Sequencing of Genomes from Environmental Single Cells

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 1712)

Abstract

Sequencing of single bacterial and archaeal cells is an important methodology that provides access to the genetic makeup of uncultivated microorganisms. We here describe the high-throughput fluorescence-activated cell sorting-based isolation of single cells from the environment, their lysis and strand displacement-mediated whole genome amplification. We further outline 16S rRNA gene sequence-based screening of single-cell amplification products, their preparation for Illumina sequencing libraries, and finally propose computational methods for read and contig level quality control of the resulting sequence data.

Key words

Single amplified genomes Fluorescence-activated cell sorting Multiple displacement amplification Tagmentation Illumina genome sequencing 
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Notes

Acknowledgment

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. We would like to thank Bill Andreopoulos for his assistance in preparing Fig. 2.

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Department of EnergyJoint Genome InstituteWalnut CreekUSA

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