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    An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community

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    Type
    Article
    Authors
    Wang, Yong
    Gao, Zhaoming
    Xu, Ying
    Li, Guangyu
    He, Lisheng
    Qian, Pei-Yuan cc
    KAUST Grant Number
    SAC0040
    UK-C0016
    Date
    2016-02-24
    Online Publication Date
    2016-02-24
    Print Publication Date
    2016-02
    Permanent link to this record
    http://hdl.handle.net/10754/623513
    
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    Abstract
    The low biomass in environmental samples is a major challenge for microbial metagenomic studies. The amplification of a genomic DNA was frequently applied to meeting the minimum requirement of the DNA for a high-throughput next-generation-sequencing technology. Using a synthetic bacterial community, the amplification efficiency of the Multiple Annealing and Looping Based Amplification Cycles (MALBAC) kit that is originally developed to amplify the single-cell genomic DNA of mammalian organisms is examined. The DNA template of 10 pg in each reaction of the MALBAC amplification may generate enough DNA for Illumina sequencing. Using 10 pg and 100 pg templates for each reaction set, the MALBAC kit shows a stable and homogeneous amplification as indicated by the highly consistent coverage of the reads from the two amplified samples on the contigs assembled by the original unamplified sample. Although GenomePlex whole genome amplification kit allows one to generate enough DNA using 100 pg of template in each reaction, the minority of the mixed bacterial species is not linearly amplified. For both of the kits, the GC-rich regions of the genomic DNA are not efficiently amplified as suggested by the low coverage of the contigs with the high GC content. The high efficiency of the MALBAC kit is supported for the amplification of environmental microbial DNA samples, and the concerns on its application are also raised to bacterial species with the high GC content.
    Citation
    Wang Y, Gao Z, Xu Y, Li G, He L, et al. (2016) An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community. Acta Oceanologica Sinica 35: 131–136. Available: http://dx.doi.org/10.1007/s13131-015-0781-x.
    Sponsors
    The Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) under contract Nos XDB06010100 and XDB06010200; the National Basic Research Program (973 Program) of China under contract No. 2012CB417304; the National Natural Science Foundation of China under contract No. U1301232; the Sanya Institute of Deep Sea Science and Engineering under contract Nos SIDSSE- 201206, SIDSSE-BR-201303 and SIDSSE-201305; the award from King Abdullah University of Science and Technology under contract No. SAC0040/ UK-C0016.
    Publisher
    Springer Nature
    Journal
    Acta Oceanologica Sinica
    DOI
    10.1007/s13131-015-0781-x
    ae974a485f413a2113503eed53cd6c53
    10.1007/s13131-015-0781-x
    Scopus Count
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