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

Volume 35 Issue 2

Turn off MathJax

Article Contents

Abstract

References

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

PDF( 2210 KB)

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

FullText(HTML)

References(24)

References

Abbai N S, Govender A, Shaik R, et al. 2012. Pyrosequence analysis of unamplified and whole genome amplified DNA from hydrocar-bon-contaminated groundwater. Molecular Biotechnology, 50(1): 39-48

Albertsen M, Hugenholtz P, Skarshewski A, et al. 2013. Genome se-quences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechno-logy, 31(6): 533-538

Bergen A W, Haque K A, Qi Ying, et al. 2005. Comparison of yield and genotyping performance of multiple displacement amplifica-tion and OmniPlex^TM whole genome amplified DNA generated from multiple DNA sources. Human Mutation, 26(3): 262-270

Dean F B, Hosono S, Fang Linhua, et al. 2002. Comprehensive hu-man genome amplification using multiple displacement ampli-fication. Proceedings of the National Academy of Sciences of the United States of America, 99(8): 5261-5266

Dean F B, Nelson J R, Giesler T L, et al. 2001. Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Re-search, 11(6): 1095-1099

Direito S O L, Zaura E, Little M, et al. 2014. Systematic evaluation of bias in microbial community profiles induced by whole gen-ome amplification. Environmental Microbiology, 16(3): 643-657

Huson D H, Mitra S, Ruscheweyh H J, et al. 2011. Integrative analysis of environmental sequences using MEGAN4. Genome Re-search, 21(9): 1552-1560

Hyatt D, Chen GwoLiang, Locascio P F, et al. 2010. Prodigal: proka-ryotic gene recognition and translation initiation site identifica-tion. BMC Bioinformatics, 11(1): 119, doi: 10.1186/1471-2105-11-119

Langmead B, Salzberg S L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4): 357-359 Langmore J P. 2002. Rubicon Genomics, Inc. Pharmacogenomics, 3(4): 557-560

Lasken R S, Stockwell T B. 2007. Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnology, 7(1): 19, doi: 10.1186/1472-6750-7-19

Li Heng, Handsaker B, Wysoker A, et al. 2009. The sequence align-ment/map format and SAMtools. Bioinformatics, 25(16): 2078-2079

Logares R, Haverkamp T H A, Kumar S, et al. 2012. Environmental microbiology through the lens of high-throughput DNA se-quencing: Synopsis of current platforms and bioinformatics ap-proaches. Journal of Microbiological Methods, 91(1): 106-113

Patel R K, Jain M. 2012. NGS QC toolkit: A toolkit for quality control of next generation sequencing data. Plos One, 7(2): e30619

Pinard R, de Winter A, Sarkis G J, et al. 2006. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics, 7(1): 216, doi: 10.1186/1471-2164-7-216

Raghunathan A, Ferguson H R Jr, Bornarth C J, et al. 2005. Genomic DNA amplification from a single bacterium. Applied and Envir-onmental Microbiology, 71(6): 3342-3347

Shi Binhai, Arunpairojana V, Palakawong S, et al. 2002. Tistrella mo-bilis gen. nov., sp. nov., a novel polyhydroxyalkanoate-produ-cing bacterium belonging to α-Proteobacteria. The Journal of General and Applied Microbiology, 48(6): 335-343

Shieh W Y, Lin Yute, Jean W D. 2004. Pseudovibrio denitrificans gen.

nov., sp. nov., a marine, facultatively anaerobic, fermentative bacterium capable of denitrification. International Journal of Systematic and Evolutionary Microbiology, 54(6): 2307-2312

Simpson J T, Wong K, Jackman S D, et al. 2009. ABySS: a parallel as-sembler for short read sequence data. Genome Research, 19(6): 1117-1123

Spits C, Le Caignec C, De Rycke M, et al. 2006. Optimization and eval-uation of single-cell whole-genome multiple displacement amplification. Human Mutation, 27(5): 496-503

Uda A, Tanabayashi K, Fujita O, et al. 2007. Comparison of whole genome amplification methods for detecting pathogenic bac-terial genomic DNA using microarray. Japanese Journal of In-fectious Diseases, 60(6): 355-361

Yilmaz S, Allgaier M, Hugenholtz P. 2010. Multiple displacement amplification compromises quantitative analysis of metagen-omes. Nature Methods, 7(12): 943-944

Zhang Kun, Martiny A C, Reppas N B, et al. 2006. Sequencing gen-omes from single cells by polymerase cloning. Nature Biotech-nology, 24(6): 680-686

Zong Chenghang, Lu Sijia, Chapman A R, et al. 2012. Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338(6114): 1622-1626

Relative Articles

Relative Articles

Supplements(0)

Cited By

Cited by

Periodical cited type(6)

1.	Yong Wang, Wenli Li, Brett J. Baker, et al. Carbon metabolism and adaptation of hyperalkaliphilic microbes in serpentinizing spring of Manleluag, the Philippines. Environmental Microbiology Reports, 2022, 14(2): 308. doi:10.1111/1758-2229.13052
2.	Jackson K. B. Cahn, Jörn Piel. Anwendungen von Einzelzellmethoden in der mikrobiellen Naturstoffforschung. Angewandte Chemie, 2021, 133(34): 18560. doi:10.1002/ange.201900532
3.	Márton Szoboszlay, Christoph C. Tebbe. Hidden heterogeneity and co‐occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. MicrobiologyOpen, 2021, 10(1) doi:10.1002/mbo3.1144
4.	Jackson K. B. Cahn, Jörn Piel. Opening up the Single‐Cell Toolbox for Microbial Natural Products Research. Angewandte Chemie International Edition, 2021, 60(34): 18412. doi:10.1002/anie.201900532
5.	Yucheng Wu, Yeliang Dai, Guangming Liu, et al. Assessment of two whole genome amplification techniques in terms of soil community profiles. Applied Soil Ecology, 2020, 150: 103455. doi:10.1016/j.apsoil.2019.103455
6.	Yong Wang, Tie Gang Li, Meng Ying Wang, et al. Archive of bacterial community in anhydrite crystals from a deep-sea basin provides evidence of past oil-spilling in a benthic environment in the Red Sea. Biogeosciences, 2016, 13(23): 6405. doi:10.5194/bg-13-6405-2016