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dc.contributor.authorNishikawa, Yohei
dc.contributor.authorKogawa, Masato
dc.contributor.authorHosokawa, Masahito
dc.contributor.authorMineta, Katsuhiko
dc.contributor.authorTakahashi, Kai
dc.contributor.authorSakanashi, Chikako
dc.contributor.authorBehzad, Hayedeh
dc.contributor.authorGojobori, Takashi
dc.contributor.authorTakeyama, Haruko
dc.date.accessioned2020-03-12T05:28:20Z
dc.date.available2020-03-12T05:28:20Z
dc.date.issued2020-03-06
dc.identifier.citationNishikawa, 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.doi10.1101/2020.03.05.962001
dc.identifier.urihttp://hdl.handle.net/10754/662102
dc.description.abstractTo 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.sponsorshipThis 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.publisherCold Spring Harbor Laboratory
dc.relation.urlhttp://biorxiv.org/lookup/doi/10.1101/2020.03.05.962001
dc.rightsArchived with thanks to Cold Spring Harbor Laboratory
dc.titleMassively parallel single-cell genome sequencing enables high-resolution analysis of soil and marine microorganisms
dc.typePreprint
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.eprint.versionPre-print
dc.contributor.institutionComputational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169–0072, Japan
dc.contributor.institutionDepartment of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162–8480, Japan
dc.contributor.institutionResearch Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo, 162–0041, Japan
dc.contributor.institutionInstitute 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.personMineta, Katsuhiko
kaust.personMineta, Katsuhiko
kaust.personBehzad, Hayedeh
kaust.personBehzad, Hayedeh
kaust.personGojobori, Takashi
kaust.personGojobori, Takashi
kaust.grant.numberURF/1/1976/03/01
refterms.dateFOA2020-03-12T05:28:44Z


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