Optimization of microbial DNA extraction from Dendrocalamus asper (buluh betung) for metagenomic sequencing.

Isolation of genomic DNA of microbial cells in the woody plants presents a special
challenge to molecular work especially when several plant metabolites such as phenolic
compound that have chemical properties similar to those of nucleic acids which cause
these compounds to co-precipitate with DNA and RNA thus resulting in low quantity
and quality of the nucleic acid. In view of the fact that none of the published protocol
has established itself as universally applicable to extract DNA of plant microbes from all
plant varieties, the commonly used techniques require adaptation before it can be used
with plant samples. In this work, attempts were made to extract a good quality DNA
from woody sample of Dendrocalamus asper (Buluh Betung) using different protocols
including conventional and extraction kit involving the use of Cetyltrimethylammonium
Bromide ( CTAB) and Sodium Dodecyl Sulphate (SDS) buffers together with Wizard
Genomic DNA purification Kit. Apart from that, the types of chemicals beside the
external factors that have significant effects on the condition of the extracted were also
emphasized in this review. The extracted genomic DNA was eventually subjected to
agarose gel electrophoresis and spectrophotometer to determine its yield and purity
levels. In comparison of all the four different protocol, it was found that the carefully
modified CTAB conventional method generally produces a consistent and higher yield
of DNA with a concentration of 19.66 ng/μL in relative to only 8.90 ng/μL of DNA
concentration for DNA extracted using SDS-based DNA extraction buffer as well as the
extraction kit. Therefore, the CTAB- based extraction buffer method was proven to be
reliable in generating a good quality of DNA from these particular genera.