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

Handle URI:
http://hdl.handle.net/10754/623513
Title:
An evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial community
Authors:
Wang, Yong; Gao, Zhaoming; Xu, Ying; Li, Guangyu; He, Lisheng; Qian, Peiyuan
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.
Publisher:
Springer Nature
Journal:
Acta Oceanologica Sinica
KAUST Grant Number:
SAC0040; UK-C0016
Issue Date:
23-Feb-2016
DOI:
10.1007/s13131-015-0781-x
Type:
Article
ISSN:
0253-505X; 1869-1099
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.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, Yongen
dc.contributor.authorGao, Zhaomingen
dc.contributor.authorXu, Yingen
dc.contributor.authorLi, Guangyuen
dc.contributor.authorHe, Lishengen
dc.contributor.authorQian, Peiyuanen
dc.date.accessioned2017-05-15T10:35:05Z-
dc.date.available2017-05-15T10:35:05Z-
dc.date.issued2016-02-23en
dc.identifier.citationWang 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.en
dc.identifier.issn0253-505Xen
dc.identifier.issn1869-1099en
dc.identifier.doi10.1007/s13131-015-0781-xen
dc.identifier.urihttp://hdl.handle.net/10754/623513-
dc.description.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.en
dc.description.sponsorshipThe 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.en
dc.publisherSpringer Natureen
dc.subjectbacterial DNAen
dc.subjectMALBACen
dc.subjectmetagenome amplificationen
dc.titleAn evaluation of multiple annealing and looping based genome amplification using a synthetic bacterial communityen
dc.typeArticleen
dc.identifier.journalActa Oceanologica Sinicaen
dc.contributor.institutionInstitute of Deep Sea Science and Engineering, Chinese Academy of Sciences (CAS), Sanya, Chinaen
dc.contributor.institutionDivision of Life Science, Hong Kong University of Science and Technology, Hong Kong, Chinaen
dc.contributor.institutionSchool of Life Science, Shenzhen University, Shenzhen, Chinaen
dc.contributor.institutionKey Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Chinaen
kaust.grant.numberSAC0040en
kaust.grant.numberUK-C0016en
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.