than dried wood samples [1][3].

  • Fresh wood samples may contain less secondary metabolites than dried wood samples, which can interfere with DNA extraction [6].

  • Extraction results from dried wood indicated no visualization in the gel [1][3].

  • DNA extraction from dried wood is generally more difficult than from fresh wood due to the highly degraded nature of the DNA [4][5][6].

  • Dried wood samples may contain more secondary metabolites than fresh wood samples, which can interfere with DNA extraction [6].

 

It is important to optimize the DNA extraction protocol for both fresh and dried wood to increase DNA yield and purity [1][3]. 

 

To practise DNA extraction use PraxiLabs

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