Evidence map›Paper›PMID 33870123›Full record

ArticleiScience2021

A single-cell genomics pipeline for environmental microbial eukaryotes.

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 and 12 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in iScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Doina CiobanuUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Alicia ClumUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Steven AhrendtUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
William B AndreopoulosUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Asaf SalamovUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Sandy ChanUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
C Alisha QuandtDepartment of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
Brian FosterUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Jan P Meier-KolthoffDepartment of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany.
Yung Tsu TangJoint BioEnergy Institute, Emeryville, CA 94608, USA.
Patrick SchwientekUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Gerald L BennyDepartment of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
Matthew E SmithDepartment of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
Diane BauerUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Shweta DeshpandeUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Kerrie BarryUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Alex CopelandUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Steven W SingerJoint BioEnergy Institute, Emeryville, CA 94608, USA.
Tanja WoykeUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Igor V GrigorievUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.
Timothy Y JamesDepartment of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
Jan-Fang ChengUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

GenomicsGeomicrobiologyMicrobiology

Identifiers

PMID33870123
PMCPMC8042348

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.