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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
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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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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies.

Anders K Krabberød1, Embla Stokke1, Ella Thoen1

  • 1Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway.

Molecular Ecology Resources
|October 21, 2024
PubMed
Summary

A new Ribosomal Operon Database (ROD) provides full-length eukaryotic rDNA operons for advanced phylogenetic studies. This resource addresses the need for longer DNA sequences driven by new sequencing technologies.

Keywords:
DNA metabarcodingamplicon sequencingenvironmental sequencingreference sequencesribosomal DNA

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Current rDNA databases focus on short DNA markers, limiting phylogenetic resolution in environmental sequencing.
  • Advances in long-read DNA sequencing necessitate longer rDNA reference sequences for improved phylogenetic analysis.

Purpose of the Study:

  • To introduce the Ribosomal Operon Database (ROD), a novel resource of eukaryotic full-length rDNA operons.
  • To provide researchers with comprehensive, long-read rDNA sequences for enhanced phylogenetic studies.

Main Methods:

  • Collected full-length rDNA operons from publicly available eukaryotic genome assemblies in NCBI.
  • Detected and analyzed operon presence, copy number, and variant clustering across diverse eukaryotic genomes.
  • Evaluated the taxonomic resolution of different rDNA regions within full-length operons.

Main Results:

  • Full-length rDNA operons were found in 34.1% of examined eukaryotic genomes.
  • Significant intragenomic operon variability and extensive length variation (4136–16,463 bp) were observed.
  • The 18S, V4, and V9 regions showed the highest conservation, offering valuable taxonomic resolution.

Conclusions:

  • The ROD database successfully compiles eukaryotic full-length rDNA operons, supporting advanced phylogenetic research.
  • The database will be regularly updated to incorporate new data and expand its utility.
  • Understanding operon variability and length is crucial for mitigating PCR bias and interpreting phylogenetic data.