An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community
Wang Yong1,2; Gao Zhaoming1,2; Xu Ying2,3; Li Guangyu4; He Lisheng1,2; Qian Peiyuan2
2016-02-01
Source PublicationACTA OCEANOLOGICA SINICA
Volume35Issue:2Pages:131-136
AbstractThe 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.
SubtypeArticle
KeywordBacterial Dna Malbac Metagenome Amplification
WOS HeadingsScience & Technology ; Physical Sciences
DOI10.1007/s13131-015-0781-x
Indexed BySCI
Language英语
WOS KeywordDISPLACEMENT AMPLIFICATION ; HIGH-THROUGHPUT ; AMPLIFIED DNA ; GEN. NOV. ; WHOLE ; METAGENOMES ; POLYMERASE ; SEQUENCES ; BIAS ; CELL
WOS SubjectOceanography
WOS IDWOS:000370614700016
Citation statistics
Cited Times:2[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.idsse.ac.cn/handle/183446/1509
Collection深海科学研究部_深海生物学研究室_海洋微生物宏基因组与分子进化研究组
Affiliation1.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Sanya 572000, Peoples R China
2.Hong Kong Univ Sci & Technol, Div Life Sci, Hong Kong, Hong Kong, Peoples R China
3.Shenzhen Univ, Sch Life Sci, Shenzhen 518000, Peoples R China
4.State Ocean Adm, Inst Oceanog 3, Key Lab Marine Biogenet Resources, Xiamen 361005, Peoples R China
First Author AffilicationInstitute of Deep-sea Science and Engineering,CAS
Recommended Citation
GB/T 7714
Wang Yong,Gao Zhaoming,Xu Ying,et al. An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community[J]. ACTA OCEANOLOGICA SINICA,2016,35(2):131-136.
APA Wang Yong,Gao Zhaoming,Xu Ying,Li Guangyu,He Lisheng,&Qian Peiyuan.(2016).An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community.ACTA OCEANOLOGICA SINICA,35(2),131-136.
MLA Wang Yong,et al."An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community".ACTA OCEANOLOGICA SINICA 35.2(2016):131-136.
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