Open AccessDNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia
Author(s) -
Jayaraj Vijaya Kumaran,
Arvind V Rajasegar Suraj,
Azrinaaini Md Yusof,
Suganthi Appalasamy,
Seri Intan Mokhtar,
Dennis Choon Yung Ten,
Tao Deng
Publication year - 2017
Publication title -
journal of tropical resources and sustainable science/journal of tropical resources and sustainable science
Language(s) - English
Resource type - Journals
eISSN - 2462-2389
pISSN - 2289-3946
DOI - 10.47253/jtrss.v5i2.587
Subject(s) - metagenomics , whale , biology , dna extraction , ecology , polymerase chain reaction , genetics , gene
The objective of this study was to determine the expected minimum number of sequence readsneeded to achieve full coverage of the microbial species found in the gut of giant panda This wasdone by first, analyzing five different mammalian metagenomes namely horse, coyote, whitetaildeer, humpback whale and the bottlenose dolphin as metagenomic references; based on anapproximate of 1,000,000 sequence read estimation. After rarefaction analysis using MG-RASTVersion 3.0 analysis pipeline, an average value of 775,075 reads was found to be sufficient formetagenomic analysis. Next, the fecal matter of giant panda was sampled at Zoo Negara, andDNA extraction was performed. DNA extraction was then subjected to DNA qualification andquantification analysis; where the results show that the samples are still viable and sufficient inyield to be used for library preparation. After library preparation, the samples were sequencedusing IlluminaTM MiSeq® next generation sequencer. The results of this research serve as afoundation for further studies of the giant panda metagenome.