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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

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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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Translation in Prokaryotes01:29

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Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
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Next-generation Sequencing03:00

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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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 19, 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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RefSeq: an update on prokaryotic genome annotation and curation.

Daniel H Haft1, Michael DiCuccio1, Azat Badretdin1

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892-6511, USA.

Nucleic Acids Research
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PubMed
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The National Center for Biotechnology Information

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial genomics

Background:

  • The National Center for Biotechnology Information's Reference Sequence (RefSeq) project provides curated genomic data.
  • Prokaryotic genomes are annotated using a standardized Prokaryotic Genome Annotation Pipeline (PGAP).

Purpose of the Study:

  • To detail recent advancements and comprehensive updates to the RefSeq prokaryotic genome annotation resource.
  • To enhance the accuracy, consistency, and utility of prokaryotic genome annotations for researchers.

Main Methods:

  • Implementation of a hierarchical evidence scheme and curation of annotation sources.
  • Addition and curation of protein profile hidden Markov models (HMMs) and release of the updated PGAP-4 pipeline.
  • Comprehensive re-annotation of RefSeq prokaryotic genomes, including antimicrobial resistance proteins and specialized protein families.

Main Results:

  • Millions of multidomain proteins have received upgraded names based on curated complex domain architectures.
  • Improved structural annotation for insertion sequence transposases and selenoproteins.
  • Introduction of a new annotation rule, BlastRules, and increased use of portable HMMs for annotation.

Conclusions:

  • RefSeq provides a consistent, accurate, and continually updated resource for prokaryotic genome annotation.
  • Recent updates enhance the functional annotation of genomes, particularly for antimicrobial resistance and complex protein structures.
  • Portable annotation rules and curated HMMs are increasingly available for reuse by the scientific community.