DNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia
The objective of this study was to determine the expected minimum number of sequence reads needed to achieve full coverage of the microbial species found in the gut of giant panda This was done by first, analyzing five different mammalian metagenomes namely horse, coyote, whitetail deer, humpback wh...
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ftumalaykelantan:oai:ojs2020.journal.umk.edu.my:article/587 2023-05-15T16:36:01+02:00 DNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia Vijaya Kumaran, Jayaraj Suraj , Arvind V Rajasegar Md Yusof, Azrinaaini Appalasamy, Suganthi Mokhtar, Seri Intan Ten, Dennis Choon Yung Deng, Tao 2017-12-31 application/pdf http://journal.umk.edu.my/index.php/jtrss/article/view/587 https://doi.org/10.47253/jtrss.v5i2.587 eng eng UMK Press http://journal.umk.edu.my/index.php/jtrss/article/view/587/397 http://journal.umk.edu.my/index.php/jtrss/article/view/587 doi:10.47253/jtrss.v5i2.587 Journal of Tropical Resources and Sustainable Science (JTRSS) Vol. 5 No. 2 (2017): Journal of Tropical Resources and Sustainable Science; 117-120 2462-2389 10.47253/jtrss.v5i2 Giant panda Illumina MiSeq metagenomic analysis info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Peer-reviewed Article 2017 ftumalaykelantan https://doi.org/10.47253/jtrss.v5i2.587 https://doi.org/10.47253/jtrss.v5i2 2022-12-03T12:34:06Z The objective of this study was to determine the expected minimum number of sequence reads needed to achieve full coverage of the microbial species found in the gut of giant panda This was done by first, analyzing five different mammalian metagenomes namely horse, coyote, whitetail deer, humpback whale and the bottlenose dolphin as metagenomic references; based on an approximate of 1,000,000 sequence read estimation. After rarefaction analysis using MG-RAST Version 3.0 analysis pipeline, an average value of 775,075 reads was found to be sufficient for metagenomic analysis. Next, the fecal matter of giant panda was sampled at Zoo Negara, and DNA extraction was performed. DNA extraction was then subjected to DNA qualification and quantification analysis; where the results show that the samples are still viable and sufficient in yield to be used for library preparation. After library preparation, the samples were sequenced using IlluminaTM MiSeq® next generation sequencer. The results of this research serve as a foundation for further studies of the giant panda metagenome. Article in Journal/Newspaper Humpback Whale Open Journal System Universiti Malaysia Kelantan (UMK) Journal of Tropical Resources and Sustainable Science (JTRSS) 5 2 117 120 |
institution |
Open Polar |
collection |
Open Journal System Universiti Malaysia Kelantan (UMK) |
op_collection_id |
ftumalaykelantan |
language |
English |
topic |
Giant panda Illumina MiSeq metagenomic analysis |
spellingShingle |
Giant panda Illumina MiSeq metagenomic analysis Vijaya Kumaran, Jayaraj Suraj , Arvind V Rajasegar Md Yusof, Azrinaaini Appalasamy, Suganthi Mokhtar, Seri Intan Ten, Dennis Choon Yung Deng, Tao DNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia |
topic_facet |
Giant panda Illumina MiSeq metagenomic analysis |
description |
The objective of this study was to determine the expected minimum number of sequence reads needed to achieve full coverage of the microbial species found in the gut of giant panda This was done by first, analyzing five different mammalian metagenomes namely horse, coyote, whitetail deer, humpback whale and the bottlenose dolphin as metagenomic references; based on an approximate of 1,000,000 sequence read estimation. After rarefaction analysis using MG-RAST Version 3.0 analysis pipeline, an average value of 775,075 reads was found to be sufficient for metagenomic analysis. Next, the fecal matter of giant panda was sampled at Zoo Negara, and DNA extraction was performed. DNA extraction was then subjected to DNA qualification and quantification analysis; where the results show that the samples are still viable and sufficient in yield to be used for library preparation. After library preparation, the samples were sequenced using IlluminaTM MiSeq® next generation sequencer. The results of this research serve as a foundation for further studies of the giant panda metagenome. |
format |
Article in Journal/Newspaper |
author |
Vijaya Kumaran, Jayaraj Suraj , Arvind V Rajasegar Md Yusof, Azrinaaini Appalasamy, Suganthi Mokhtar, Seri Intan Ten, Dennis Choon Yung Deng, Tao |
author_facet |
Vijaya Kumaran, Jayaraj Suraj , Arvind V Rajasegar Md Yusof, Azrinaaini Appalasamy, Suganthi Mokhtar, Seri Intan Ten, Dennis Choon Yung Deng, Tao |
author_sort |
Vijaya Kumaran, Jayaraj |
title |
DNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia |
title_short |
DNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia |
title_full |
DNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia |
title_fullStr |
DNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia |
title_full_unstemmed |
DNA Extraction and Library Preparation Optimization for Metagenomic Analysis of Giant Panda in Malaysia |
title_sort |
dna extraction and library preparation optimization for metagenomic analysis of giant panda in malaysia |
publisher |
UMK Press |
publishDate |
2017 |
url |
http://journal.umk.edu.my/index.php/jtrss/article/view/587 https://doi.org/10.47253/jtrss.v5i2.587 |
genre |
Humpback Whale |
genre_facet |
Humpback Whale |
op_source |
Journal of Tropical Resources and Sustainable Science (JTRSS) Vol. 5 No. 2 (2017): Journal of Tropical Resources and Sustainable Science; 117-120 2462-2389 10.47253/jtrss.v5i2 |
op_relation |
http://journal.umk.edu.my/index.php/jtrss/article/view/587/397 http://journal.umk.edu.my/index.php/jtrss/article/view/587 doi:10.47253/jtrss.v5i2.587 |
op_doi |
https://doi.org/10.47253/jtrss.v5i2.587 https://doi.org/10.47253/jtrss.v5i2 |
container_title |
Journal of Tropical Resources and Sustainable Science (JTRSS) |
container_volume |
5 |
container_issue |
2 |
container_start_page |
117 |
op_container_end_page |
120 |
_version_ |
1766026335861342208 |