Massively parallel single-cell genome sequencing enables high-resolution analysis of soil and marine microorganisms

Abstract
To improve our understanding of the environmental microbiome, we developed a single-cell genome sequencing platform, named SAG-gel, which utilizes gel beads for single-cell isolation, cell lysis, and whole genome amplification (WGA) for sequencing. SAG-gel enables serial, parallel and independent reactions of > 100,000 single cells in a single tube, delivering high-quality genome recovery with storable randomized single-cell genome libraries. From soil and marine environmental sources, we acquired 734 partial genomes that are recapitulated in 231 species, 35% of which were assigned as high-to-medium qualities. We found that each genome to be almost unique and 98.7% of them were newly identified, implying the complex genetic diversities across 44 phyla. The various metabolic capabilities including virulence factors and biosynthetic gene clusters were found across the lineages at single-cell resolution. This technology will accelerate the accumulation of reference genomes of uncharacterized environmental microbes and provide us new insights for their roles.

Citation
Nishikawa, Y., Kogawa, M., Hosokawa, M., Mineta, K., Takahashi, K., Sakanashi, C., … Takeyama, H. (2020). Massively parallel single-cell genome sequencing enables high-resolution analysis of soil and marine microorganisms. doi:10.1101/2020.03.05.962001

Acknowledgements
This work was supported by JST-PRESTO grant number JPMJPR15FA, MEXT KAKENHI grant numbers 18H01801 and 17H06158, and the funding from King Abdullah University of Science and Technology (KAUST), under award numbers URF/1/1976/03/01, URF/1/1976/17/01, URF/1/1976/20/01 and FCS/1/3326/01/01. The super-computing resource was provided by the Human Genome Center (University of Tokyo).

Publisher
Cold Spring Harbor Laboratory

DOI
10.1101/2020.03.05.962001

Additional Links
http://biorxiv.org/lookup/doi/10.1101/2020.03.05.962001

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