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Related Concept Videos

Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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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.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
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Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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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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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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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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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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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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Related Experiment Videos

Large-scale comparative analysis of microbial pan-genomes using PanOCT.

Jason M Inman1, Granger G Sutton1, Erin Beck1

  • 1Department of Informatics, J. Craig Venter Institute, Rockville, MD, USA.

Bioinformatics (Oxford, England)
|August 31, 2018
PubMed
Summary

The JCVI Pan-Genome Pipeline analyzes prokaryotic genomes using PanOCT (pan-genome ortholog clustering tool). This tool aids in understanding genetic variations and identifying important genes like antimicrobial resistance genes.

Related Experiment Videos

Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Pan-genome analysis is crucial for understanding genetic diversity in closely related prokaryotic species.
  • Existing tools require efficient and integrated pipelines for comprehensive analysis.

Purpose of the Study:

  • To introduce the JCVI Pan-Genome Pipeline, a comprehensive toolset for prokaryotic pan-genome analysis.
  • To extend the capabilities of the PanOCT tool for enhanced genome comparison and feature identification.

Main Methods:

  • The pipeline integrates various command-line utilities and third-party tools, including NCBI Blast+.
  • It automates genome preparation, PanOCT execution, consensus pan-genome generation, and feature annotation.
  • The pipeline supports hierarchical mode to optimize resource utilization (RAM and compute).

Main Results:

  • The JCVI Pan-Genome Pipeline facilitates the analysis of closely related prokaryotic species or strains.
  • It enables the detection of specific gene sets, such as antimicrobial resistance (AMR) genes.
  • The pipeline generates visualizations including figures, tables, and HTML pages for results interpretation.

Conclusions:

  • The JCVI Pan-Genome Pipeline provides a robust and efficient solution for prokaryotic pan-genome analysis.
  • Its integrated approach and resource optimization offer significant advantages for researchers in the field.