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Related Concept Videos

Ribosomes01:27

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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
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Fungi are a diverse group of eukaryotes more closely related to animals than other eukaryotes. Fungal cell walls comprise chitin, a polysaccharide that provides structural strength, and glucans, which contribute to flexibility and integrity. Other polysaccharides, such as mannans and galactosans, may supplement or replace chitin in some fungi. These adaptations, along with their preference for acidic environments and tolerance for high osmotic pressure, enable fungi to thrive in various...
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Related Experiment Video

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DNA Fingerprinting of Mycobacterium leprae Strains Using Variable Number Tandem Repeat VNTR - Fragment Length Analysis FLA
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Introducing ribosomal tandem repeat barcoding for fungi.

Christian Wurzbacher1,2,3, Ellen Larsson1,3, Johan Bengtsson-Palme4,5

  • 1Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.

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|September 22, 2018
PubMed
Summary
This summary is machine-generated.

New primers amplify all fungal ribosomal genetic markers, enabling high-throughput sequencing and closing gaps in fungal reference databases. This facilitates fungal identification and description using advanced sequencing technologies.

Keywords:
IGSNanoporePacBioSangerribosomal operonthird-generation sequencing

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Area of Science:

  • Mycology
  • Genomics
  • Molecular Biology

Background:

  • Ribosomal genetic markers are key for fungal identification, but current databases have significant gaps in taxonomic and marker coverage.
  • Environmental fungal lineages are often known only from DNA data, highlighting limitations in existing reference datasets.

Purpose of the Study:

  • To develop general primers for amplifying the complete ribosomal operon, covering all major ribosomal markers (ETS, SSU, ITS1, 5.8S, ITS2, LSU, IGS).
  • To facilitate the integration of diverse ribosomal marker data into reference sequence databases.
  • To enable high-throughput generation of high-quality fungal reference data.

Main Methods:

  • Design and application of three sets of general primers for ribosomal operon amplification.
  • Coupling primers with third-generation sequencing technologies (PacBio and Nanopore).
  • Testing the approach on diverse fungal specimens including Basidiomycota, Chytridiomycota, and Nephridiophagidae.

Main Results:

  • Successful amplification and sequencing of the complete ribosomal operon across different fungal groups.
  • Generation of high-quality reference data using Nanopore sequencing (99.85% accuracy) in a high-throughput manner.
  • Demonstration that reference data generation is feasible on standard desktop computers.

Conclusions:

  • The developed primers and methods effectively address gaps in fungal reference data.
  • Nanopore sequencing offers a viable, accessible, and high-throughput method for generating accurate fungal genomic data.
  • This work aims to establish a new standard for comprehensive ribosomal reference data to improve fungal classification and discovery.