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

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• 作者：Yong Wang ; Zhaoming Gao ; Ying Xu ; Guangyu Li ; Lisheng He…
• 刊名：Acta Oceanologica Sinica
• 出版年：2016
• 出版时间：February 2016
• 年：2016
• 卷：35
• 期：2
• 页码：131-136
• 全文大小：656 KB
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• 作者单位：Yong Wang (1) (2)
  Zhaoming Gao (1) (2)
  Ying Xu (2) (3)
  Guangyu Li (4)
  Lisheng He (1) (2)
  Peiyuan Qian (2)
  
  1. Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences (CAS), Sanya, 572000, China
  2. Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
  3. School of Life Science, Shenzhen University, Shenzhen, 518000, China
  4. Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, China
  
• 刊物主题：Oceanography; Climatology; Ecology; Engineering Fluid Dynamics; Marine & Freshwater Sciences; Environmental Chemistry;
• 出版者：Springer Berlin Heidelberg
• ISSN：1869-1099

文摘

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.