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    Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counts Obtained for per g of Seawater Sample

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    Type
    Book Chapter
    Authors
    Kudo, Toshiaki
    Reza, Md. Shaheed
    Kobiyama, Atsushi
    Rashid, Jonaira
    Yamada, Yuichiro
    Ikeda, Yuri
    Ikeda, Daisuke
    Mizusawa, Nanami
    Yanagisawa, Saki
    Ikeo, Kazuho
    Sato, Shigeru
    Ogata, Takehiko
    Kaga, Shinnosuke
    Watanabe, Shiho
    Naiki, Kimiaki
    Kaga, Yoshimasa
    Segawa, Satoshi
    Mineta, Katsuhiko cc
    Bajic, Vladimir B. cc
    Gojobori, Takashi cc
    Watabe, Shugo
    KAUST Department
    Computational Bioscience Research Center (CBRC)
    Applied Mathematics and Computational Science Program
    Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
    Bioscience Program
    Biological and Environmental Sciences and Engineering (BESE) Division
    Date
    2019-07-25
    Online Publication Date
    2019-07-25
    Print Publication Date
    2019
    Embargo End Date
    2020-07-25
    Permanent link to this record
    http://hdl.handle.net/10754/656340
    
    Metadata
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    Abstract
    Development of high-throughput DNA sequencing technologies has enabled scientists to generate vast amounts of genetic information that may provide a comprehensive understanding of key roles played by environmental microorganisms. Generally the microorganisms inhabit a particular niche and correlate well with environmental changes. It is accepted that the read counts obtained through metagenomic analyses correlate semi-quantitatively with the relative abundance of bacterial species. In our marine metagenomic study conducted on the Ofunato Bay, Iwate Prefecture, Japan, we observed such correlation which exists for bacterioplankton Candidatus Pelagibacter ubique, identified as the dominant bacterial species of the bay. Shotgun metagenomic analyses identified three strains of Ca. Pelagibacter in the bay, viz., dmdA-HTCC1062, dmdA-HTCC9022, and O19-dmdA, that showed a dynamic change throughout the year particularly in the 10-m depth zone. Interestingly, the total abundances of those strains that fall in the Ca. Pelagibacter genus were found to correlate well with the read counts per g seawater samples used for analyses. It is assumed that whole-genome sequence (WGS) reads for members of the metagenome would show similar trend provided that proper precautions are taken to ensure collection of representative sample from the environment.
    Citation
    Kudo, T., Reza, M. S., Kobiyama, A., Rashid, J., Yamada, Y., Ikeda, Y., … Watabe, S. (2019). Marine Metagenomic Sequence Counts of Reads Assigned to Taxa Consistently Proportionate to Read Counts Obtained for per g of Seawater Sample. Marine Metagenomics, 183–188. doi:10.1007/978-981-13-8134-8_12
    Publisher
    Springer Nature
    DOI
    10.1007/978-981-13-8134-8_12
    Additional Links
    http://link.springer.com/10.1007/978-981-13-8134-8_12
    ae974a485f413a2113503eed53cd6c53
    10.1007/978-981-13-8134-8_12
    Scopus Count
    Collections
    Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Book Chapters; Computer, Electrical and Mathematical Science and Engineering (CEMSE) Division

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