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

WANG Yong; GAO Zhaoming; XU Ying; LI Guangyu; HE Lisheng; QIAN Peiyuan

doi:10.1007/s13131-015-0781-x

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Article Navigation > Acta Oceanologica Sinica > 2016 > 35(2): 131-136

WANG Yong, GAO Zhaoming, XU Ying, LI Guangyu, HE Lisheng, QIAN Peiyuan. An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community[J]. Acta Oceanologica Sinica, 2016, 35(2): 131-136. doi: 10.1007/s13131-015-0781-x

Citation:

WANG Yong, GAO Zhaoming, XU Ying, LI Guangyu, HE Lisheng, QIAN Peiyuan. An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community[J]. Acta Oceanologica Sinica, 2016, 35(2): 131-136. doi: 10.1007/s13131-015-0781-x

Citation:

WANG Yong, GAO Zhaoming, XU Ying, LI Guangyu, HE Lisheng, QIAN Peiyuan. An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community[J]. Acta Oceanologica Sinica, 2016, 35(2): 131-136. doi: 10.1007/s13131-015-0781-x

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

doi: 10.1007/s13131-015-0781-x

1.
Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences (CAS), Sanya 572000, China;Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
2.
Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China;School of Life Science, Shenzhen University, Shenzhen 518000, China
3.
Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
4.
Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China

Received Date: 2014-08-20
Rev Recd Date: 2014-12-26

Abstract

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.
- bacterial DNA,
- MALBAC,
- metagenome amplification

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