A single-cell genomics pipeline for environmental microbial eukaryotes
Summary: 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...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-04-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004221002583 |
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doaj-506f8b6c69dd41728994c0947e3f3bf7 |
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Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Doina Ciobanu Alicia Clum Steven Ahrendt William B. Andreopoulos Asaf Salamov Sandy Chan C. Alisha Quandt Brian Foster Jan P. Meier-Kolthoff Yung Tsu Tang Patrick Schwientek Gerald L. Benny Matthew E. Smith Diane Bauer Shweta Deshpande Kerrie Barry Alex Copeland Steven W. Singer Tanja Woyke Igor V. Grigoriev Timothy Y. James Jan-Fang Cheng |
| spellingShingle |
Doina Ciobanu Alicia Clum Steven Ahrendt William B. Andreopoulos Asaf Salamov Sandy Chan C. Alisha Quandt Brian Foster Jan P. Meier-Kolthoff Yung Tsu Tang Patrick Schwientek Gerald L. Benny Matthew E. Smith Diane Bauer Shweta Deshpande Kerrie Barry Alex Copeland Steven W. Singer Tanja Woyke Igor V. Grigoriev Timothy Y. James Jan-Fang Cheng A single-cell genomics pipeline for environmental microbial eukaryotes iScience Genomics Geomicrobiology Microbiology |
| author_facet |
Doina Ciobanu Alicia Clum Steven Ahrendt William B. Andreopoulos Asaf Salamov Sandy Chan C. Alisha Quandt Brian Foster Jan P. Meier-Kolthoff Yung Tsu Tang Patrick Schwientek Gerald L. Benny Matthew E. Smith Diane Bauer Shweta Deshpande Kerrie Barry Alex Copeland Steven W. Singer Tanja Woyke Igor V. Grigoriev Timothy Y. James Jan-Fang Cheng |
| author_sort |
Doina Ciobanu |
| title |
A single-cell genomics pipeline for environmental microbial eukaryotes |
| title_short |
A single-cell genomics pipeline for environmental microbial eukaryotes |
| title_full |
A single-cell genomics pipeline for environmental microbial eukaryotes |
| title_fullStr |
A single-cell genomics pipeline for environmental microbial eukaryotes |
| title_full_unstemmed |
A single-cell genomics pipeline for environmental microbial eukaryotes |
| title_sort |
single-cell genomics pipeline for environmental microbial eukaryotes |
| publisher |
Elsevier |
| series |
iScience |
| issn |
2589-0042 |
| publishDate |
2021-04-01 |
| description |
Summary: 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. |
| topic |
Genomics Geomicrobiology Microbiology |
| url |
http://www.sciencedirect.com/science/article/pii/S2589004221002583 |
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doaj-506f8b6c69dd41728994c0947e3f3bf72021-04-26T05:57:40ZengElsevieriScience2589-00422021-04-01244102290A single-cell genomics pipeline for environmental microbial eukaryotesDoina Ciobanu0Alicia Clum1Steven Ahrendt2William B. Andreopoulos3Asaf Salamov4Sandy Chan5C. Alisha Quandt6Brian Foster7Jan P. Meier-Kolthoff8Yung Tsu Tang9Patrick Schwientek10Gerald L. Benny11Matthew E. Smith12Diane Bauer13Shweta Deshpande14Kerrie Barry15Alex Copeland16Steven W. Singer17Tanja Woyke18Igor V. Grigoriev19Timothy Y. James20Jan-Fang Cheng21US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA; Corresponding authorUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA; Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USADepartment of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USADepartment of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, GermanyJoint BioEnergy Institute, Emeryville, CA 94608, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USADepartment of Plant Pathology, University of Florida, Gainesville, FL 32611, USADepartment of Plant Pathology, University of Florida, Gainesville, FL 32611, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USAJoint BioEnergy Institute, Emeryville, CA 94608, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USADepartment of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USAUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2589004221002583GenomicsGeomicrobiologyMicrobiology |