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Related Concept Videos

Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Microorganisms play a pivotal role in maintaining ecosystem balance by recycling essential elements such as carbon, nitrogen, and phosphorus, as well as supporting processes like bioremediation, wastewater treatment, and biofuel production.Microbes in Elemental CyclesIn the carbon cycle, microorganisms decompose organic matter, releasing carbon dioxide via aerobic respiration. This carbon dioxide is subsequently used by photosynthetic organisms to synthesize organic compounds, closing the...
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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
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A single-cell genomics pipeline for environmental microbial eukaryotes.

Doina Ciobanu1, Alicia Clum1, Steven Ahrendt1,2

  • 1US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.

Iscience
|April 19, 2021
PubMed
Summary
This summary is machine-generated.

We developed a cost-effective, seven-step single-cell genomics pipeline to recover whole genomes from rare, uncultivated eukaryotic microbes. This method yields high-quality genomes comparable to reference genomes for ecological studies.

Keywords:
GenomicsGeomicrobiologyMicrobiology

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Area of Science:

  • Microbial Ecology
  • Genomics
  • Eukaryotic Microbiology

Background:

  • Single-cell sequencing is crucial for microbial ecology.
  • Recovering whole genomes from uncultivated eukaryotes is challenging due to low abundance, large genomes, and tough cell walls.

Purpose of the Study:

  • To develop and validate a comprehensive pipeline for large-scale, targeted single-cell genome recovery of uncultivated eukaryotic microorganisms.
  • To address limitations in current single-cell genomics for environmental eukaryotes.

Main Methods:

  • A seven-step pipeline integrating state-of-the-art single-cell genomics tools and protocols.
  • Optimization for low-abundance, difficult-to-lyse eukaryotic cells.
  • Quality control checkpoints at each step for cost-effectiveness and high genome quality.

Main Results:

  • Successful application of the pipeline to environmental samples and cultures of early-diverging fungi and Chromista/SAR.
  • Generated high-quality eukaryotic microbial genomes.
  • The resulting genomes are suitable for functional and comparative genomics.

Conclusions:

  • The developed pipeline significantly advances the ability to study uncultivated microbial eukaryotes.
  • It provides a cost-effective solution for whole-genome recovery, enabling deeper insights into microbial ecology.
  • This approach yields genomes comparable to reference genomes for downstream analyses.