Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea

Yong Wang; On On Lee; Jiang Ke Yang; Tie Gang Li; Pei Yuan Qian

doi:10.7717/peerj.69

Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea

Yong Wang, On On Lee, Jiang Ke Yang, Tie Gang Li, Pei Yuan Qian

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

The Multiple Displacement Amplification (MDA) protocol is reported to introduce different artifacts into DNA samples with impurities. In this study, we report an artifactual effect ofMDA with sediment DNA samples froma deep-sea brine basin in the Red Sea. In the metagenomes, we showed the presence of abundant artifactual 454 pyrosequencing reads over sizes of 50 to 220bp. Gene fragments translocated from neighboring gene regions were identified in these reads. Occasionally, the translocation occurred between the gene fragments from different species. Reads containing these gene fragments could form a strong stem-loop structure. More than 60% of the artifactual reads could fit the structural models. MDA amplification is probably responsible for the massive generation of the artifactual reads with the secondary structure in the metagenomes. Possible sources of the translocations and structures are discussed. © 2013 Wang et al.

Original language	English (US)
Pages (from-to)	e69
Journal	PEERJ
Volume	1
Issue number	1
DOIs	https://doi.org/10.7717/peerj.69
State	Published - 2013
Externally published	Yes

Bibliographical note

KAUST Repository Item: Exported on 2021-09-21
Acknowledgements: China 973 Program: No. 2012CB417304.
Award from Deepsea Institute of Chinese Academy of Science.
Award from the King Abdullah University of Science and Technology: SA-C0040/UKC0016.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

General Agricultural and Biological Sciences
General Biochemistry, Genetics and Molecular Biology
General Medicine
General Neuroscience

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Cite this

@article{f66ac77f7ac14045b20edf5830299056,

title = "Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea",

abstract = "The Multiple Displacement Amplification (MDA) protocol is reported to introduce different artifacts into DNA samples with impurities. In this study, we report an artifactual effect ofMDA with sediment DNA samples froma deep-sea brine basin in the Red Sea. In the metagenomes, we showed the presence of abundant artifactual 454 pyrosequencing reads over sizes of 50 to 220bp. Gene fragments translocated from neighboring gene regions were identified in these reads. Occasionally, the translocation occurred between the gene fragments from different species. Reads containing these gene fragments could form a strong stem-loop structure. More than 60% of the artifactual reads could fit the structural models. MDA amplification is probably responsible for the massive generation of the artifactual reads with the secondary structure in the metagenomes. Possible sources of the translocations and structures are discussed. {\textcopyright} 2013 Wang et al.",

author = "Yong Wang and Lee, {On On} and Yang, {Jiang Ke} and Li, {Tie Gang} and Qian, {Pei Yuan}",

note = "KAUST Repository Item: Exported on 2021-09-21 Acknowledgements: China 973 Program: No. 2012CB417304. Award from Deepsea Institute of Chinese Academy of Science. Award from the King Abdullah University of Science and Technology: SA-C0040/UKC0016. This publication acknowledges KAUST support, but has no KAUST affiliated authors.",

year = "2013",

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T1 - Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea

AU - Wang, Yong

AU - Lee, On On

AU - Yang, Jiang Ke

AU - Li, Tie Gang

AU - Qian, Pei Yuan

N1 - KAUST Repository Item: Exported on 2021-09-21 Acknowledgements: China 973 Program: No. 2012CB417304. Award from Deepsea Institute of Chinese Academy of Science. Award from the King Abdullah University of Science and Technology: SA-C0040/UKC0016. This publication acknowledges KAUST support, but has no KAUST affiliated authors.

PY - 2013

Y1 - 2013

N2 - The Multiple Displacement Amplification (MDA) protocol is reported to introduce different artifacts into DNA samples with impurities. In this study, we report an artifactual effect ofMDA with sediment DNA samples froma deep-sea brine basin in the Red Sea. In the metagenomes, we showed the presence of abundant artifactual 454 pyrosequencing reads over sizes of 50 to 220bp. Gene fragments translocated from neighboring gene regions were identified in these reads. Occasionally, the translocation occurred between the gene fragments from different species. Reads containing these gene fragments could form a strong stem-loop structure. More than 60% of the artifactual reads could fit the structural models. MDA amplification is probably responsible for the massive generation of the artifactual reads with the secondary structure in the metagenomes. Possible sources of the translocations and structures are discussed. © 2013 Wang et al.

AB - The Multiple Displacement Amplification (MDA) protocol is reported to introduce different artifacts into DNA samples with impurities. In this study, we report an artifactual effect ofMDA with sediment DNA samples froma deep-sea brine basin in the Red Sea. In the metagenomes, we showed the presence of abundant artifactual 454 pyrosequencing reads over sizes of 50 to 220bp. Gene fragments translocated from neighboring gene regions were identified in these reads. Occasionally, the translocation occurred between the gene fragments from different species. Reads containing these gene fragments could form a strong stem-loop structure. More than 60% of the artifactual reads could fit the structural models. MDA amplification is probably responsible for the massive generation of the artifactual reads with the secondary structure in the metagenomes. Possible sources of the translocations and structures are discussed. © 2013 Wang et al.

UR - http://hdl.handle.net/10754/671345

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JF - PEERJ

IS - 1

ER -

Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea

Abstract

Bibliographical note

ASJC Scopus subject areas

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