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A single-cell genomics pipeline for environmental microbial eukaryotes.
Ciobanu, Doina; Clum, Alicia; Ahrendt, Steven; Andreopoulos, William B; Salamov, Asaf; Chan, Sandy; Quandt, C Alisha; Foster, Brian; Meier-Kolthoff, Jan P; Tang, Yung Tsu; Schwientek, Patrick; Benny, Gerald L; Smith, Matthew E; Bauer, Diane; Deshpande, Shweta; Barry, Kerrie; Copeland, Alex; Singer, Steven W; Woyke, Tanja; Grigoriev, Igor V; James, Timothy Y; Cheng, Jan-Fang.
Afiliación
  • Ciobanu D; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Clum A; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Ahrendt S; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Andreopoulos WB; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.
  • Salamov A; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Chan S; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Quandt CA; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Foster B; Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
  • Meier-Kolthoff JP; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
  • Tang YT; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Schwientek P; Department of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
  • Benny GL; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
  • Smith ME; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Bauer D; Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
  • Deshpande S; Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
  • Barry K; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Copeland A; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Singer SW; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Woyke T; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Grigoriev IV; Joint BioEnergy Institute, Emeryville, CA 94608, USA.
  • James TY; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
  • Cheng JF; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
iScience ; 24(4): 102290, 2021 Apr 23.
Article en En | MEDLINE | ID: mdl-33870123
ABSTRACT
Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: IScience Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Añadir a Mi BVS
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: IScience Año: 2021 Tipo del documento: Article País de afiliación: Estados Unidos