SSU rRNA and LSU rRNA

  • SSU rRNA (small subunit rRNA)
    • 16S rRNA in bacteria, archea and plastid
    • 18S rRNA in eukaryotes
    • 12S rRNA in mitochondria
  • LSU rRNA (large subunit rRNA)
    • 23S rRNA in bacteria, archea and plastid
    • 5.8S & 28S rRNA in eukaryotes. The 5.8S rRNA is homologous to the 5’ end of non-eukaryotic LSU rRNA. In eukaryotes, the insertion of ITS2 breaks LSU rRNA into 5.8S and 28S rRNAs.
    • 16S in Mitochondria
    • 5S rRNA
  • Biogenesis
    • In bacteria, 16S rRNA, 23S rRNA, and 5S rRNA are typically organized as a co-transcribed operon.
    • In eukaryotes, the 28S, 5.8S, and 18S rRNAs are encoded by a single transcription unit (45S) separated by 2 internally transcribed spacers, and transcribed by RNA polymerase I. 5S rRNA is transcribed independetly by RNA polymerase III.

Where to get rRNA data

  • barrnap is widely used tool for rRNA annotation, SortMeRNA is a tool to sort out rRNA from NGS data. Here list data resources used by these two tools
  • We can see two major sources of rRNA information come from:
    • The silva database. Provide sequence alignments, focus on metagenomics (16S rRNA is the most wildely used marker gene in metagenomics).
    • Also see
      • greengenes for 16S rRNA
      • RDP Bacterial and Archaeal 16S rRNA sequences, and Fungal 28S rRNA
    • The Rfam database. Provide sequence alignments, reference structure and covariance model.
      • 5S and 5.8S rRNA presents in ribosome large subunit, but not included in SILVA LSU. barrnap and SortMeRNA use Rfam for 5S and 5.8S rRNA annotation.
      • 5S rRNA: RF00001
      • 5.8S rRNA: RF00002

rRNA sequence in reference genome assembly

  • rRNA is generally recognized as repeat sequence in eukaryotic genomes, and abscent from some genome assemblies.

  • Human genome
  • rRNAs have considerable variation among populations