Massively parallel single-cell genome sequencing enables high-resolution analysis of soil and marine microorganisms
dc.contributor.author | Nishikawa, Yohei | |
dc.contributor.author | Kogawa, Masato | |
dc.contributor.author | Hosokawa, Masahito | |
dc.contributor.author | Mineta, Katsuhiko | |
dc.contributor.author | Takahashi, Kai | |
dc.contributor.author | Sakanashi, Chikako | |
dc.contributor.author | Behzad, Hayedeh | |
dc.contributor.author | Gojobori, Takashi | |
dc.contributor.author | Takeyama, Haruko | |
dc.date.accessioned | 2020-03-12T05:28:20Z | |
dc.date.available | 2020-03-12T05:28:20Z | |
dc.date.issued | 2020-03-06 | |
dc.identifier.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 | |
dc.identifier.doi | 10.1101/2020.03.05.962001 | |
dc.identifier.uri | http://hdl.handle.net/10754/662102 | |
dc.description.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. | |
dc.description.sponsorship | 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). | |
dc.publisher | Cold Spring Harbor Laboratory | |
dc.relation.url | http://biorxiv.org/lookup/doi/10.1101/2020.03.05.962001 | |
dc.rights | Archived with thanks to Cold Spring Harbor Laboratory | |
dc.title | Massively parallel single-cell genome sequencing enables high-resolution analysis of soil and marine microorganisms | |
dc.type | Preprint | |
dc.contributor.department | Biological and Environmental Sciences and Engineering (BESE) Division | |
dc.contributor.department | Bioscience Program | |
dc.contributor.department | Computational Bioscience Research Center (CBRC) | |
dc.contributor.department | Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division | |
dc.eprint.version | Pre-print | |
dc.contributor.institution | Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169–0072, Japan | |
dc.contributor.institution | Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162–8480, Japan | |
dc.contributor.institution | Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162–0041, Japan | |
dc.contributor.institution | Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan. | |
kaust.person | Mineta, Katsuhiko | |
kaust.person | Mineta, Katsuhiko | |
kaust.person | Behzad, Hayedeh | |
kaust.person | Behzad, Hayedeh | |
kaust.person | Gojobori, Takashi | |
kaust.person | Gojobori, Takashi | |
kaust.grant.number | URF/1/1976/03/01 | |
refterms.dateFOA | 2020-03-12T05:28:44Z |
Files in this item
This item appears in the following Collection(s)
-
Biological and Environmental Sciences and Engineering (BESE) Division
For more information visit: https://bese.kaust.edu.sa/ -
Preprints
-
Bioscience Program
For more information visit: https://bese.kaust.edu.sa/study/Pages/Bioscience.aspx -
Computational Bioscience Research Center (CBRC)
-
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
For more information visit: https://cemse.kaust.edu.sa/