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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Genomic DNA in Prokaryotes00:46

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

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Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
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Prokaryotic Cells01:28

Prokaryotic Cells

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Prokaryotes are small unicellular organisms that include the domains — Archaea and Bacteria. Bacteria include many common microorganisms, such as Salmonella and E. coli, while the Archaea include extremophiles that live in harsh environments, such as volcanic springs.
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Prokaryotic Cells01:51

Prokaryotic Cells

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Prokaryotes are small unicellular organisms that include the domains—Archaea and Bacteria. Bacteria include many common organisms, such as Salmonella and E. coli, while the Archaea include extremophiles that live in harsh environments, such as volcanic springs.
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Related Experiment Video

Updated: Feb 24, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Using KBase to Assemble and Annotate Prokaryotic Genomes.

Benjamin Allen1, Meghan Drake1, Nomi Harris2

  • 1Bioinformatics Group, Oak Ridge National Laboratory, Oak Ridge, Tennessee.

Current Protocols in Microbiology
|August 12, 2017
PubMed
Summary
This summary is machine-generated.

The DOE Systems Biology Knowledgebase (KBase) provides bioinformatics tools for analyzing microbial genomes. This workflow demonstrates reproducible prokaryotic genome assembly and annotation for microbiologists.

Keywords:
KBaseannotationassemblygenomicssystems biology

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Area of Science:

  • Systems biology
  • Bioinformatics
  • Genomics

Background:

  • The DOE Systems Biology Knowledgebase (KBase) is an open-access platform for biological data analysis.
  • It supports the analysis of plants, microbes, and microbial communities.
  • KBase facilitates reproducible research by enabling data sharing and collaboration.

Purpose of the Study:

  • To demonstrate a comparative and iterative workflow for prokaryotic genome assembly and annotation using KBase.
  • To provide microbiologists with a rapid and reproducible method for isolate analysis.
  • To showcase KBase's capabilities for analyzing structural and functional genomic features.

Main Methods:

  • Utilizing the DOE Systems Biology Knowledgebase (KBase) platform.
  • Implementing analysis tools for quality control and assessment of Next-Generation Sequencing reads.
  • Performing de novo assembly and genome annotation for prokaryotic genomes.
  • Applying a comparative and iterative approach to genome analysis.

Main Results:

  • A demonstrated workflow for prokaryotic genome assembly and annotation was presented.
  • The workflow enables rapid and reproducible isolate analysis.
  • KBase tools facilitate comprehensive analysis of genomic structural and functional features.

Conclusions:

  • The DOE Systems Biology Knowledgebase (KBase) offers valuable tools for prokaryotic genome analysis.
  • The demonstrated workflow enhances reproducibility and efficiency in microbial genomics research.
  • KBase empowers microbiologists to conduct in-depth analysis of microbial genomes.